1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 2243 2244 2245 2246 2247 2248 2249 2250 2251 2252 2253 2254 2255 2256 2257 2258 2259 2260 2261 2262 2263 2264 2265 2266 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 2280 2281 2282 2283 2284 2285 2286 2287 2288 2289 2290 2291 2292 2293 2294 2295 2296 2297 2298 2299 2300 2301 2302 2303 2304 2305 2306 2307 2308 2309 2310 2311 2312 2313 2314 2315 2316 2317 2318 2319 2320 2321 2322 2323 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 2335 2336 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355 2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385 2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400 2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415 2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460 2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 2685 2686 2687 2688 2689 2690 2691 2692 2693 2694 2695 2696 2697 2698 2699 2700 2701 2702 2703 2704 2705 2706 2707 2708 2709 2710 2711 2712 2713 2714 2715 2716 2717 2718 2719 2720 2721 2722 2723 2724 2725 2726 2727 2728 2729 2730 2731 2732 2733 2734 2735 2736 2737 2738 2739 2740 2741 2742 2743 2744 2745 2746 2747 2748 2749 2750 2751 2752 2753 2754 2755 2756 2757 2758 2759 2760 2761 2762 2763 2764 2765 2766 2767 2768 2769 2770 2771 2772 2773 2774 2775 2776 2777 2778 2779 2780 2781 2782 2783 2784 2785 2786 2787 2788 2789 2790 2791 2792 2793 2794 2795 2796 2797 2798 2799 2800 2801 2802 2803 2804 2805 2806 2807 2808 2809 2810 2811 2812 2813 2814 2815 2816 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827 2828 2829 2830 2831 2832 2833 2834 2835 2836 2837 2838 2839 2840 2841 2842 2843 2844 2845 2846 2847 2848 2849 2850 2851 2852 2853 2854 2855 2856 2857 2858 2859 2860 2861 2862 2863 2864 2865 2866 2867 2868 2869 2870 2871 2872 2873 2874 2875 2876 2877 2878 2879 2880 2881 2882 2883 2884 2885 2886 2887 2888 2889 2890 2891 2892 2893 2894 2895 2896 2897 2898 2899 2900 2901 2902 2903 2904 2905 2906 2907 2908 2909 2910 2911 2912 2913 2914 2915 2916 2917 2918 2919 2920 2921 2922 2923 2924 2925 2926 2927 2928 2929 2930 2931 2932 2933 2934 2935 2936 2937 2938 2939 2940 2941 2942 2943 2944 2945 2946 2947 2948 2949 2950 2951 2952 2953 2954 2955 2956 2957 2958 2959 2960 2961 2962 2963 2964 2965 2966 2967 2968 2969 2970 2971 2972 2973 2974 2975 2976 2977 2978 2979 2980 2981 2982 2983 2984 2985 2986 2987 2988 2989 2990 2991 2992 2993 2994 2995 2996 2997 2998 2999 3000 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3011 3012 3013 3014 3015 3016 3017 3018 3019 3020 3021 3022 3023 3024 3025 3026 3027 3028 3029 3030 3031 3032 3033 3034 3035 3036 3037 3038 3039 3040 3041 3042 3043 3044 3045 3046 3047 3048 3049 3050 3051 3052 3053 3054 3055 3056 3057 3058 3059 3060 3061 3062 3063 3064 3065 3066 3067 3068 3069 3070 3071 3072 3073 3074 3075 3076 3077 3078 3079 3080 3081 3082 3083 3084 3085 3086 3087 3088 3089 3090 3091 3092 3093 3094 3095 3096 3097 3098 3099 3100 3101 3102 3103 3104 3105 3106 3107 3108 3109 3110 3111 3112 3113 3114 3115 3116 3117 3118 3119 3120 3121 3122 3123 3124 3125 3126 3127 3128 3129 3130 3131 3132 3133 3134 3135 3136 3137 3138 3139 3140 3141 3142 3143 3144 3145 3146 3147 3148 3149 3150 3151 3152 3153 3154 3155 3156 3157 3158 3159 3160 3161 3162 3163 3164 3165 3166 3167 3168 3169 3170 3171 3172 3173 3174 3175 3176 3177 3178 3179 3180 3181 3182 3183 3184 3185 3186 3187 3188 3189 3190 3191 3192 3193 3194 3195 3196 3197 3198 3199 3200 3201 3202 3203 3204 3205 3206 3207 3208 3209 3210 3211 3212 3213 3214 3215 3216 3217 3218 3219 3220 3221 3222 3223 3224 3225 3226 3227 3228 3229 3230 3231 3232 3233 3234 3235 3236 3237 3238 3239 3240 3241 3242 3243 3244 3245 3246 3247 3248 3249 3250 3251 3252 3253 3254 3255 3256 3257 3258 3259 3260 3261 3262 3263 3264 3265 3266 3267 3268 3269 3270 3271 3272 3273 3274 3275 3276 3277 3278 3279 3280 3281 3282 3283 3284 3285 3286 3287 3288 3289 3290 3291 3292 3293 3294 3295 3296 3297 3298 3299 3300 3301 3302 3303 3304 3305 3306 3307 3308 3309 3310 3311 3312 3313 3314 3315 3316 3317 3318 3319 3320 3321 3322 3323 3324 3325 3326 3327 3328 3329 3330 3331 3332 3333 3334 3335 3336 3337 3338 3339 3340 3341 3342 3343 3344 3345 3346 3347 3348 3349 3350 3351 3352 3353 3354 3355 3356 3357 3358 3359 3360 3361 3362 3363 3364 3365 3366 3367 3368 3369 3370 3371 3372 3373 3374 3375 3376 3377 3378 3379 3380 3381 3382 3383 3384 3385 3386 3387 3388 3389 3390 3391 3392 3393 3394 3395 3396 3397 3398 3399 3400 3401 3402 3403 3404 3405 3406 3407 3408 3409 3410 3411 3412 3413 3414 3415 3416 3417 3418 3419 3420 3421 3422 3423 3424 3425 3426 3427 3428 3429 3430 3431 3432 3433 3434 3435 3436 3437 3438 3439 3440 3441 3442 3443 3444 3445 3446 3447 3448 3449 3450 3451 3452 3453 3454 3455 3456 3457 3458 3459 3460 3461 3462 3463 3464 3465 3466 3467 3468 3469 3470 3471 3472 3473 3474 3475 3476 3477 3478 3479 3480 3481 3482 3483 3484 3485 3486 3487 3488 3489 3490 3491 3492 3493 3494 3495 3496 3497 3498 3499 3500 3501 3502 3503 3504 3505 3506 3507 3508 3509 3510 3511 3512 3513 3514 3515 3516 3517 3518 3519 3520 3521 3522 3523 3524 3525 3526 3527 3528 3529 3530 3531 3532 3533 3534 3535 3536 3537 3538 3539 3540 3541 3542 3543 3544 3545 3546 3547 3548 3549 3550 3551 3552 3553 3554 3555 3556 3557 3558 3559 3560 3561 3562 3563 3564 3565 3566 3567 3568 3569 3570 3571 3572 3573 3574 3575 3576 3577 3578 3579 3580 3581 3582 3583 3584 3585 3586 3587 3588 3589 3590 3591 3592 3593 3594 3595 3596 3597 3598 3599 3600 3601 3602 3603 3604 3605 3606 3607 3608 3609 3610 3611 3612 3613 3614 3615 3616 3617 3618 3619 3620 3621 3622 3623 3624 3625 3626 3627 3628 3629 3630 3631 3632 3633 3634 3635 3636 3637 3638 3639 3640 3641 3642 3643 3644 3645 3646 3647 3648 3649 3650 3651 3652 3653 3654 3655 3656 3657 3658 3659 3660 3661 3662 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 3673 3674 3675 3676 3677 3678 3679 3680 3681 3682 3683 3684 3685 3686 3687 3688 3689 3690 3691 3692 3693 3694 3695 3696 3697 3698 3699 3700 3701 3702 3703 3704 3705 3706 3707 3708 3709 3710 3711 3712 3713 3714 3715 3716 3717 3718 3719 3720 3721 3722 3723 3724 3725 3726 3727 3728 3729 3730 3731 3732 3733 3734 3735 3736 3737 3738 3739 3740 3741 3742 3743 3744 3745 3746 3747 3748 3749 3750 3751 3752 3753 3754 3755 3756 3757 3758 3759 3760 3761 3762 3763 3764 3765 3766 3767 3768 3769 3770 3771 3772 3773 3774 3775 3776 3777 3778 3779 3780 3781 3782 3783 3784 3785 3786 3787 3788 3789 3790 3791 3792 3793 3794 3795 3796 3797 3798 3799 3800 3801 3802 3803 3804 3805 3806 3807 3808 3809 3810 3811 3812 3813 3814 3815 3816 3817 3818 3819 3820 3821 3822 3823 3824 3825 3826 3827 3828 3829 3830 3831 3832 3833 3834 3835 3836 3837 3838 3839 3840 3841 3842 3843 3844 3845 3846 3847 3848 3849 3850 3851 3852 3853 3854 3855 3856 3857 3858 3859 3860 3861 3862 3863 3864 3865 3866 3867 3868 3869 3870 3871 3872 3873 3874 3875 3876 3877 3878 3879 3880 3881 3882 3883 3884 3885 3886 3887 3888 3889 3890 3891 3892 3893 3894 3895 3896 3897 3898 3899 3900 3901 3902 3903 3904 3905 3906 3907 3908 3909 3910 3911 3912 3913 3914 3915 3916 3917 3918 3919 3920 3921 3922 3923 3924 3925 3926 3927 3928 3929 3930 3931 3932 3933 3934 3935 3936 3937 3938 3939 3940 3941 3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956 3957 3958 3959 3960 3961 3962 3963 3964 3965 3966 3967 3968 3969 3970 3971 3972 3973 3974 3975 3976 3977 3978 3979 3980 3981 3982 3983 3984 3985 3986 3987 3988 3989 3990 3991 3992 3993 3994 3995 3996 3997 3998 3999 4000 4001 4002 4003 4004 4005 4006 4007 4008 4009 4010 4011 4012 4013 4014 4015 4016 4017 4018 4019 4020 4021 4022 4023 4024 4025 4026 4027 4028 4029 4030 4031 4032 4033 4034 4035 4036 4037 4038 4039 4040 4041 4042 4043 4044 4045 4046 4047 4048 4049 4050 4051 4052 4053 4054 4055 4056 4057 4058 4059 4060 4061 4062 4063 4064 4065 4066 4067 4068 4069 4070 4071 4072 4073 4074 4075 4076 4077 4078 4079 4080 4081 4082 4083 4084 4085 4086 4087 4088 4089 4090 4091 4092 4093 4094 4095 4096 4097 4098 4099 4100 4101 4102 4103 4104 4105 4106 4107 4108 4109 4110 4111 4112 4113 4114 4115 4116 4117 4118 4119 4120 4121 4122 4123 4124 4125 4126 4127 4128 4129 4130 4131 4132 4133 4134 4135 4136 4137 4138 4139 4140 4141 4142 4143 4144 4145 4146 4147 4148 4149 4150 4151 4152 4153 4154 4155 4156 4157 4158 4159 4160 4161 4162 4163 4164 4165 4166 4167 4168 4169 4170 4171 4172 4173 4174 4175 4176 4177 4178 4179 4180 4181 4182 4183 4184 4185 4186 4187 4188 4189 4190 4191 4192 4193 4194 4195 4196 4197 4198 4199 4200 4201 4202 4203 4204 4205 4206 4207 4208 4209 4210 4211 4212 4213 4214 4215 4216 4217 4218 4219 4220 4221 4222 4223 4224 4225 4226 4227 4228 4229 4230 4231 4232 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 4243 4244 4245 4246 4247 4248 4249 4250 4251 4252 4253 4254 4255 4256 4257 4258 4259 4260 4261 4262 4263 4264 4265 4266 4267 4268 4269 4270 4271 4272 4273 4274 4275 4276 4277 4278 4279 4280 4281 4282 4283 4284 4285 4286 4287 4288 4289 4290 4291 4292 4293 4294 4295 4296 4297 4298 4299 4300 4301 4302 4303 4304 4305 4306 4307 4308 4309 4310 4311 4312 4313 4314 4315 4316 4317 4318 4319 4320 4321 4322 4323 4324 4325 4326 4327 4328 4329 4330 4331 4332 4333 4334 4335 4336 4337 4338 4339 4340 4341 4342 4343 4344 4345 4346 4347 4348 4349 4350 4351 4352 4353 4354 4355 4356 4357 4358 4359 4360 4361 4362 4363 4364 4365 4366 4367 4368 4369 4370 4371 4372 4373 4374 4375 4376 4377 4378 4379 4380 4381 4382 4383 4384 4385 4386 4387 4388 4389 4390 4391 4392 4393 4394 4395 4396 4397 4398 4399 4400 4401 4402 4403 4404 4405 4406 4407 4408 4409 4410 4411 4412 4413 4414 4415 4416 4417 4418 4419 4420 4421 4422 4423 4424 4425 4426 4427 4428 4429 4430 4431 4432 4433 4434 4435 4436 4437 4438 4439 4440 4441 4442 4443 4444 4445 4446 4447 4448 4449 4450 4451 4452 4453 4454 4455 4456 4457 4458 4459 4460 4461 4462 4463 4464 4465 4466 4467 4468 4469 4470 4471 4472 4473 4474 4475 4476 4477 4478 4479 4480 4481 4482 4483 4484 4485 4486 4487 4488 4489 4490 4491 4492 4493 4494 4495 4496 4497 4498 4499 4500 4501 4502 4503 4504 4505 4506 4507 4508 4509 4510 4511 4512 4513 4514 4515 4516 4517 4518 4519 4520 4521 4522 4523 4524 4525 4526 4527 4528 4529 4530 4531 4532 4533 4534 4535 4536 4537 4538 4539 4540 4541 4542 4543 4544 4545 4546 4547 4548 4549 4550 4551 4552 4553 4554 4555 4556 4557 4558 4559 4560 4561 4562 4563 4564 4565 4566 4567 4568 4569 4570 4571 4572 4573 4574 4575 4576 4577 4578 4579 4580 4581 4582 4583 4584 4585 4586 4587 4588 4589 4590 4591 4592 4593 4594 4595 4596 4597 4598 4599 4600 4601 4602 4603 4604 4605 4606 4607 4608 4609 4610 4611 4612 4613 4614 4615 4616 4617 4618 4619 4620 4621 4622 4623 4624 4625 4626 4627 4628 4629 4630 4631 4632 4633 4634 4635 4636 4637 4638 4639 4640 4641 4642 4643 4644 4645 4646 4647 4648 4649 4650 4651 4652 4653 4654 4655 4656 4657 4658 4659 4660 4661 4662 4663 4664 4665 4666 4667 4668 4669 4670 4671 4672 4673 4674 4675 4676 4677 4678 4679 4680 4681 4682 4683 4684 4685 4686 4687 4688 4689 4690 4691 4692 4693 4694 4695 4696 4697 4698 4699 4700 4701 4702 4703 4704 4705 4706 4707 4708 4709 4710 4711 4712 4713 4714 4715 4716 4717 4718 4719 4720 4721 4722 4723 4724 4725 4726 4727 4728 4729 4730 4731 4732 4733 4734 4735 4736 4737 4738 4739 4740 4741 4742 4743 4744 4745 4746 4747 4748 4749 4750 4751 4752 4753 4754 4755 4756 4757 4758 4759 4760 4761 4762 4763 4764 4765 4766 4767 4768 4769 4770 4771 4772 4773 4774 4775 4776 4777 4778 4779 4780 4781 4782 4783 4784 4785 4786 4787 4788 4789 4790 4791 4792 4793 4794 4795 4796 4797 4798 4799 4800 4801 4802 4803 4804 4805 4806 4807 4808 4809 4810 4811 4812 4813 4814 4815 4816 4817 4818 4819 4820 4821 4822 4823 4824 4825 4826 4827 4828 4829 4830 4831 4832 4833 4834 4835 4836 4837 4838 4839 4840 4841 4842 4843 4844 4845 4846 4847 4848 4849 4850 4851 4852 4853 4854 4855 4856 4857 4858 4859 4860 4861 4862 4863 4864 4865 4866 4867 4868 4869 4870 4871 4872 4873 4874 4875 4876 4877 4878 4879 4880 4881 4882 4883 4884 4885 4886 4887 4888 4889 4890 4891 4892 4893 4894 4895 4896 4897 4898 4899 4900 4901 4902 4903 4904 4905 4906 4907 4908 4909 4910 4911 4912 4913 4914 4915 4916 4917 4918 4919 4920 4921 4922 4923 4924 4925 4926 4927 4928 4929 4930 4931 4932 4933 4934 4935 4936 4937 4938 4939 4940 4941 4942 4943 4944 4945 4946 4947 4948 4949 4950 4951 4952 4953 4954 4955 4956 4957 4958 4959 4960 4961 4962 4963 4964 4965 4966 4967 4968 4969 4970 4971 4972 4973 4974 4975 4976 4977 4978 4979 4980 4981 4982 4983 4984 4985 4986 4987 4988 4989 4990 4991 4992 4993 4994 4995 4996 4997 4998 4999 5000 5001 5002 5003 5004 5005 5006 5007 5008 5009 5010 5011 5012 5013 5014 5015 5016 5017 5018 5019 5020 5021 5022 5023 5024 5025 5026 5027 5028 5029 5030 5031 5032 5033 5034 5035 5036 5037 5038 5039 5040 5041 5042 5043 5044 5045 5046 5047 5048 5049 5050 5051 5052 5053 5054 5055 5056 5057 5058 5059 5060 5061 5062 5063 5064 5065 5066 5067 5068 5069 5070 5071 5072 5073 5074 5075 5076 5077 5078 5079 5080 5081 5082 5083 5084 5085 5086 5087 5088 5089 5090 5091 5092 5093 5094 5095 5096 5097 5098 5099 5100 5101 5102 5103 5104 5105 5106 5107 5108 5109 5110 5111 5112 5113 5114 5115 5116 5117 5118 5119 5120 5121 5122 5123 5124 5125 5126 5127 5128 5129 5130 5131 5132 5133 5134 5135 5136 5137 5138 5139 5140 5141 5142 5143 5144 5145 5146 5147 5148 5149 5150 5151 5152 5153 5154 5155 5156 5157 5158 5159 5160 5161 5162 5163 5164 5165 5166 5167 5168 5169 5170 5171 5172 5173 5174 5175 5176 5177 5178 5179 5180 5181 5182 5183 5184 5185 5186 5187 5188 5189 5190 5191 5192 5193 5194 5195 5196 5197 5198 5199 5200 5201 5202 5203 5204 5205 5206 5207 5208 5209 5210 5211 5212 5213 5214 5215 5216 5217 5218 5219 5220 5221 5222 5223 5224 5225 5226 5227 5228 5229 5230 5231 5232 5233 5234 5235 5236 5237 5238 5239 5240 5241 5242 5243 5244 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257 5258 5259 5260 5261 5262 5263 5264 5265 5266 5267 5268 5269 5270 5271 5272 5273 5274 5275 5276 5277 5278 5279 5280 5281 5282 5283 5284 5285 5286 5287 5288 5289 5290 5291 5292 5293 5294 5295 5296 5297 5298 5299 5300 5301 5302 5303 5304 5305 5306 5307 5308 5309 5310 5311 5312 5313 5314 5315 5316 5317 5318 5319 5320 5321 5322 5323 5324 5325 5326 5327 5328 5329 5330 5331 5332 5333 5334 5335 5336 5337 5338 5339 5340 5341 5342 5343 5344 5345 5346 5347 5348 5349 5350 5351 5352 5353 5354 5355 5356 5357 5358 5359 5360 5361 5362 5363 5364 5365 5366 5367 5368 5369 5370 5371 5372 5373 5374 5375 5376 5377 5378 5379 5380 5381 5382 5383 5384 5385 5386 5387 5388 5389 5390 5391 5392 5393 5394 5395 5396 5397 5398 5399 5400 5401 5402 5403 5404 5405 5406 5407 5408 5409 5410 5411 5412 5413 5414 5415 5416 5417 5418 5419 5420 5421 5422 5423 5424 5425 5426 5427 5428 5429 5430 5431 5432 5433 5434 5435 5436 5437 5438 5439 5440 5441 5442 5443 5444 5445 5446 5447 5448 5449 5450 5451 5452 5453 5454 5455 5456 5457 5458 5459 5460 5461 5462 5463 5464 5465 5466 5467 5468 5469 5470 5471 5472 5473 5474 5475 5476 5477 5478 5479 5480 5481 5482 5483 5484 5485 5486 5487 5488 5489 5490 5491 5492 5493 5494 5495 5496 5497 5498 5499 5500 5501 5502 5503 5504 5505 5506 5507 5508 5509 5510 5511 5512 5513 5514 5515 5516 5517 5518 5519 5520 5521 5522 5523 5524 5525 5526 5527 5528 5529 5530 5531 5532 5533 5534 5535 5536 5537 5538 5539 5540 5541 5542 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 5553 5554 5555 5556 5557 5558 5559 5560 5561 5562 5563 5564 5565 5566 5567 5568 5569 5570 5571 5572 5573 5574 5575 5576 5577 5578 5579 5580 5581 5582 5583 5584 5585 5586 5587 5588 5589 5590 5591 5592 5593 5594 5595 5596 5597 5598 5599 5600 5601 5602 5603 5604 5605 5606 5607 5608 5609 5610 5611 5612 5613 5614 5615 5616 5617 5618 5619 5620 5621 5622 5623 5624 5625 5626 5627 5628 5629 5630 5631 5632 5633 5634 5635 5636 5637 5638 5639 5640 5641 5642 5643 5644 5645 5646 5647 5648 5649 5650 5651 5652 5653 5654 5655 5656 5657 5658 5659 5660 5661 5662 5663 5664 5665 5666 5667 5668 5669 5670 5671 5672 5673 5674 5675 5676 5677 5678 5679 5680 5681 5682 5683 5684 5685 5686 5687 5688 5689 5690 5691 5692 5693 5694 5695 5696 5697 5698 5699 5700 5701 5702 5703 5704 5705 5706 5707 5708 5709 5710 5711 5712 5713 5714 5715 5716 5717 5718 5719 5720 5721 5722 5723 5724 5725 5726 5727 5728 5729 5730 5731 5732 5733 5734 5735 5736 5737 5738 5739 5740 5741 5742 5743 5744 5745 5746 5747 5748 5749 5750 5751 5752 5753 5754 5755 5756 5757 5758 5759 5760 5761 5762 5763 5764 5765 5766 5767 5768 5769 5770 5771 5772 5773 5774 5775 5776 5777 5778 5779 5780 5781 5782 5783 5784 5785 5786 5787 5788 5789 5790 5791 5792 5793 5794 5795 5796 5797 5798 5799 5800 5801 5802 5803 5804 5805 5806 5807 5808 5809 5810 5811 5812 5813 5814 5815 5816 5817 5818 5819 5820 5821 5822 5823 5824 5825 5826 5827 5828 5829 5830 5831 5832 5833 5834 5835 5836 5837 5838 5839 5840 5841 5842 5843 5844 5845 5846 5847 5848 5849 5850 5851 5852 5853 5854 5855 5856 5857 5858 5859 5860 5861 5862 5863 5864 5865 5866 5867 5868 5869 5870 5871 5872 5873 5874 5875 5876 5877 5878 5879 5880 5881 5882 5883 5884 5885 5886 5887 5888 5889 5890 5891 5892 5893 5894 5895 5896 5897 5898 5899 5900 5901 5902 5903 5904 5905 5906 5907 5908 5909 5910 5911 5912 5913 5914 5915 5916 5917 5918 5919 5920 5921 5922 5923 5924 5925 5926 5927 5928 5929 5930 5931 5932 5933 5934 5935 5936 5937 5938 5939 5940 5941 5942 5943 5944 5945 5946 5947 5948 5949 5950 5951 5952 5953 5954 5955 5956 5957 5958 5959 5960 5961 5962 5963 5964 5965 5966 5967 5968 5969 5970 5971 5972 5973 5974 5975 5976 5977 5978 5979 5980 5981 5982 5983 5984 5985 5986 5987 5988 5989 5990 5991 5992 5993 5994 5995 5996 5997 5998 5999 6000 6001 6002 6003 6004 6005 6006 6007 6008 6009 6010 6011 6012 6013 6014 6015 6016 6017 6018 6019 6020 6021 6022 6023 6024 6025 6026 6027 6028 6029 6030 6031 6032 6033 6034 6035 6036 6037 6038 6039 6040 6041 6042 6043 6044 6045 6046 6047 6048 6049 6050 6051 6052 6053 6054 6055 6056 6057 6058 6059 6060 6061 6062 6063 6064 6065 6066 6067 6068 6069 6070 6071 6072 6073 6074 6075 6076 6077 6078 6079 6080 6081 6082 6083 6084 6085 6086 6087 6088 6089 6090 6091 6092 6093 6094 6095 6096 6097 6098 6099 6100 6101 6102 6103 6104 6105 6106 6107 6108 6109 6110 6111 6112 6113 6114 6115 6116 6117 6118 6119 6120 6121 6122 6123 6124 6125 6126 6127 6128 6129 6130 6131 6132 6133 6134 6135 6136 6137 6138 6139 6140 6141 6142 6143 6144 6145 6146 6147 6148 6149 6150 6151 6152 6153 6154 6155 6156 6157 6158 6159 6160 6161 6162 6163 6164 6165 6166 6167 6168 6169 6170 6171 6172 6173 6174 6175 6176 6177 6178 6179 6180 6181 6182 6183 6184 6185 6186 6187 6188 6189 6190 6191 6192 6193 6194 6195 6196 6197 6198 6199 6200 6201 6202 6203 6204 6205 6206 6207 6208 6209 6210 6211 6212 6213 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 6224 6225 6226 6227 6228 6229 6230 6231 6232 6233 6234 6235 6236 6237 6238 6239 6240 6241 6242 6243 6244 6245 6246 6247 6248 6249 6250 6251 6252 6253 6254 6255 6256 6257 6258 6259 6260 6261 6262 6263 6264 6265 6266 6267 6268 6269 6270 6271 6272 6273 6274 6275 6276 6277 6278 6279 6280 6281 6282 6283 6284 6285 6286 6287 6288 6289 6290 6291 6292 6293 6294 6295 6296 6297 6298 6299 6300 6301 6302 6303 6304 6305 6306 6307 6308 6309 6310 6311 6312 6313 6314 6315 6316 6317 6318 6319 6320 6321 6322 6323 6324 6325 6326 6327 6328 6329 6330 6331 6332 6333 6334 6335 6336 6337 6338 6339 6340 6341 6342 6343 6344 6345 6346 6347 6348 6349 6350 6351 6352 6353 6354 6355 6356 6357 6358 6359 6360 6361 6362 6363 6364 6365 6366 6367 6368 6369 6370 6371 6372 6373 6374 6375 6376 6377 6378 6379 6380 6381 6382 6383 6384 6385 6386 6387 6388 6389 6390 6391 6392 6393 6394 6395 6396 6397 6398 6399 6400 6401 6402 6403 6404 6405 6406 6407 6408 6409 6410 6411 6412 6413 6414 6415 6416 6417 6418 6419 6420 6421 6422 6423 6424 6425 6426 6427 6428 6429 6430 6431 6432 6433 6434 6435 6436 6437 6438 6439 6440 6441 6442 6443 6444 6445 6446 6447 6448 6449 6450 6451 6452 6453 6454 6455 6456 6457 6458 6459 6460 6461 6462 6463 6464 6465 6466 6467 6468 6469 6470 6471 6472 6473 6474 6475 6476 6477 6478 6479 6480 6481 6482 6483 6484 6485 6486 6487 6488 6489 6490 6491 6492 6493 6494 6495 6496 6497 6498 6499 6500 6501 6502 6503 6504 6505 6506 6507 6508 6509 6510 6511 6512 6513 6514 6515 6516 6517 6518 6519 6520 6521 6522 6523 6524 6525 6526 6527 6528 6529 6530 6531 6532 6533 6534 6535 6536 6537 6538 6539 6540 6541 6542 6543 6544 6545 6546 6547 6548 6549 6550 6551 6552 6553 6554 6555 6556 6557 6558 6559 6560 6561 6562 6563 6564 6565 6566 6567 6568 6569 6570 6571 6572 6573 6574 6575 6576 6577 6578 6579 6580 6581 6582 6583 6584 6585 6586 6587 6588 6589 6590 6591 6592 6593 6594 6595 6596 6597 6598 6599 6600 6601 6602 6603 6604 6605 6606 6607 6608 6609 6610 6611 6612 6613 6614 6615 6616 6617 6618 6619 6620 6621 6622 6623 6624 6625 6626 6627 6628 6629 6630 6631 6632 6633 6634 6635 6636 6637 6638 6639 6640 6641 6642 6643 6644 6645 6646 6647 6648 6649 6650 6651 6652 6653 6654 6655 6656 6657 6658 6659 6660 6661 6662 6663 6664 6665 6666 6667 6668 6669 6670 6671 6672 6673 6674 6675 6676 6677 6678 6679 6680 6681 6682 6683 6684 6685 6686 6687 6688 6689 6690 6691 6692 6693 6694 6695 6696 6697 6698 6699 6700 6701 6702 6703 6704 6705 6706 6707 6708 6709 6710 6711 6712 6713 6714 6715 6716 6717 6718 6719 6720 6721 6722 6723 6724 6725 6726 6727 6728 6729 6730 6731 6732 6733 6734 6735 6736 6737 6738 6739 6740 6741 6742 6743 6744 6745 6746 6747 6748 6749 6750 6751 6752 6753 6754 6755 6756 6757 6758 6759 6760 6761 6762 6763 6764 6765 6766 6767 6768 6769 6770 6771 6772 6773 6774 6775 6776 6777 6778 6779 6780 6781 6782 6783 6784 6785 6786 6787 6788 6789 6790 6791 6792 6793 6794 6795 6796 6797 6798 6799 6800 6801 6802 6803 6804 6805 6806 6807 6808 6809 6810 6811 6812 6813 6814 6815 6816 6817 6818 6819 6820 6821 6822 6823 6824 6825 6826 6827 6828 6829 6830 6831 6832 6833 6834 6835 6836 6837 6838 6839 6840 6841 6842 6843 6844 6845 6846 6847 6848 6849 6850 6851 6852 6853 6854 6855 6856 6857 6858 6859 6860 6861 6862 6863 6864 6865 6866 6867 6868 6869 6870 6871 6872 6873 6874 6875 6876 6877 6878 6879 6880 6881 6882 6883 6884 6885 6886 6887 6888 6889 6890 6891 6892 6893 6894 6895 6896 6897 6898 6899 6900 6901 6902 6903 6904 6905 6906 6907 6908 6909 6910 6911 6912 6913 6914 6915 6916 6917 6918 6919 6920 6921 6922 6923 6924 6925 6926 6927 6928 6929 6930 6931 6932 6933 6934 6935 6936 6937 6938 6939 6940 6941 6942 6943 6944 6945 6946 6947 6948 6949 6950 6951 6952 6953 6954 6955 6956 6957 6958 6959 6960 6961 6962 6963 6964 6965 6966 6967 6968 6969 6970 6971 6972 6973 6974 6975 6976 6977 6978 6979 6980 6981 6982 6983 6984 6985 6986 6987 6988 6989 6990 6991 6992 6993 6994 6995 6996 6997 6998 6999 7000 7001 7002 7003 7004 7005 7006 7007 7008 7009 7010 7011 7012 7013 7014 7015 7016 7017 7018 7019 7020 7021 7022 7023 7024 7025 7026 7027 7028 7029 7030 7031 7032 7033 7034 7035 7036 7037 7038 7039 7040 7041 7042 7043 7044 7045 7046 7047 7048 7049 7050 7051 7052 7053 7054 7055 7056 7057 7058 7059 7060 7061 7062 7063 7064 7065 7066 7067 7068 7069 7070 7071 7072 7073 7074 7075 7076 7077 7078 7079 7080 7081 7082 7083 7084 7085 7086 7087 7088 7089 7090 7091 7092 7093 7094 7095 7096 7097 7098 7099 7100 7101 7102 7103 7104 7105 7106 7107 7108 7109 7110 7111 7112 7113 7114 7115 7116 7117 7118 7119 7120 7121 7122 7123 7124 7125 7126 7127 7128 7129 7130 7131 7132 7133 7134 7135 7136 7137 7138 7139 7140 7141 7142 7143 7144 7145 7146 7147 7148 7149 7150 7151 7152 7153 7154 7155 7156 7157 7158 7159 7160 7161 7162 7163 7164 7165 7166 7167 7168 7169 7170 7171 7172 7173 7174 7175 7176 7177 7178 7179 7180 7181 7182 7183 7184 7185 7186 7187 7188 7189 7190 7191 7192 7193 7194 7195 7196 7197 7198 7199 7200 7201 7202 7203 7204 7205 7206 7207 7208 7209 7210 7211 7212 7213 7214 7215 7216 7217 7218 7219 7220 7221 7222 7223 7224 7225 7226 7227 7228 7229 7230 7231 7232 7233 7234 7235 7236 7237 7238 7239 7240 7241 7242 7243 7244 7245 7246 7247 7248 7249 7250 7251 7252 7253 7254 7255 7256 7257 7258 7259 7260 7261 7262 7263 7264 7265 7266 7267 7268 7269 7270 7271 7272 7273 7274 7275 7276 7277 7278 7279 7280 7281 7282 7283 7284 7285 7286 7287 7288 7289 7290 7291 7292 7293 7294 7295 7296 7297 7298 7299 7300 7301 7302 7303 7304 7305 7306 7307 7308 7309 7310 7311 7312 7313 7314 7315 7316 7317 7318 7319 7320 7321 7322 7323 7324 7325 7326 7327 7328 7329 7330 7331 7332 7333 7334 7335 7336 7337 7338 7339 7340 7341 7342 7343 7344 7345 7346 7347 7348 7349 7350 7351 7352 7353 7354 7355 7356 7357 7358 7359 7360 7361 7362 7363 7364 7365 7366 7367 7368 7369 7370 7371 7372 7373 7374 7375 7376 7377 7378 7379 7380 7381 7382 7383 7384 7385 7386 7387 7388 7389 7390 7391 7392 7393 7394 7395 7396 7397 7398 7399 7400 7401 7402 7403 7404 7405 7406 7407 7408 7409 7410 7411 7412 7413 7414 7415 7416 7417 7418 7419 7420 7421 7422 7423 7424 7425 7426 7427 7428 7429 7430 7431 7432 7433 7434 7435 7436 7437 7438 7439 7440 7441 7442 7443 7444 7445 7446 7447 7448 7449 7450 7451 7452 7453 7454 7455 7456 7457 7458 7459 7460 7461 7462 7463 7464 7465 7466 7467 7468 7469 7470 7471 7472 7473 7474 7475 7476 7477 7478 7479 7480 7481 7482 7483 7484 7485 7486 7487 7488 7489 7490 7491 7492 7493 7494 7495 7496 7497 7498 7499 7500 7501 7502 7503 7504 7505 7506 7507 7508 7509 7510 7511 7512 7513 7514 7515 7516 7517 7518 7519 7520 7521 7522 7523 7524 7525 7526 7527 7528 7529 7530 7531 7532 7533 7534 7535 7536 7537 7538 7539 7540 7541 7542 7543 7544 7545 7546 7547 7548 7549 7550 7551 7552 7553 7554 7555 7556 7557 7558 7559 7560 7561 7562 7563 7564 7565 7566 7567 7568 7569 7570 7571 7572 7573 7574 7575 7576 7577 7578 7579 7580 7581 7582 7583 7584 7585 7586 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 7597 7598 7599 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 7610 7611 7612 7613 7614 7615 7616 7617 7618 7619 7620 7621 7622 7623 7624 7625 7626 7627 7628 7629 7630 7631 7632 7633 7634 7635 7636 7637 7638 7639 7640 7641 7642 7643 7644 7645 7646 7647 7648 7649 7650 7651 7652 7653 7654 7655 7656 7657 7658 7659 7660 7661 7662 7663 7664 7665 7666 7667 7668 7669 7670 7671 7672 7673 7674 7675 7676 7677 7678 7679 7680 7681 7682 7683 7684 7685 7686 7687 7688 7689 7690 7691 7692 7693 7694 7695 7696 7697 7698 7699 7700 7701 7702 7703 7704 7705 7706 7707 7708 7709 7710 7711 7712 7713 7714 7715 7716 7717 7718 7719 7720 7721 7722 7723 7724 7725 7726 7727 7728 7729 7730 7731 7732 7733 7734 7735 7736 7737 7738 7739 7740 7741 7742 7743 7744 7745 7746 7747 7748 7749 7750 7751 7752 7753 7754 7755 7756 7757 7758 7759 7760 7761 7762 7763 7764 7765 7766 7767 7768 7769 7770 7771 7772 7773 7774 7775 7776 7777 7778 7779 7780 7781 7782 7783 7784 7785 7786 7787 7788 7789 7790 7791 7792 7793 7794 7795 7796 7797 7798 7799 7800 7801 7802 7803 7804 7805 7806 7807 7808 7809 7810 7811 7812 7813 7814 7815 7816 7817 7818 7819 7820 7821 7822 7823 7824 7825 7826 7827 7828 7829 7830 7831 7832 7833 7834 7835 7836 7837 7838 7839 7840 7841 7842 7843 7844 7845 7846 7847 7848 7849 7850 7851 7852 7853 7854 7855 7856 7857 7858 7859 7860 7861 7862 7863 7864 7865 7866 7867 7868 7869 7870 7871 7872 7873 7874 7875 7876 7877 7878 7879 7880 7881 7882 7883 7884 7885 7886 7887 7888 7889 7890 7891 7892 7893 7894 7895 7896 7897 7898 7899 7900 7901 7902 7903 7904 7905 7906 7907 7908 7909 7910 7911 7912 7913 7914 7915 7916 7917 7918 7919 7920 7921 7922 7923 7924 7925 7926 7927 7928 7929 7930 7931 7932 7933 7934 7935 7936 7937 7938 7939 7940 7941 7942 7943 7944 7945 7946 7947 7948 7949 7950 7951 7952 7953 7954 7955 7956 7957 7958 7959 7960 7961 7962 7963 7964 7965 7966 7967 7968 7969 7970 7971 7972 7973 7974 7975 7976 7977 7978 7979 7980 7981 7982 7983 7984 7985 7986 7987 7988 7989 7990 7991 7992 7993 7994 7995 7996 7997 7998 7999 8000 8001 8002 8003 8004 8005 8006 8007 8008 8009 8010 8011 8012 8013 8014 8015 8016 8017 8018 8019 8020 8021 8022 8023 8024 8025 8026 8027 8028 8029 8030 8031 8032 8033 8034 8035 8036 8037 8038 8039 8040 8041 8042 8043 8044 8045 8046 8047 8048 8049 8050 8051 8052 8053 8054 8055 8056 8057 8058 8059 8060 8061 8062 8063 8064 8065 8066 8067 8068 8069 8070 8071 8072 8073 8074 8075 8076 8077 8078 8079 8080 8081 8082 8083 8084 8085 8086 8087 8088 8089 8090 8091 8092 8093 8094 8095 8096 8097 8098 8099 8100 8101 8102 8103 8104 8105 8106 8107 8108 8109 8110 8111 8112 8113 8114 8115 8116 8117 8118 8119 8120 8121 8122 8123 8124 8125 8126 8127 8128 8129 8130 8131 8132 8133 8134 8135 8136 8137 8138 8139 8140 8141 8142 8143 8144 8145 8146 8147 8148 8149 8150 8151 8152 8153 8154 8155 8156 8157 8158 8159 8160 8161 8162 8163 8164 8165 8166 8167 8168 8169 8170 8171 8172 8173 8174 8175 8176 8177 8178 8179 8180 8181 8182 8183 8184 8185 8186 8187 8188 8189 8190 8191 8192 8193 8194 8195 8196 8197 8198 8199 8200 8201 8202 8203 8204 8205 8206 8207 8208 8209 8210 8211 8212 8213 8214 8215 8216 8217 8218 8219 8220 8221 8222 8223 8224 8225 8226 8227 8228 8229 8230 8231 8232 8233 8234 8235 8236 8237 8238 8239 8240 8241 8242 8243 8244 8245 8246 8247 8248 8249 8250 8251 8252 8253 8254 8255 8256 8257 8258 8259 8260 8261 8262 8263 8264 8265 8266 8267 8268 8269 8270 8271 8272 8273 8274 8275 8276 8277 8278 8279 8280 8281 8282 8283 8284 8285 8286 8287 8288 8289 8290 8291 8292 8293 8294 8295 8296 8297 8298 8299 8300 8301 8302 8303 8304 8305 8306 8307 8308 8309 8310 8311 8312 8313 8314 8315 8316 8317 8318 8319 8320 8321 8322 8323 8324 8325 8326 8327 8328 8329 8330 8331 8332 8333 8334 8335 8336 8337 8338 8339 8340 8341 8342 8343 8344 8345 8346 8347 8348 8349 8350 8351 8352 8353 8354 8355 8356 8357 8358 8359 8360 8361 8362 8363 8364 8365 8366 8367 8368 8369 8370 8371 8372 8373 8374 8375 8376 8377 8378 8379 8380 8381 8382 8383 8384 8385 8386 8387 8388 8389 8390 8391 8392 8393 8394 8395 8396 8397 8398 8399 8400 8401 8402 8403 8404 8405 8406 8407 8408 8409 8410 8411 8412 8413 8414 8415 8416 8417 8418 8419 8420 8421 8422 8423 8424 8425 8426 8427 8428 8429 8430 8431 8432 8433 8434 8435 8436 8437 8438 8439 8440 8441 8442 8443 8444 8445 8446 8447 8448 8449 8450 8451 8452
|
* 2018-04-28(Tal Galili) update docs |4cb6652|
| NAMESPACE | 1 +
| man/colored_dots.Rd | 192 ++++++++++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 193 insertions(+)
* 2018-04-28(Tal Galili) temp rename 2 |2be950c|
| R/colored_dots.R | 441 ++++++++++++++++++++++++++++++++++++++++++++++++++
| R/colored_dots111.R | 441 --------------------------------------------------
| 2 files changed, 441 insertions(+), 441 deletions(-)
* 2018-04-28(Tal Galili) temp rename |d8b1ce7|
| R/colored_Dots.R | 441 --------------------------------------------------
| R/colored_dots.R | 441 --------------------------------------------------
| R/colored_dots111.R | 441 ++++++++++++++++++++++++++++++++++++++++++++++++++
| 3 files changed, 441 insertions(+), 882 deletions(-)
* 2018-04-28(Tal Galili) stlyr the colored_dots file/functions |3f9da97|
| NEWS | 9 +
| R/colored_Dots.R | 493 ++++++++++++++++++++++++++---------------------------
| R/colored_dots.R | 493 ++++++++++++++++++++++++++---------------------------
| 3 files changed, 485 insertions(+), 510 deletions(-)
* 2018-04-28(Tal Galili) rename color_dots file to be lower case |c1351e3|
| R/colored_dots.R | 458 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 458 insertions(+)
* 2018-04-28(Tal Galili) Added Chase Clark as a contributor |949cebf|
| DESCRIPTION | 10 +++++++---
| 1 file changed, 7 insertions(+), 3 deletions(-)
* 2018-03-03(Chase Clark) Added Roxygen, added examples similar to "colored_bars" |9cb4b46|
| R/colored_Dots.R | 504 ++++++++++++++++++++++++++++++++++++++++-------------
| 1 file changed, 385 insertions(+), 119 deletions(-)
* 2018-01-15(Chase Clark) Add two comments |cbd2e2d|
| R/colored_Dots.R | 8 +++++---
| 1 file changed, 5 insertions(+), 3 deletions(-)
* 2018-01-01(Chase Clark) Create colored_Dots.R |501fa8b|
| R/colored_Dots.R | 190 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 190 insertions(+)
* 2018-03-16(Tal Galili) Update version and added Manuela Hummel as author of: branches_attr_by_lists - Change col/lwd/lty of branches from the root down to clusters defined by list of labels of respective members |26f20b6|
| DESCRIPTION | 8 +++++---
| NEWS | 9 +++++++++
| 2 files changed, 14 insertions(+), 3 deletions(-)
* 2018-03-14(Hummel) added test unit for branches_attr_by_labels |6cf0d62|
| tests/testthat/test-branches_attr_by.R | 32 ++++++++++++++++++++++++++++++++
| 1 file changed, 32 insertions(+)
* 2018-02-28(Hummel) added documentation for branches_attr_by_lists |1950401|
| man/branches_attr_by_lists.Rd | 59 +++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 59 insertions(+)
* 2018-02-28(Hummel) added documentation for branches_attr_by_lists |e02f1ef|
| man/set.Rd | 21 +++++++++++++++++----
| 1 file changed, 17 insertions(+), 4 deletions(-)
* 2018-02-28(Hummel) added function branches_attr_by_lists |11a232f|
| NAMESPACE | 1 +
| R/branches_attr_by.R | 75 ++++++++++++++++++++++++++++++++++++++++++++++++++
| R/set.dendrogram.R | 24 ++++++++++++++--
| 3 files changed, 97 insertions(+), 3 deletions(-)
* 2018-02-10(Tal Galili) remove labeltodendro. |49dde87|
| DESCRIPTION | 2 +-
| NEWS | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2018-02-10(Tal Galili) Fix: Rd line widths ... NOTE |54b9889|
| R/get_subdendrograms.R | 6 ++++--
| man/find_dendrogram.Rd | 3 ++-
| man/get_subdendrograms.Rd | 3 ++-
| 3 files changed, 8 insertions(+), 4 deletions(-)
* 2018-02-10(Tal Galili) update NEWS.md |c13a2c6|
| ChangeLog | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 16 ++++++++++++++++
| 2 files changed, 69 insertions(+)
* 2018-02-10(Tal Galili) Remove NMF from suggested |846f881|
| DESCRIPTION | 3 +--
| NEWS | 7 +++++--
| vignettes/introduction.Rmd | 34 ++++++++++++++++++++--------------
| 3 files changed, 26 insertions(+), 18 deletions(-)
* 2018-01-19(Tal Galili) add docs and fix #61 |1d12d13|
| NAMESPACE | 2 ++
| man/find_dendrogram.Rd | 39 ++++++++++++++++++++++++++++++
| man/get_subdendrograms.Rd | 59 +++++++++++++++++++++++++++++++++++++++++++++
| man/seriate_dendrogram.Rd | 4 +--
| 4 files changed, 102 insertions(+), 2 deletions(-)
* 2018-01-19(Tal Galili) Updated NEWS and added storaged as a contributor |dccff9b|
| DESCRIPTION | 10 ++++++----
| NEWS | 13 +++++++++++++
| 2 files changed, 19 insertions(+), 4 deletions(-)
* 2018-01-19(Tal Galili) update get_dendrograms example to demonstrate how to plot it in a heatmap.2 |f9c576e|
| R/get_subdendrograms.R | 24 ++++++++++++++++++++++--
| 1 file changed, 22 insertions(+), 2 deletions(-)
* 2018-01-19(Tal Galili) styler the functions |e02364d|
| R/get_subdendrograms.R | 52 ++++++++++++++++++++++++------------------------
| 1 file changed, 26 insertions(+), 26 deletions(-)
* 2018-01-19(Tal Galili) move to using _ instead of . |cb1f7bb|
| R/get_subdendrograms.R | 34 +++++++++++++++-------------------
| 1 file changed, 15 insertions(+), 19 deletions(-)
* 2018-01-11(storaged) Functions that help to extract subdendrogram structures based on given number of expected stuctures |14130e4|
| R/get_subdendrograms.R | 77 ++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 77 insertions(+)
* 2017-12-19(Tal Galili) Merge pull request #58 from Alanocallaghan/master |7d11920
|\
| * 2017-12-19(Alan O'Callaghan) Bugfix seriate_dendrogram |e77e2be
|/ |
| R/seriate_dendrogram.R | 32 ++++++++++++++++----------------
| 1 file changed, 16 insertions(+), 16 deletions(-)
* 2017-12-10(Tal Galili) Adding some #' par(mfrow = c(1,2)) |f5ad443|
| R/color_branches.R | 7 ++++++-
| man/color_branches.Rd | 7 ++++++-
| 2 files changed, 12 insertions(+), 2 deletions(-)
* 2017-11-13(Tal Galili) Bump version to 0.16.0 |879d98c|
| ChangeLog | 275 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| DESCRIPTION | 2 +-
| NEWS | 2 +-
| NEWS.md | 198 ++++++++++++++++++++++++------------------
| 4 files changed, 390 insertions(+), 87 deletions(-)
* 2017-11-13(Tal Galili) fix long url: |3e9f0d6|
| R/color_branches.R | 2 +-
| man/color_branches.Rd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2017-11-13(Tal Galili) Fix: (invalid URL) |e0386e1|
| vignettes/introduction.Rmd | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2017-11-13(Tal Galili) how to cite |eeb1c1e|
| README.md | 23 +++++++++++++++++++++++
| 1 file changed, 23 insertions(+)
* 2017-10-26(Tal Galili) typo |c806acf|
| inst/CITATION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2017-09-27(Tal Galili) Another example for color_branches |99bfa39|
| R/color_branches.R | 34 ++++++++++++++++++++++++++++++++++
| man/color_branches.Rd | 21 +++++++++++++++++++++
| 2 files changed, 55 insertions(+)
* 2017-09-27(Tal Galili) circlize_dendrogram - can now handle dendrograms with non unique labels. A warning is issued, and a running number is padded to the labels. |44d1ca9|
| DESCRIPTION | 2 +-
| NEWS | 3 ++-
| R/circlize.R | 8 ++++++++
| 3 files changed, 11 insertions(+), 2 deletions(-)
* 2017-06-10(Tal Galili) update date |2a303ef|
| DESCRIPTION | 2 +-
| NEWS | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2017-06-10(Tal Galili) Added min_depth, max_depth - measures the min/max depth of a tree (from the root to the closest/furtherest leaf). |d88249c|
| NAMESPACE | 2 ++
| NEWS | 1 +
| R/depth.R | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| man/depth.Rd | 34 +++++++++++++++++++++++++++++++++
| 4 files changed, 97 insertions(+)
* 2017-05-31(Tal Galili) Updating pvrect2 example |33efee8|
| R/pvclust.R | 4 ++--
| man/pvrect2.Rd | 4 ++--
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2017-05-29(Tal Galili) Fix rect.dendrogram - it now deals much better with setting the lower part of the rectangle to be below the labels. |a756d9a|
| NEWS | 2 ++
| R/rect.dendrogram.R | 21 +++++++++++++++++++--
| 2 files changed, 21 insertions(+), 2 deletions(-)
* 2017-05-29(Tal Galili) pvrect2 function added - Draw Rectangles Around a Dendrogram's Clusters with High/Low P-values |56f9e92|
| DESCRIPTION | 4 +-
| NAMESPACE | 1 +
| NEWS | 187 +++++++++++++++++++++++++++++--------------------------
| R/pvclust.R | 114 +++++++++++++++++++++++++++++++--
| man/pvrect2.Rd | 61 ++++++++++++++++++
| 5 files changed, 271 insertions(+), 96 deletions(-)
* 2017-05-28(Tal Galili) Update bioinformatics link |82a3df7|
| DESCRIPTION | 6 +++---
| inst/CITATION | 4 ++--
| 2 files changed, 5 insertions(+), 5 deletions(-)
* 2017-05-19(Tal Galili) Fix #38 by using alternative default for prune (i.e.: reindex_dend=TRUE). Also added examples in the doc to demonstrate its use. |8b948b6|
| R/prune.R | 28 ++++++++++++++++++++--------
| man/prune.Rd | 19 +++++++++++++++----
| man/reindex_dend.Rd | 2 +-
| 3 files changed, 36 insertions(+), 13 deletions(-)
* 2017-05-19(Tal Galili) * refactor reindex_dend to use order.dendrogram * Simpler consolidation of the prune documentation. * added reindex_dend parameter to allow the leaves of a pruned dendrogram to be of the vector of 1:nleaves |f5f09f7|
| NAMESPACE | 2 +-
| NEWS | 2 +-
| R/prune.R | 72 ++++++++++++++++++++-----------------------------
| man/prune.Rd | 10 +++++--
| man/reindex_dend.Rd | 45 +++++++++++++++++++++++++++++++
| man/reindex_dendro.Rd | 43 -----------------------------
| 6 files changed, 84 insertions(+), 90 deletions(-)
* 2017-05-19(Tal Galili) Added John Ma as contributor |10d732d|
| DESCRIPTION | 7 ++++---
| NEWS | 6 +++++-
| 2 files changed, 9 insertions(+), 4 deletions(-)
* 2017-05-19(Tal Galili) Added reindex_dendro doc |9cc6ca6|
| NAMESPACE | 1 +
| man/reindex_dendro.Rd | 43 +++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 44 insertions(+)
* 2017-05-19(Tal Galili) Merge pull request #39 from JohnMCMa/master |b02dcca
|\
| * 2017-03-30(John Ma) Adding function reindex_dendro to resolve problems with as.hclust |1e25e5b| |
| | R/prune.R | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++--
| | 1 file changed, 54 insertions(+), 2 deletions(-)
* | 2017-05-17(Tal Galili) Fix print.ggdend |c3c0a00| |
| | R/ggdend.R | 2 +-
| | 1 file changed, 1 insertion(+), 1 deletion(-)
* | 2017-05-17(Tal Galili) refresh .Rd files. |8b0df89| |
| | man/Bk.Rd | 1 -
| | man/Bk_permutations.Rd | 1 -
| | man/Bk_plot.Rd | 1 -
| | man/DendSer.dendrogram.Rd | 1 -
| | man/FM_index.Rd | 1 -
| | man/FM_index_R.Rd | 1 -
| | man/FM_index_permutation.Rd | 1 -
| | man/FM_index_profdpm.Rd | 1 -
| | man/all.equal.dendrogram.Rd | 3 +--
| | man/all_couple_rotations_at_k.Rd | 1 -
| | man/all_unique.Rd | 1 -
| | man/as.dendlist.Rd | 1 -
| | man/as.phylo.dendrogram.Rd | 1 -
| | man/as_hclust_fixed.Rd | 1 -
| | man/assign_dendextend_options.Rd | 1 -
| | man/assign_values_to_branches_edgePar.Rd | 1 -
| | man/assign_values_to_leaves_edgePar.Rd | 1 -
| | man/assign_values_to_leaves_nodePar.Rd | 1 -
| | man/assign_values_to_nodes_nodePar.Rd | 1 -
| | man/bakers_gamma_for_2_k_matrix.Rd | 1 -
| | man/branches_attr_by_clusters.Rd | 1 -
| | man/branches_attr_by_labels.Rd | 1 -
| | man/circlize_dendrogram.Rd | 7 +++----
| | man/click_rotate.Rd | 7 +++----
| | man/collapse_branch.Rd | 1 -
| | man/color_branches.Rd | 9 ++++-----
| | man/color_labels.Rd | 1 -
| | man/color_unique_labels.Rd | 1 -
| | man/colored_bars.Rd | 9 ++++-----
| | man/common_subtrees_clusters.Rd | 1 -
| | man/cor.dendlist.Rd | 1 -
| | man/cor_FM_index.Rd | 1 -
| | man/cor_common_nodes.Rd | 1 -
| | man/cor_cophenetic.Rd | 1 -
| | man/count_terminal_nodes.Rd | 1 -
| | man/cut_lower_fun.Rd | 7 +++----
| | man/cutree_1h.dendrogram.Rd | 7 +++----
| | man/cutree_1k.dendrogram.Rd | 7 +++----
| | man/dend_diff.Rd | 3 +--
| | man/dendextend-package.Rd | 3 +--
| | man/dendextend_labels.dendrogram.Rd | 1 -
| | man/dendextend_options.Rd | 1 -
| | man/dendlist.Rd | 1 -
| | man/dist.dendlist.Rd | 1 -
| | man/dist_long.Rd | 1 -
| | man/distinct_edges.Rd | 1 -
| | man/duplicate_leaf.Rd | 1 -
| | man/entanglement.Rd | 5 ++---
| | man/fac2num.Rd | 1 -
| | man/find_dend.Rd | 1 -
| | man/find_k.Rd | 1 -
| | man/fix_members_attr.dendrogram.Rd | 1 -
| | man/flatten.dendrogram.Rd | 1 -
| | man/flip_leaves.Rd | 1 -
| | man/get_branches_heights.Rd | 3 +--
| | man/get_childrens_heights.Rd | 1 -
| | man/get_leaves_attr.Rd | 1 -
| | man/get_leaves_branches_attr.Rd | 1 -
| | man/get_leaves_branches_col.Rd | 1 -
| | man/get_leaves_edgePar.Rd | 1 -
| | man/get_leaves_nodePar.Rd | 1 -
| | man/get_nodes_attr.Rd | 1 -
| | man/get_nodes_xy.Rd | 1 -
| | man/get_root_branches_attr.Rd | 1 -
| | man/hang.dendrogram.Rd | 1 -
| | man/has_component_in_attribute.Rd | 1 -
| | man/heights_per_k.dendrogram.Rd | 3 +--
| | man/highlight_branches.Rd | 3 +--
| | man/highlight_distinct_edges.Rd | 3 +--
| | man/identify.dendrogram.Rd | 1 -
| | man/intersect_trees.Rd | 1 -
| | man/is.natural.number.Rd | 7 +++----
| | man/is_null_list.Rd | 1 -
| | man/is_some_class.Rd | 9 ++++-----
| | man/khan.Rd | 1 -
| | man/labels-assign.Rd | 11 +++++------
| | man/labels_cex.Rd | 1 -
| | man/labels_colors.Rd | 3 +--
| | man/ladderize.Rd | 3 +--
| | man/leaf_Colors.Rd | 7 +++----
| | man/lowest_common_branch.Rd | 1 -
| | man/match_order_by_labels.Rd | 1 -
| | man/match_order_dendrogram_by_old_order.Rd | 1 -
| | man/na_locf.Rd | 1 -
| | man/nleaves.Rd | 3 +--
| | man/nnodes.Rd | 1 -
| | man/noded_with_condition.Rd | 1 -
| | man/order.dendrogram-assign.Rd | 1 -
| | man/order.hclust.Rd | 1 -
| | man/partition_leaves.Rd | 1 -
| | man/plot_horiz.dendrogram.Rd | 1 -
| | man/prune.Rd | 1 -
| | man/prune_common_subtrees.dendlist.Rd | 1 -
| | man/prune_leaf.Rd | 1 -
| | man/pvclust_show_signif.Rd | 1 -
| | man/pvclust_show_signif_gradient.Rd | 1 -
| | man/raise.dendrogram.Rd | 1 -
| | man/rank_branches.Rd | 1 -
| | man/rank_order.dendrogram.Rd | 1 -
| | man/rank_values_with_clusters.Rd | 1 -
| | man/rect.dendrogram.Rd | 1 -
| | man/reexports.Rd | 4 ++--
| | man/remove_branches_edgePar.Rd | 1 -
| | man/remove_leaves_nodePar.Rd | 1 -
| | man/remove_nodes_nodePar.Rd | 1 -
| | man/rllply.Rd | 1 -
| | man/rotate.Rd | 5 ++---
| | man/rotate_DendSer.Rd | 1 -
| | man/sample.dendrogram.Rd | 1 -
| | man/seriate_dendrogram.Rd | 1 -
| | man/set.Rd | 5 ++---
| | man/set_labels.Rd | 9 ++++-----
| | man/shuffle.Rd | 3 +--
| | man/sort_2_clusters_vectors.Rd | 1 -
| | man/sort_dist_mat.Rd | 1 -
| | man/sort_levels_values.Rd | 1 -
| | man/tanglegram.Rd | 13 ++++++-------
| | man/theme_dendro.Rd | 7 +++----
| | man/unbranch.Rd | 1 -
| | man/unclass_dend.Rd | 1 -
| | man/untangle.Rd | 11 +++++------
| | man/untangle_DendSer.Rd | 1 -
| | man/untangle_random_search.Rd | 1 -
| | man/untangle_step_rotate_1side.Rd | 1 -
| | man/untangle_step_rotate_2side.Rd | 1 -
| | man/which_leaf.Rd | 1 -
| | man/which_node.Rd | 1 -
| | 127 files changed, 75 insertions(+), 201 deletions(-)
* | 2017-05-17(Tal Galili) Add print.ggdend - a wrapper for ggplot2::ggplot of a ggdend object. |95ae952| |
| | DESCRIPTION | 2 +-
| | NAMESPACE | 1 +
| | NEWS | 3 +++
| | R/ggdend.R | 8 +++++++-
| | man/cor_bakers_gamma.Rd | 6 ++++--
| | man/cutree-methods.Rd | 11 +++++------
| | man/ggdend.Rd | 18 ++++++++++--------
| | 7 files changed, 31 insertions(+), 18 deletions(-)
* | 2017-05-04(Tal Galili) Mention that dendextendRcpp is no longer supported. |f3e28e6
|/ |
| README.md | 8 ++++----
| 1 file changed, 4 insertions(+), 4 deletions(-)
* 2017-03-27(Tal Galili) remove dendextendRcpp further |af9921e|
| DESCRIPTION | 4 ++--
| NEWS | 3 ++-
| vignettes/introduction.Rmd | 12 +++++++-----
| 3 files changed, 11 insertions(+), 8 deletions(-)
* 2017-03-27(Tal Galili) Rollback viridisLite to viridis (to check if this is what's breaking everything) |abe5348|
| DESCRIPTION | 2 +-
| NAMESPACE | 2 +-
| R/zzz.R | 2 +-
| 3 files changed, 3 insertions(+), 3 deletions(-)
* 2017-03-27(Tal Galili) Fix viridis to viridisLite in NAMESPACE |7ae8a29|
| NAMESPACE | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2017-03-27(Tal Galili) viridis to viridisLite |d183226|
| DESCRIPTION | 6 +++---
| R/zzz.R | 2 +-
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2017-03-27(Tal Galili) Remove dendextendRcpp :( (from tests and suggests) |986bce1|
| DESCRIPTION | 1 -
| NEWS | 5 +++++
| tests/test-all.R | 4 ++--
| 3 files changed, 7 insertions(+), 3 deletions(-)
* 2017-03-24(Tal Galili) update NEWS |ba11350|
| ChangeLog | 131 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
| NEWS.md | 16 +++++++-
| 2 files changed, 142 insertions(+), 5 deletions(-)
* 2017-03-24(Tal Galili) 1.5.0 |d574b43|
| DESCRIPTION | 4 ++--
| NEWS | 9 ++-------
| 2 files changed, 4 insertions(+), 9 deletions(-)
* 2017-03-24(Tal Galili) # this is behaving different for R 3.3.3 and 3.4 - I'm not sure why... (removing the test for now) |57042f7|
| tests/testthat/test-untangle.R | 23 ++++++++++++++++-------
| 1 file changed, 16 insertions(+), 7 deletions(-)
* 2017-03-19(Tal Galili) description not details! |6c7a8b0|
| R/find_dend.R | 2 +-
| man/find_dend.Rd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2017-03-19(Tal Galili) Get cor_cophenetic to work with hclust again |3ee25a1|
| R/cor_cophenetic.R | 8 ++++----
| 1 file changed, 4 insertions(+), 4 deletions(-)
* 2017-03-19(Tal Galili) dend_expend and find_dend - functions for finding a "good" dendrogram for a dist |350de5d|
| NAMESPACE | 2 +
| NEWS | 5 +++
| R/find_dend.R | 111 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| man/find_dend.Rd | 58 ++++++++++++++++++++++++++++
| 4 files changed, 176 insertions(+)
* 2017-03-19(Tal Galili) cor_cophenetic - dend2 can now also be a dist object (allowing to check how close is some clustering to the original distance matrix). |76a479c|
| DESCRIPTION | 4 ++--
| NEWS | 4 ++++
| R/cor_cophenetic.R | 12 ++++++++++--
| man/cor_cophenetic.Rd | 2 +-
| 4 files changed, 17 insertions(+), 5 deletions(-)
* 2017-02-15(Tal Galili) Fix "Undocumented arguments in documentation object 'find_k' ‘x’" |496294c|
| R/find_k.R | 1 +
| man/find_k.Rd | 2 ++
| 2 files changed, 3 insertions(+)
* 2017-02-15(Tal Galili) Fix "is_some_class" from being exported. |ef537ff|
| NAMESPACE | 5 ++---
| R/is.functions.R | 1 -
| 2 files changed, 2 insertions(+), 4 deletions(-)
* 2017-02-15(Tal Galili) document new ggplot S3 methods. |348d8ab|
| man/ggdend.Rd | 7 ++++---
| 1 file changed, 4 insertions(+), 3 deletions(-)
* 2017-02-15(Tal Galili) Simplified the roxygen2 code by using @rdname (and removing many instances of @allias and @usage) |71c8a0d|
| DESCRIPTION | 4 +-
| NAMESPACE | 12 ++++-
| NEWS | 10 ++++
| R/cor_bakers_gamma.R | 18 +++----
| R/cor_cophenetic.R | 16 ++-----
| R/cutree.dendrogram.R | 29 ++----------
| R/dendlist.R | 9 +---
| R/distinct_edges.R | 34 +++-----------
| R/entanglement.R | 25 ++--------
| R/find_k.R | 5 +-
| R/ggdend.R | 29 +++---------
| R/highlight_branches.R | 13 ++----
| R/is.functions.R | 54 +++++++++------------
| R/labels.R | 38 ++-------------
| R/labels_colors.R | 22 +++------
| R/nleaves.R | 53 ++++++---------------
| R/rotate.R | 68 +++++++--------------------
| R/set.dendrogram.R | 47 ++-----------------
| R/tanglegram.R | 69 ++++-----------------------
| R/unbranch.R | 20 ++------
| R/untangle.R | 51 ++++++--------------
| man/click_rotate.Rd | 5 +-
| man/cor_bakers_gamma.Rd | 14 ++++--
| man/cor_cophenetic.Rd | 18 +++----
| man/cutree-methods.Rd | 37 +++++++--------
| man/dend_diff.Rd | 9 ++--
| man/entanglement.Rd | 12 ++---
| man/find_k.Rd | 7 +++
| man/ggdend.Rd | 20 ++++----
| man/highlight_branches.Rd | 18 +++----
| man/highlight_distinct_edges.Rd | 13 ++----
| man/is.dendlist.Rd | 24 ----------
| man/is.dendrogram.Rd | 18 -------
| man/is.dist.Rd | 24 ----------
| man/is.hclust.Rd | 18 -------
| man/is.phylo.Rd | 18 -------
| man/is_some_class.Rd | 41 ++++++++++++++++
| man/labels-assign.Rd | 7 +--
| man/labels_colors.Rd | 4 +-
| man/ladderize.Rd | 4 +-
| man/nleaves.Rd | 2 +
| man/nnodes.Rd | 2 +
| man/rotate.Rd | 13 ++++--
| man/set.Rd | 38 ++++-----------
| man/shuffle.Rd | 2 +
| man/tanglegram.Rd | 98 ++++++++++++++++++---------------------
| man/unbranch.Rd | 8 +++-
| man/untangle.Rd | 21 +++++----
| 48 files changed, 370 insertions(+), 751 deletions(-)
* 2017-02-14(Tal Galili) Fix dend_diff.dendrogram to return to original mfrow after finish plotting. ( fix issue #37 ) |a75223c|
| R/distinct_edges.R | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2017-01-22(Tal Galili) highlight_distinct_edges is now value 3 instead of 2 for tanglegram - so that the gap from lty are not too wide. |01d4a47|
| NEWS | 2 +-
| R/tanglegram.R | 4 ++--
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2017-01-21(Tal Galili) Namespace in Imports field not imported from: 'datasets' |89a52f4|
| NAMESPACE | 1 +
| R/zzz.R | 1 +
| 2 files changed, 2 insertions(+)
* 2017-01-21(Tal Galili) Fix Undocumented arguments in documentation object 'has_component_in_attribute': 'the_attrib' |4e90cf3|
| R/has_edgePar.R | 2 ++
| man/has_component_in_attribute.Rd | 3 +++
| 2 files changed, 5 insertions(+)
* 2017-01-21(Tal Galili) If dend is not a dendrogram, then has_edgePar will return FALSE. |25f4b4d|
| R/has_edgePar.R | 3 +++
| man/has_component_in_attribute.Rd | 1 +
| 2 files changed, 4 insertions(+)
* 2017-01-21(Tal Galili) update dates |c612a6e|
| ChangeLog | 254 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| DESCRIPTION | 2 +-
| NEWS | 6 +-
| NEWS.md | 19 +++++
| 4 files changed, 277 insertions(+), 4 deletions(-)
* 2017-01-21(Tal Galili) tanglegram function now highlights branches only if these parameters are NOT already set in the object. If the tree already has lty/lwd/col - these will not be updated by this parameter. These parameters can be removed from the tree by using `dend %>% set("clear_branches")`. |aef480e|
| NEWS | 2 +-
| R/has_edgePar.R | 2 ++
| R/tanglegram.R | 28 ++++++++++++++++++++++------
| man/has_component_in_attribute.Rd | 2 ++
| man/tanglegram.Rd | 18 +++++++++++++++---
| 5 files changed, 42 insertions(+), 10 deletions(-)
* 2017-01-21(Tal Galili) New functions has_edgePar, has_nodePar - Does a dendrogram has an edgePar/nodePar component? |28ec998|
| NAMESPACE | 3 +++
| NEWS | 3 ++-
| R/has_edgePar.R | 50 +++++++++++++++++++++++++++++++++++++
| man/has_component_in_attribute.Rd | 43 +++++++++++++++++++++++++++++++
| 4 files changed, 98 insertions(+), 1 deletion(-)
* 2017-01-20(Tal Galili) https://cran.r-project.org/web/packages to https://CRAN.R-project.org/package= |531f990|
| R/bk_method.R | 2 +-
| R/magrittr.R | 4 ++--
| README.md | 2 +-
| vignettes/Quick_Introduction.Rmd | 2 +-
| vignettes/dendextend-tutorial.bib | 2 +-
| vignettes/introduction.Rmd | 4 ++--
| 6 files changed, 8 insertions(+), 8 deletions(-)
* 2017-01-20(Tal Galili) Fix "\examples lines wider than 100 characters:" |dd84df4|
| R/highlight_branches.R | 9 ++++++---
| man/highlight_branches.Rd | 9 ++++++---
| 2 files changed, 12 insertions(+), 6 deletions(-)
* 2017-01-20(Tal Galili) http://cran.r-project to https://cran.r-project |460b3aa|
| R/bk_method.R | 4 ++--
| R/colored_bars.R | 2 +-
| R/distinct_edges.R | 2 +-
| R/ggdendro.R | 2 +-
| R/magrittr.R | 10 +++++-----
| R/pvclust.R | 2 +-
| man/colored_bars.Rd | 2 +-
| vignettes/Quick_Introduction.Rmd | 2 +-
| vignettes/dendextend-tutorial.bib | 18 +++++++++---------
| vignettes/disabled/dendextend-tutorial.rnw | 2 +-
| vignettes/introduction.Rmd | 14 +++++++-------
| 11 files changed, 30 insertions(+), 30 deletions(-)
* 2017-01-20(Tal Galili) "Possibly mis-spelled words in DESCRIPTION:" |b9cf5d3|
| DESCRIPTION | 8 ++++----
| 1 file changed, 4 insertions(+), 4 deletions(-)
* 2017-01-07(Tal Galili) Adding highlight_branches to the vignette. |e2cad21|
| vignettes/introduction.Rmd | 53 +++++++++++++++++++++++++++++++++++++++++++-
| 1 file changed, 52 insertions(+), 1 deletion(-)
* 2017-01-07(Tal Galili) Fix colored_bars example to work. props to Jerome Bartholome |4818699|
| vignettes/introduction.Rmd | 19 ++++++++++++++++++-
| 1 file changed, 18 insertions(+), 1 deletion(-)
* 2016-12-25(Tal Galili) highlight_branches - added a heatmap example. |ececc60|
| DESCRIPTION | 1 +
| R/highlight_branches.R | 19 +++++++++++++++++++
| man/highlight_branches.Rd | 19 +++++++++++++++++++
| 3 files changed, 39 insertions(+)
* 2016-12-24(Tal Galili) highlight_branches_col - remove the yellow color (so that the leaves will be visible). |cae9254|
| R/highlight_branches.R | 6 +++---
| man/highlight_branches.Rd | 2 +-
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2016-12-24(Tal Galili) This fixes #33 - although it might be worth improving get_leaves_branches_col in the future. |8976a92|
| R/attr_access.R | 4 ++++
| R/tanglegram.R | 20 ++++++++++++++++++--
| man/get_leaves_branches_col.Rd | 5 +++++
| man/tanglegram.Rd | 5 ++++-
| 4 files changed, 31 insertions(+), 3 deletions(-)
* 2016-12-24(Tal Galili) fix bug in branches_attr_by_clusters (should have values and not value) |93795d0|
| R/branches_attr_by.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2016-12-24(Tal Galili) using TRUE and FALSE instead of T and F. Also moved to using dendextend_get_branches_heights instead of get_branches_heights (so to be more robust). |57054dc|
| R/highlight_branches.R | 14 +++++++-------
| R/zzz.R | 1 +
| man/highlight_branches.Rd | 6 +++---
| 3 files changed, 11 insertions(+), 10 deletions(-)
* 2016-12-24(Tal Galili) added viridis to the example. |eb4f21b|
| R/highlight_branches.R | 1 +
| man/highlight_branches.Rd | 1 +
| 2 files changed, 2 insertions(+)
* 2016-12-24(Tal Galili) Pass include_leaves in get_branches_heights (otherwise it will result in an error) |69461a4|
| R/attr_access.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2016-12-24(Tal Galili) Added example for set("highlight_branches_col") |b083f57|
| R/set.dendrogram.R | 6 ++++++
| man/set.Rd | 6 ++++++
| 2 files changed, 12 insertions(+)
* 2016-12-24(Tal Galili) Updated NEWS about the new "highlight_branches" capabilities. |9e2930c|
| DESCRIPTION | 2 +-
| NEWS | 5 ++++-
| 2 files changed, 5 insertions(+), 2 deletions(-)
* 2016-12-24(Tal Galili) tanglegram - added highlight_branches_col (FALSE) and highlight_branches_lwd (TRUE) parameters. |38346d5|
| R/tanglegram.R | 22 +++++++++++++++++++---
| man/tanglegram.Rd | 6 ++++++
| 2 files changed, 25 insertions(+), 3 deletions(-)
* 2016-12-24(Tal Galili) get_branches_heights - fix missing docs |cdfa4c7|
| R/attr_access.R | 2 +-
| man/get_branches_heights.Rd | 7 ++++---
| 2 files changed, 5 insertions(+), 4 deletions(-)
* 2016-12-24(Tal Galili) set - added highlight_branches_col and highlight_branches_lwd |21562f3|
| R/set.dendrogram.R | 8 ++++++++
| man/set.Rd | 4 ++++
| 2 files changed, 12 insertions(+)
* 2016-12-24(Tal Galili) New functions: highlight_branches, highlight_branches_col, highlight_branches_lwd - Highlight a dendrogram's branches heights via color and line-width. resolves #34 |a576a9e|
| NAMESPACE | 4 ++
| R/highlight_branches.R | 166 ++++++++++++++++++++++++++++++++++++++++++++
| man/highlight_branches.Rd | 79 +++++++++++++++++++++
| 3 files changed, 249 insertions(+)
* 2016-12-24(Tal Galili) Adding viridis to imports |e095aa8|
| DESCRIPTION | 3 ++-
| R/zzz.R | 9 ++++++++-
| 2 files changed, 10 insertions(+), 2 deletions(-)
* 2016-12-24(Tal Galili) Add "include_leaves" to dendextend_get_branches_heights (required in highlight_branches) |4e07e26|
| R/attr_access.R | 5 +++--
| man/get_branches_heights.Rd | 2 ++
| 2 files changed, 5 insertions(+), 2 deletions(-)
* 2016-11-08(Tal Galili) Fix " \examples lines wider than 100 characters:" |e8cee13|
| R/set.dendrogram.R | 11 +++++++----
| man/set.Rd | 11 +++++++----
| 2 files changed, 14 insertions(+), 8 deletions(-)
* 2016-11-08(Tal Galili) fix "checking S3 generic/method consistency ... WARNING" |08b09f0|
| R/Hmisc.R | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2016-11-08(Tal Galili) Added as.dendrogram.varclus |87b1b5c|
| DESCRIPTION | 6 +++---
| NAMESPACE | 1 +
| NEWS | 5 ++++-
| R/Hmisc.R | 24 ++++++++++++++++++++++++
| man/set.Rd | 4 ++--
| 5 files changed, 34 insertions(+), 6 deletions(-)
* 2016-11-02(Tal Galili) set - added the parameter `order_value` to easily use values which are in the order of the original data. (related to issue #31 ) |8ea84b2|
| DESCRIPTION | 4 ++--
| NEWS | 4 ++++
| R/set.dendrogram.R | 19 +++++++++++++++++--
| man/set.Rd | 18 +++++++++++++++---
| 4 files changed, 38 insertions(+), 7 deletions(-)
* 2016-10-21(Tal Galili) Credit for recent pull request. |9db0f99|
| DESCRIPTION | 8 +++++---
| NEWS | 3 ++-
| 2 files changed, 7 insertions(+), 4 deletions(-)
* 2016-10-21(Tal Galili) How to cite. |ee6ceb9|
| R/zzz.R | 2 ++
| 1 file changed, 2 insertions(+)
* 2016-10-21(Tal Galili) Return the missing par reset from tanglegram. |1a21101|
| R/tanglegram.R | 10 ++++++++++
| 1 file changed, 10 insertions(+)
* 2016-10-21(Tal Galili) misc |8191070|
| TODO | 5 +++++
| 1 file changed, 5 insertions(+)
* 2016-10-21(Tal Galili) Merge pull request #30 from CathG/master |81796b6
|\
| * 2016-10-19(Cath) Update tanglegram.R |69dd9b7| |
| | R/tanglegram.R | 8 ++++----
| | 1 file changed, 4 insertions(+), 4 deletions(-)
| * 2016-10-18(Cath) Add files via upload |407c394| |
| | man/tanglegram.Rd | 2 +-
| | 1 file changed, 1 insertion(+), 1 deletion(-)
| * 2016-10-18(Cath) Add files via upload |8896856| |
| | R/tanglegram.R | 2 +-
| | 1 file changed, 1 insertion(+), 1 deletion(-)
| * 2016-10-18(Cath) Update tanglegram.R |1432a24| |
| | R/tanglegram.R | 2 +-
| | 1 file changed, 1 insertion(+), 1 deletion(-)
| * 2016-10-18(Cath) Update tanglegram.R |a9639f2| |
| | R/tanglegram.R | 2 +-
| | 1 file changed, 1 insertion(+), 1 deletion(-)
| * 2016-10-18(Cath) Update tanglegram.R |6301067| |
| | R/tanglegram.R | 2 +-
| | 1 file changed, 1 insertion(+), 1 deletion(-)
| * 2016-10-18(Cath) Update tanglegram.R |2806ee9| |
| | R/tanglegram.R | 2 ++
| | 1 file changed, 2 insertions(+)
| * 2016-10-17(Cath) Add files via upload |8177483
| * 2016-10-17(Cath) Update tanglegram.R |41d96be| |
| | R/tanglegram.R | 2 +-
| | 1 file changed, 1 insertion(+), 1 deletion(-)
| * 2016-10-17(Cath) Update tanglegram.R |0107d70| |
| | R/tanglegram.R | 6 +++---
| | 1 file changed, 3 insertions(+), 3 deletions(-)
| * 2016-10-17(Cath) Delete tanglegram.Rd |5e932f5| |
| | tanglegram.Rd | 273 ------------------------------------------------------
| | 1 file changed, 273 deletions(-)
| * 2016-10-17(Cath) Add files via upload |080218e| |
| | man/tanglegram.Rd | 541 +++++++++++++++++++++++++-------------------------
| | 1 file changed, 273 insertions(+), 268 deletions(-)
| * 2016-10-17(Cath) Add files via upload |3bd61a7| |
| | tanglegram.Rd | 273 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
| | 1 file changed, 273 insertions(+)
| * 2016-10-17(Cath) Update tanglegram.R |f7fe826
|/ |
| R/tanglegram.R | 14 ++++++++------
| 1 file changed, 8 insertions(+), 6 deletions(-)
* 2016-10-12(Tal Galili) Add FAQ example: Plot a "mirror" (labels on the left) horizontal dendrogram |c1645ed|
| vignettes/FAQ.Rmd | 31 +++++++++++++++++++++++++++++++
| 1 file changed, 31 insertions(+)
* 2016-10-06(Tal Galili) find_k - now includes `k` in the output, which is a copy of `nc`. This is to make it easier to extract the value (i.e.: the suggested number of clusters). |ced7cc6|
| DESCRIPTION | 4 ++--
| NEWS | 7 +++++++
| R/find_k.R | 2 ++
| man/find_k.Rd | 1 +
| 4 files changed, 12 insertions(+), 2 deletions(-)
* 2016-08-27(Tal Galili) 1.3.0 |7a8fb04|
| ChangeLog | 31 +++++++++++++++++++++++++++++++
| 1 file changed, 31 insertions(+)
* 2016-08-27(Tal Galili) another http to https |cb9d1ab|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2016-08-27(Tal Galili) v1.3.0 |abb2d7f|
| NEWS.md | 13 +++++++++++++
| 1 file changed, 13 insertions(+)
* 2016-08-27(Tal Galili) http to https |fc6f403|
| DESCRIPTION | 2 +-
| man/set_labels.Rd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2016-07-15(Tal Galili) Fix "labels_colors<-" - make it more robust for combinations of using it with assign_values_to_leaves_nodePar (as used in set("labels_colors", ...) for example) |1fa259e|
| DESCRIPTION | 2 +-
| NEWS | 5 ++++-
| R/attr_access.R | 2 ++
| R/labels_colors.R | 3 ++-
| man/assign_values_to_leaves_nodePar.Rd | 2 ++
| tests/testthat/test-labels_colors.R | 19 +++++++++++++++++++
| 6 files changed, 30 insertions(+), 3 deletions(-)
* 2016-07-06(Tal Galili) Added set_labels and place_labels. These are convenience functions for updating the labels of a dendrogram. Props to Garrett Grolemund for the idea. |ccc43bc|
| DESCRIPTION | 4 +--
| NAMESPACE | 2 ++
| NEWS | 10 +++++++
| R/labels.R | 85 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| man/set_labels.Rd | 69 +++++++++++++++++++++++++++++++++++++++++++
| 5 files changed, 168 insertions(+), 2 deletions(-)
* 2016-06-22(Tal Galili) update log files. |962ea87|
| ChangeLog | 164 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 28 +++++++++++
| 2 files changed, 192 insertions(+)
* 2016-06-21(Tal Galili) Improve vignette size for CRAN (moving to html_vignette) |ad2880c|
| .Rbuildignore | 1 +
| NEWS | 1 +
| vignettes/Cluster_Analysis.Rmd | 17 +++++++++--------
| vignettes/FAQ.Rmd | 5 +++--
| vignettes/Quick_Introduction.Rmd | 3 ++-
| vignettes/introduction.Rmd | 9 +++++----
| 6 files changed, 21 insertions(+), 15 deletions(-)
* 2016-06-21(Tal Galili) add requireNamespace("seriation") (since I can't use imports) |8c5ae04|
| R/seriate_dendrogram.R | 2 ++
| 1 file changed, 2 insertions(+)
* 2016-06-21(Tal Galili) Added seriate_dendrogram - rotates a dendrogram to fit the optimal ordering (via OLO or GW) of some distance matrix (very useful for heatmaps) |113c354|
| DESCRIPTION | 4 ++-
| NAMESPACE | 2 ++
| NEWS | 3 +-
| R/seriate_dendrogram.R | 79 +++++++++++++++++++++++++++++++++++++++++++++
| man/seriate_dendrogram.Rd | 48 +++++++++++++++++++++++++++
| 5 files changed, 134 insertions(+), 2 deletions(-)
* 2016-06-21(Tal Galili) reduce dpi to deal with vignette size |5245c28|
| vignettes/Cluster_Analysis.Rmd | 2 +-
| vignettes/introduction.Rmd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2016-06-21(Tal Galili) trying a new untangle method (didn't work) |77e933c|
| R/untangle.R | 44 ++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 44 insertions(+)
* 2016-06-21(Tal Galili) copyright notice |c2b044b|
| R/find_k.R | 18 ++++++++++++++++++
| 1 file changed, 18 insertions(+)
* 2016-06-21(Tal Galili) added is.dist |d508a51|
| NEWS | 1 +
| R/is.functions.R | 18 ++++++++++++++++++
| man/is.dist.Rd | 24 ++++++++++++++++++++++++
| 3 files changed, 43 insertions(+)
* 2016-06-18(Tal Galili) reminder to myself on how to add SSH to github and connect it to RStudio |e59b44d|
| R/zzz.R | 29 +++++++++++++++++++++++++++++
| 1 file changed, 29 insertions(+)
* 2016-06-18(Tal Galili) bump date |3fd6e7f|
| DESCRIPTION | 2 +-
| NAMESPACE | 4 ++--
| NEWS | 2 +-
| 3 files changed, 4 insertions(+), 4 deletions(-)
* 2016-06-18(Tal Galili) find_k can now deal with smaller trees (n<10) by default. |3ff51db|
| R/find_k.R | 2 +-
| man/find_k.Rd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2016-06-13(Tal Galili) ggplot2 is now imported (instead of just suggested). This is because the use of dendextend for transforming dendrograms into ggplot2 has become more important (thanks to the new plotly package). |3ab1886|
| DESCRIPTION | 2 +-
| NEWS | 6 ++++++
| 2 files changed, 7 insertions(+), 1 deletion(-)
* 2016-06-13(Tal Galili) Fix the tiny notch in angle of the branches (in ggplot.ggdend) |b085046|
| R/ggdend.R | 4 +++-
| 1 file changed, 3 insertions(+), 1 deletion(-)
* 2016-06-12(Tal Galili) import(ggplot2) (instead of manually copying each function - which is NOT a good way to do this) |7de4df9|
| NAMESPACE | 1 +
| R/ggdend.R | 32 +++++++++++++++++++-------------
| 2 files changed, 20 insertions(+), 13 deletions(-)
* 2016-06-12(Tal Galili) New function: find_k - Find the (estimated) number of clusters for a dendrogram using average silhouette width |5b6a666|
| DESCRIPTION | 5 ++--
| NAMESPACE | 3 +++
| NEWS | 9 +++++--
| R/find_k.R | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| man/find_k.Rd | 52 ++++++++++++++++++++++++++++++++++++
| 5 files changed, 146 insertions(+), 4 deletions(-)
* 2016-06-12(Tal Galili) allow NEWS.md to be listed on CRAN |dbfd35c|
| .Rbuildignore | 1 -
| 1 file changed, 1 deletion(-)
* 2016-05-26(Tal Galili) would this help codecov to work?! |6a0d6f8|
| .travis.yml | 8 +++++---
| 1 file changed, 5 insertions(+), 3 deletions(-)
* 2016-05-26(Tal Galili) http -> https |68350b2|
| DESCRIPTION | 4 ++--
| README.md | 15 ++++++++-------
| 2 files changed, 10 insertions(+), 9 deletions(-)
* 2016-05-25(Tal Galili) Update Startup Message |b529c5f|
| R/ggdend.R | 2 +-
| R/zzz.R | 49 +++++++++++++++++++++++++++++++++----------------
| 2 files changed, 34 insertions(+), 17 deletions(-)
* 2016-05-23(Tal Galili) Fix (as is done now in dplyr): Warning: replacing previous import 'dendextend::%>%' by 'plotly::%>%' when loading 'heatmaply' |f97c47b|
| NAMESPACE | 1 +
| R/magrittr.R | 24 ++----------------------
| man/pipe.Rd | 33 ---------------------------------
| man/reexports.Rd | 16 ++++++++++++++++
| 4 files changed, 19 insertions(+), 55 deletions(-)
* 2016-05-08(Tal Galili) more info on the statistical use of E_FM and V_FM |08351a2|
| vignettes/introduction.Rmd | 15 +++++++++++++++
| 1 file changed, 15 insertions(+)
* 2016-04-25(Tal Galili) Use test_check instead of test_package |7af67a3|
| tests/test-all.R | 13 +++++++++++--
| 1 file changed, 11 insertions(+), 2 deletions(-)
* 2016-04-25(Tal Galili) check if the tests now work (if I place them in the tests\\testthat |362e0b0|
| tests/test-all.R | 29 ++++++++++++++++++-----------
| 1 file changed, 18 insertions(+), 11 deletions(-)
* 2016-04-24(Tal Galili) alternative name of Baker's Gamma |270dd40|
| R/cor_bakers_gamma.R | 3 ++-
| man/cor_bakers_gamma.Rd | 3 ++-
| man/entanglement.Rd | 2 +-
| 3 files changed, 5 insertions(+), 3 deletions(-)
* 2016-04-24(Tal Galili) ^ instead of ** |884c01d|
| R/entanglement.R | 6 +++---
| 1 file changed, 3 insertions(+), 3 deletions(-)
* 2016-03-24(Tal Galili) update documentation of the functions' location. |1325bbb|
| man/fac2num.Rd | 2 +-
| man/is.dendlist.Rd | 2 +-
| man/is.dendrogram.Rd | 2 +-
| man/is.hclust.Rd | 2 +-
| man/is.phylo.Rd | 2 +-
| 5 files changed, 5 insertions(+), 5 deletions(-)
* 2016-03-17(Tal Galili) Move is.X style functions to a new file: is.functions.R |2b533fe|
| DESCRIPTION | 4 +--
| NEWS | 9 +++++
| R/cutree.dendrogram.R | 52 ----------------------------
| R/dendlist.R | 15 ---------
| R/is.functions.R | 90 +++++++++++++++++++++++++++++++++++++++++++++++++
| 5 files changed, 101 insertions(+), 69 deletions(-)
* 2016-02-10(Tal Galili) until tests\\testthat will work. |dd25ff2|
| tests/test-all.R | 8 ++++++--
| 1 file changed, 6 insertions(+), 2 deletions(-)
* 2016-02-10(Tal Galili) 1.1.8 bump |6e490e0|
| DESCRIPTION | 2 +-
| NEWS | 5 +++++
| 2 files changed, 6 insertions(+), 1 deletion(-)
* 2016-02-10(Tal Galili) some updates |634511f|
| TODO | 34 ----------------------------------
| 1 file changed, 34 deletions(-)
* 2016-02-10(Tal Galili) ideas |90a4627|
| TODO | 51 ++++++++++++++++++++++++++++++++++++++++++++++++++-
| 1 file changed, 50 insertions(+), 1 deletion(-)
* 2016-02-10(Tal Galili) Added "tryCatch" to deal with the tests issue. + updated changelog and NEWS |3f2c1a2|
| ChangeLog | 366 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS | 2 +-
| NEWS.md | 47 +++++++
| tests/test-all.R | 7 +-
| 4 files changed, 419 insertions(+), 3 deletions(-)
* 2016-02-10(Tal Galili) another fix for the warning. |3708e45|
| tests/testthat/test-cutree.dendrogram.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2016-02-10(Tal Galili) Added rmarkdown in Suggests of DESCRIPTION |881733a|
| DESCRIPTION | 3 ++-
| NEWS | 7 +++++++
| 2 files changed, 9 insertions(+), 1 deletion(-)
* 2016-02-10(Tal Galili) typo |77ccd5f|
| R/zzz.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2016-02-10(Tal Galili) Tests fixed to deal with the new R's ability to run as.hclust on dendrogram with ties. |f0ee811|
| DESCRIPTION | 4 ++--
| NEWS | 1 +
| R/cutree.dendrogram.R | 2 +-
| tests/testthat/test-cutree.dendrogram.R | 9 ++++++++-
| 4 files changed, 12 insertions(+), 4 deletions(-)
* 2016-02-10(Tal Galili) Moved `inst/tests/` to `tests/testthat/` |b4c7fbc|
| NEWS | 7 +
| inst/tests/test-attr_access.R | 232 -------------
| inst/tests/test-bk_method.R | 286 ----------------
| inst/tests/test-branches_attr_by.R | 97 ------
| inst/tests/test-common_subtrees.R | 49 ---
| inst/tests/test-cor_bakers_gamma.R | 48 ---
| inst/tests/test-cor_cophenetic.R | 44 ---
| inst/tests/test-cut_lower_fun.R | 110 -------
| inst/tests/test-cutree.dendrogram.R | 520 ------------------------------
| inst/tests/test-dendlist.R | 97 ------
| inst/tests/test-distinct_edges.R | 45 ---
| inst/tests/test-entanglement.R | 142 --------
| inst/tests/test-general.R | 15 -
| inst/tests/test-ggdend.R | 79 -----
| inst/tests/test-labels-assign.R | 202 ------------
| inst/tests/test-labels_colors.R | 118 -------
| inst/tests/test-nleaves.R | 68 ----
| inst/tests/test-rect.dendrogram.R | 26 --
| inst/tests/test-rotate.R | 91 ------
| inst/tests/test-set.dendrogram.R | 160 ---------
| inst/tests/test-trim.R | 81 -----
| inst/tests/test-unbranch.R | 48 ---
| inst/tests/test-untangle.R | 162 ----------
| tests/test-all.R | 2 +-
| tests/testthat/test-attr_access.R | 232 +++++++++++++
| tests/testthat/test-bk_method.R | 286 ++++++++++++++++
| tests/testthat/test-branches_attr_by.R | 97 ++++++
| tests/testthat/test-common_subtrees.R | 49 +++
| tests/testthat/test-cor_bakers_gamma.R | 48 +++
| tests/testthat/test-cor_cophenetic.R | 44 +++
| tests/testthat/test-cut_lower_fun.R | 110 +++++++
| tests/testthat/test-cutree.dendrogram.R | 520 ++++++++++++++++++++++++++++++
| tests/testthat/test-dendlist.R | 97 ++++++
| tests/testthat/test-distinct_edges.R | 45 +++
| tests/testthat/test-entanglement.R | 142 ++++++++
| tests/testthat/test-general.R | 15 +
| tests/testthat/test-ggdend.R | 79 +++++
| tests/testthat/test-labels-assign.R | 202 ++++++++++++
| tests/testthat/test-labels_colors.R | 118 +++++++
| tests/testthat/test-nleaves.R | 68 ++++
| tests/testthat/test-rect.dendrogram.R | 26 ++
| tests/testthat/test-rotate.R | 91 ++++++
| tests/testthat/test-set.dendrogram.R | 160 +++++++++
| tests/testthat/test-trim.R | 81 +++++
| tests/testthat/test-unbranch.R | 48 +++
| tests/testthat/test-untangle.R | 162 ++++++++++
| 46 files changed, 2728 insertions(+), 2721 deletions(-)
* 2016-01-06(Tal Galili) Adding Gregory Jefferis as an author (thanks to his work on dendroextras, which was later reused in the dendextend package) |818aa14|
| DESCRIPTION | 4 ++--
| NEWS | 6 ++++--
| 2 files changed, 6 insertions(+), 4 deletions(-)
* 2016-01-05(Tal Galili) remove sort_cluster_numbers from another place... |d42be6f|
| R/color_branches.R | 3 +--
| R/cutree.dendrogram.R | 2 +-
| inst/tests/test-cutree.dendrogram.R | 8 ++++----
| man/color_branches.Rd | 3 +--
| vignettes/disabled/dendextend-tutorial.rnw | 4 ++--
| 5 files changed, 9 insertions(+), 11 deletions(-)
* 2016-01-05(Tal Galili) Fix #18 by removing the sort_cluster_numbers parameter. |287b1fd|
| DESCRIPTION | 4 ++--
| NEWS | 7 +++++++
| R/color_branches.R | 8 ++++----
| R/colored_bars.R | 4 ++--
| R/cutree.dendrogram.R | 21 ++++++---------------
| man/color_branches.Rd | 4 ++--
| man/cutree-methods.Rd | 12 ------------
| 7 files changed, 23 insertions(+), 37 deletions(-)
* 2016-01-02(Tal Galili) Add legend to a SO example |655a0aa|
| vignettes/FAQ.Rmd | 5 ++++-
| 1 file changed, 4 insertions(+), 1 deletion(-)
* 2016-01-02(Tal Galili) Added many description elements in .Rd files. |d10d082|
| NEWS | 10 +++++++---
| R/attr_access.R | 5 +++++
| R/bk_method.R | 3 ++-
| R/color_branches.R | 7 +++++--
| R/colored_bars.R | 6 ++++--
| R/cor_bakers_gamma.R | 1 +
| R/cor_cophenetic.R | 3 ++-
| R/cutree.dendrogram.R | 5 +++++
| R/dendextend_options.R | 2 ++
| R/dendlist.R | 2 ++
| R/dist_long.R | 1 +
| R/distinct_edges.R | 3 ++-
| R/get_nodes_xy.R | 3 ++-
| R/labels.R | 1 +
| R/labels_colors.R | 2 ++
| R/nleaves.R | 1 +
| R/prune.R | 5 +++--
| R/pvclust.R | 6 ++++--
| R/unbranch.R | 7 ++++++-
| man/all_unique.Rd | 3 +++
| man/assign_dendextend_options.Rd | 3 +++
| man/bakers_gamma_for_2_k_matrix.Rd | 3 +++
| man/color_branches.Rd | 3 ++-
| man/colored_bars.Rd | 6 ++++--
| man/dist_long.Rd | 3 +++
| man/distinct_edges.Rd | 5 ++++-
| man/get_branches_heights.Rd | 3 +++
| man/get_childrens_heights.Rd | 3 +++
| man/get_leaves_attr.Rd | 3 +++
| man/get_leaves_nodePar.Rd | 3 +++
| man/get_nodes_xy.Rd | 5 ++++-
| man/get_root_branches_attr.Rd | 3 +++
| man/heights_per_k.dendrogram.Rd | 4 ++++
| man/is.dendlist.Rd | 3 +++
| man/is.dendrogram.Rd | 3 +++
| man/is.hclust.Rd | 3 +++
| man/is.phylo.Rd | 3 +++
| man/is_null_list.Rd | 3 +++
| man/labels_cex.Rd | 3 +++
| man/labels_colors.Rd | 3 +++
| man/leaf_Colors.Rd | 2 +-
| man/order.hclust.Rd | 3 +++
| man/prune_leaf.Rd | 5 ++++-
| man/pvclust_show_signif.Rd | 5 ++++-
| man/pvclust_show_signif_gradient.Rd | 5 ++++-
| man/raise.dendrogram.Rd | 3 +++
| man/sort_2_clusters_vectors.Rd | 5 ++++-
| man/sort_dist_mat.Rd | 5 ++++-
| man/unbranch.Rd | 3 +++
| man/unclass_dend.Rd | 3 +++
| 50 files changed, 156 insertions(+), 27 deletions(-)
* 2016-01-01(Tal Galili) change update to set in the document |758eb9b|
| R/colored_bars.R | 10 +++++-----
| man/colored_bars.Rd | 2 +-
| 2 files changed, 6 insertions(+), 6 deletions(-)
* 2016-01-01(Tal Galili) having colored_bars more robust to various types of vectors. And updated the introduction vignette to use sort_by_labels_order properly in the example. |f0f96c5|
| R/colored_bars.R | 6 ++++--
| vignettes/introduction.Rmd | 4 +++-
| 2 files changed, 7 insertions(+), 3 deletions(-)
* 2016-01-01(Tal Galili) Updated the vignette (and removed the check in colored_bars for matrix/vector) |8aa9e78|
| DESCRIPTION | 2 +-
| R/colored_bars.R | 5 +++--
| vignettes/FAQ.Rmd | 46 ++++++++++++++++++++++++++++++++++++++++++++++
| 3 files changed, 50 insertions(+), 3 deletions(-)
* 2016-01-01(Tal Galili) colored_bars - updated example (a new mtcars example) |a89df04|
| R/colored_bars.R | 39 +++++++++++++++++++++++++++
| man/colored_bars.Rd | 73 +++++++++++++++++++++++++++++++++++++++++----------
| 2 files changed, 98 insertions(+), 14 deletions(-)
* 2016-01-01(Tal Galili) colored_bars - Fixed many bugs (in the horiz string location, and in the display of multiple bars) |b394170|
| R/colored_bars.R | 23 ++++++++++-------------
| 1 file changed, 10 insertions(+), 13 deletions(-)
* 2016-01-01(Tal Galili) Fixes to the bars' positions for horiz = TRUE |6cf4e2e|
| R/colored_bars.R | 10 +++++-----
| 1 file changed, 5 insertions(+), 5 deletions(-)
* 2016-01-01(Tal Galili) colored_bars - Major corrections to the way the bars are located automatically (it is now positioned underneath the labels automatically!) |ce47da4|
| R/colored_bars.R | 226 +++++++++++++++++++++++++++++++++++------------------
| 1 file changed, 152 insertions(+), 74 deletions(-)
* 2016-01-01(Tal Galili) rxoygen2 edit |ccbbf4f|
| NAMESPACE | 2 +-
| R/dendextend_options.R | 8 +--
| R/rotate.R | 2 +-
| man/Bk.Rd | 19 +++---
| man/Bk_permutations.Rd | 19 +++---
| man/Bk_plot.Rd | 37 +++++------
| man/DendSer.dendrogram.Rd | 4 +-
| man/FM_index.Rd | 17 ++---
| man/FM_index_R.Rd | 13 ++--
| man/FM_index_permutation.Rd | 9 +--
| man/FM_index_profdpm.Rd | 15 +++--
| man/all.equal.dendrogram.Rd | 9 +--
| man/all_couple_rotations_at_k.Rd | 5 +-
| man/all_unique.Rd | 7 +-
| man/as.dendlist.Rd | 4 +-
| man/as.phylo.dendrogram.Rd | 8 +--
| man/as_hclust_fixed.Rd | 10 +--
| man/assign_dendextend_options.Rd | 5 +-
| man/assign_values_to_branches_edgePar.Rd | 7 +-
| man/assign_values_to_leaves_edgePar.Rd | 6 +-
| man/assign_values_to_leaves_nodePar.Rd | 10 +--
| man/assign_values_to_nodes_nodePar.Rd | 22 ++++---
| man/bakers_gamma_for_2_k_matrix.Rd | 5 +-
| man/branches_attr_by_clusters.Rd | 15 +++--
| man/branches_attr_by_labels.Rd | 16 ++---
| man/circlize_dendrogram.Rd | 9 +--
| man/click_rotate.Rd | 7 +-
| man/collapse_branch.Rd | 7 +-
| man/color_branches.Rd | 56 ++++++++--------
| man/color_labels.Rd | 14 ++--
| man/color_unique_labels.Rd | 3 +-
| man/common_subtrees_clusters.Rd | 5 +-
| man/cor.dendlist.Rd | 9 +--
| man/cor_FM_index.Rd | 4 +-
| man/cor_bakers_gamma.Rd | 36 ++++++-----
| man/cor_common_nodes.Rd | 8 ++-
| man/cor_cophenetic.Rd | 40 ++++++------
| man/count_terminal_nodes.Rd | 10 +--
| man/cut_lower_fun.Rd | 8 ++-
| man/cutree-methods.Rd | 79 +++++++++++-----------
| man/cutree_1h.dendrogram.Rd | 18 +++---
| man/cutree_1k.dendrogram.Rd | 30 +++++----
| man/d3dendro_options.Rd | 8 +--
| man/d3dendrogram.Rd | 8 +--
| man/dend_diff.Rd | 14 ++--
| man/dendextend-package.Rd | 2 +-
| man/dendextend_labels.dendrogram.Rd | 4 +-
| man/dendextend_options.Rd | 4 +-
| man/dendlist.Rd | 8 ++-
| man/dist.dendlist.Rd | 14 ++--
| man/dist_long.Rd | 6 +-
| man/distinct_edges.Rd | 7 +-
| man/duplicate_leaf.Rd | 4 +-
| man/entanglement.Rd | 27 ++++----
| man/fac2num.Rd | 4 +-
| man/fix_members_attr.dendrogram.Rd | 5 +-
| man/flatten.dendrogram.Rd | 4 +-
| man/flip_leaves.Rd | 3 +-
| man/get_branches_heights.Rd | 7 +-
| man/get_childrens_heights.Rd | 10 +--
| man/get_leaves_attr.Rd | 21 +++---
| man/get_leaves_branches_attr.Rd | 8 ++-
| man/get_leaves_branches_col.Rd | 12 ++--
| man/get_leaves_edgePar.Rd | 5 +-
| man/get_leaves_nodePar.Rd | 8 +--
| man/get_nodes_attr.Rd | 29 +++++----
| man/get_nodes_xy.Rd | 17 ++---
| man/get_root_branches_attr.Rd | 7 +-
| man/ggdend.Rd | 43 ++++++------
| man/hang.dendrogram.Rd | 13 ++--
| man/heights_per_k.dendrogram.Rd | 17 ++---
| man/highlight_distinct_edges.Rd | 28 ++++----
| man/identify.dendrogram.Rd | 23 +++----
| man/intersect_trees.Rd | 5 +-
| man/is.dendlist.Rd | 5 +-
| man/is.dendrogram.Rd | 5 +-
| man/is.hclust.Rd | 5 +-
| man/is.natural.number.Rd | 3 +-
| man/is.phylo.Rd | 5 +-
| man/is_null_list.Rd | 7 +-
| man/khan.Rd | 40 ++++++------
| man/labels-assign.Rd | 22 +++----
| man/labels_cex.Rd | 8 +--
| man/labels_colors.Rd | 11 ++--
| man/ladderize.Rd | 8 ++-
| man/leaf_Colors.Rd | 5 +-
| man/lowest_common_branch.Rd | 4 +-
| man/match_order_by_labels.Rd | 4 +-
| man/match_order_dendrogram_by_old_order.Rd | 12 ++--
| man/na_locf.Rd | 8 ++-
| man/nleaves.Rd | 16 ++---
| man/nnodes.Rd | 4 +-
| man/noded_with_condition.Rd | 9 +--
| man/order.dendrogram-assign.Rd | 5 +-
| man/order.hclust.Rd | 15 ++---
| man/partition_leaves.Rd | 4 +-
| man/pipe.Rd | 8 +--
| man/plot_horiz.dendrogram.Rd | 26 ++++----
| man/prune.Rd | 2 +-
| man/prune_common_subtrees.dendlist.Rd | 6 +-
| man/prune_leaf.Rd | 7 +-
| man/pvclust_show_signif.Rd | 11 ++--
| man/pvclust_show_signif_gradient.Rd | 15 ++---
| man/raise.dendrogram.Rd | 5 +-
| man/rank_branches.Rd | 13 ++--
| man/rank_order.dendrogram.Rd | 6 +-
| man/rank_values_with_clusters.Rd | 5 +-
| man/rect.dendrogram.Rd | 33 +++++-----
| man/remove_branches_edgePar.Rd | 4 +-
| man/remove_leaves_nodePar.Rd | 4 +-
| man/remove_nodes_nodePar.Rd | 4 +-
| man/rllply.Rd | 10 +--
| man/rotate.Rd | 61 ++++++++---------
| man/rotate_DendSer.Rd | 2 +-
| man/sample.dendrogram.Rd | 16 +++--
| man/set.Rd | 97 ++++++++++++++--------------
| man/shuffle.Rd | 8 ++-
| man/sort_2_clusters_vectors.Rd | 10 ++-
| man/sort_dist_mat.Rd | 5 +-
| man/sort_levels_values.Rd | 16 +++--
| man/tanglegram.Rd | 46 ++++++-------
| man/theme_dendro.Rd | 4 +-
| man/unbranch.Rd | 5 +-
| man/unclass_dend.Rd | 13 ++--
| man/untangle.Rd | 12 ++--
| man/untangle_DendSer.Rd | 2 +-
| man/untangle_random_search.Rd | 17 ++---
| man/untangle_step_rotate_1side.Rd | 23 +++----
| man/untangle_step_rotate_2side.Rd | 19 +++---
| man/which_leaf.Rd | 6 +-
| man/which_node.Rd | 7 +-
| 131 files changed, 891 insertions(+), 834 deletions(-)
* 2015-12-31(Tal Galili) colored_bars - Fix the default position of the bars when dend is provided. |28eb04d|
| NEWS | 5 ++++-
| R/colored_bars.R | 14 +++++++++-----
| 2 files changed, 13 insertions(+), 6 deletions(-)
* 2015-12-31(Tal Galili) Fix the example in the documentation of `colored_bars` |d49f883|
| DESCRIPTION | 5 +++--
| NEWS | 7 +++++++
| R/colored_bars.R | 8 ++++----
| man/colored_bars.Rd | 26 ++++++++++++++------------
| 4 files changed, 28 insertions(+), 18 deletions(-)
* 2015-11-07(Tal Galili) ::: instead of :: (does it work?) |c80aa2e|
| R/dendextend_options.R | 8 ++++----
| 1 file changed, 4 insertions(+), 4 deletions(-)
* 2015-11-07(Tal Galili) ... not used |2454971|
| R/labels_colors.R | 2 +-
| man/color_unique_labels.Rd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2015-11-07(Tal Galili) color_unique_labels - a function to Color unique labels in a dendrogram |3d385af|
| DESCRIPTION | 4 ++--
| NAMESPACE | 1 +
| NEWS | 9 +++++++++
| R/labels_colors.R | 48 ++++++++++++++++++++++++++++++++++++++++++++
| man/color_unique_labels.Rd | 30 +++++++++++++++++++++++++++
| 5 files changed, 90 insertions(+), 2 deletions(-)
* 2015-11-07(Tal Galili) update citation. (bioinformatics paper is published :) ) |5751356|
| DESCRIPTION | 2 +-
| inst/CITATION | 4 ++--
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2015-10-31(Tal Galili) ignore caching and an old tutorial |8f58f47|
| .Rbuildignore | 2 ++
| dendextend.Rproj | 1 +
| 2 files changed, 3 insertions(+)
* 2015-10-31(Tal Galili) # Use ylim to deal with long labels in ggplot2 |50eb921|
| R/ggdend.R | 8 ++++++++
| man/ggdend.Rd | 8 ++++++++
| 2 files changed, 16 insertions(+)
* 2015-10-30(Tal Galili) update changelog and NEWS |4ab0bcc|
| ChangeLog | 71 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 17 +++++++++++++++
| R/zzz.R | 2 +-
| 3 files changed, 89 insertions(+), 1 deletion(-)
* 2015-10-30(Tal Galili) update citations |483b935|
| DESCRIPTION | 4 ++--
| NEWS | 5 ++++-
| inst/CITATION | 4 ++--
| 3 files changed, 8 insertions(+), 5 deletions(-)
* 2015-10-01(Tal Galili) added counter badges |b53cba4|
| README.md | 2 ++
| 1 file changed, 2 insertions(+)
* 2015-09-20(Tal Galili) rect.dendrogram and identify.dendrogram - gain the stop_if_out parameter. The defaults for this parameter makes the error of "Error in rect.dendrogram(x, k = k, x = X$x, cluster = cluster[, k - 1], : k must be between 2 and 10" - to become less common (since it replaces it with a warning). |9b0ea47|
| DESCRIPTION | 4 ++--
| NEWS | 4 +++-
| R/rect.dendrogram.R | 28 ++++++++++++++++++++++------
| man/identify.dendrogram.Rd | 6 +++++-
| man/rect.dendrogram.Rd | 7 ++++++-
| 5 files changed, 38 insertions(+), 11 deletions(-)
* 2015-09-06(Tal Galili) as.ggdend.dendrogram - can now handle different label heights. (for example, the ones produces when using hang.dendrogram) |6548b02|
| DESCRIPTION | 2 +-
| NEWS | 4 ++--
| R/ggdend.R | 2 ++
| 3 files changed, 5 insertions(+), 3 deletions(-)
* 2015-09-03(Tal Galili) Fix 2 warnings |0e05202|
| R/labels.R | 18 +-----------------
| man/labels-assign.Rd | 19 +------------------
| 2 files changed, 2 insertions(+), 35 deletions(-)
* 2015-09-03(Tal Galili) Removed functions labels.matrix and labels<-.matrix, in order to avoid conflicts with arules (and since these functions are not really used in other parts of the package)- reported by Maja Alicja. |ebcae92|
| DESCRIPTION | 2 +-
| NAMESPACE | 2 -
| NEWS | 3 +-
| R/labels.R | 111 ++++++++++++++++++--------------------
| inst/tests/test-labels-assign.R | 43 ++++++++-------
| man/labels-assign.Rd | 5 --
| 6 files changed, 79 insertions(+), 87 deletions(-)
* 2015-08-28(Tal Galili) intersect_trees - return dendlist() and a warning if there are no shared labels between the two trees. |9de3f36|
| DESCRIPTION | 2 +-
| NEWS | 5 ++++-
| R/prune.R | 5 +++++
| 3 files changed, 10 insertions(+), 2 deletions(-)
* 2015-08-14(Tal Galili) Basic test for as.ggdend |f1ab77f|
| inst/tests/test-ggdend.R | 29 +++++++++++++++++++++++++++++
| 1 file changed, 29 insertions(+)
* 2015-08-14(Tal Galili) as.ggdend.dendrogram - fix "Error in FUN(X[[i]], ...) : subscript out of bounds" problem for some (more) trees. Fixes bug #12 |15ce942|
| DESCRIPTION | 4 ++--
| NEWS | 8 ++++++++
| R/ggdend.R | 6 ++++--
| 3 files changed, 14 insertions(+), 4 deletions(-)
* 2015-07-30(Tal Galili) Remove d3heatmap example so to reduce package size |81c707d|
| vignettes/Cluster_Analysis.Rmd | 6 +++---
| 1 file changed, 3 insertions(+), 3 deletions(-)
* 2015-07-30(Tal Galili) reduce sizes of files (for CRAN) |c62be8e|
| ...ts - enhanced with the dendextend package.html | 191 +++++------
| inst/ignored/Introduction to dendextend.html | 356 +++++++++++++-------
| vignettes/Cluster_Analysis.Rmd | 2 +-
| vignettes/FAQ.Rmd | 6 +-
| vignettes/introduction.Rmd | 2 +-
| 5 files changed, 310 insertions(+), 247 deletions(-)
* 2015-07-30(Tal Galili) misc |c85c6ee|
| ChangeLog | 187 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 46 +++++++++++++++
| 2 files changed, 233 insertions(+)
* 2015-07-30(Tal Galili) Added an example for using NMF::aheatmap |9d75974|
| DESCRIPTION | 1 +
| vignettes/introduction.Rmd | 26 ++++++++++++++++++++++++--
| 2 files changed, 25 insertions(+), 2 deletions(-)
* 2015-07-30(Tal Galili) Added a link to the paper from the DESCRIPTION |5d3763e|
| DESCRIPTION | 3 ++-
| 1 file changed, 2 insertions(+), 1 deletion(-)
* 2015-07-30(Tal Galili) Added a CITATION file |086d89e|
| DESCRIPTION | 2 +-
| NEWS | 6 +++++-
| inst/CITATION | 19 +++++++++++++++++++
| 3 files changed, 25 insertions(+), 2 deletions(-)
* 2015-07-17(Tal Galili) Another step towards 1.1.0 (but not there yet...) |5d141ea|
| DESCRIPTION | 2 +-
| NEWS | 6 ++++--
| 2 files changed, 5 insertions(+), 3 deletions(-)
* 2015-07-17(Tal Galili) minor typo fixes and doc-inter-linking |abcc402|
| R/untangle.R | 11 ++++++++++-
| man/set.Rd | 3 +++
| man/untangle.Rd | 1 +
| man/untangle_step_rotate_1side.Rd | 2 +-
| man/untangle_step_rotate_2side.Rd | 8 ++++++++
| 5 files changed, 23 insertions(+), 2 deletions(-)
* 2015-07-17(Tal Galili) Adding a d3heatmap example |c5de02c|
| ...ta sets - enhanced with the dendextend package.html | 16 ++++++++++++++++
| vignettes/Cluster_Analysis.Rmd | 14 ++++++++++++++
| 2 files changed, 30 insertions(+)
* 2015-07-17(Tal Galili) Updated FAQ HTML file. |cc851f6|
| inst/ignored/Frequently asked questions.html | 143 +++++++++++++++++++++----
| 1 file changed, 123 insertions(+), 20 deletions(-)
* 2015-07-17(Tal Galili) Rename vignette files |2dd4fcd|
| README.md | 4 +-
| inst/ignored/Frequantly asked questions.html | 325 ----------
| inst/ignored/Frequently asked questions.html | 325 ++++++++++
| ...ts - enhanced with the dendextend package.html | 668 ++++++++++++++++++++
| ...ts - enhanced with the dendextend package.html | 668 --------------------
| 5 files changed, 995 insertions(+), 995 deletions(-)
* 2015-07-17(Tal Galili) added a circular example of Iris |4848a5d|
| vignettes/Cluster_Analysis.Rmd | 18 ++++++++++++++++--
| 1 file changed, 16 insertions(+), 2 deletions(-)
* 2015-07-17(Tal Galili) implemented various fixes |5455bdc|
| ...ts - enhanced with the dendextend package.html | 240 +++++++++++---------
| 1 file changed, 131 insertions(+), 109 deletions(-)
* 2015-07-16(Tal Galili) Various fixes to spelling and grammatical mistakes |e9ea9f9|
| vignettes/Cluster_Analysis.Rmd | 137 +++++++++++++++++++--------------------
| vignettes/FAQ.Rmd | 16 ++---
| 2 files changed, 76 insertions(+), 77 deletions(-)
* 2015-07-15(Tal Galili) set - added "branches_k_lty" parameter |a81ca28|
| DESCRIPTION | 4 ++--
| NEWS | 5 ++++-
| R/color_branches.R | 13 +++++++++++++
| R/set.dendrogram.R | 13 ++++++++++---
| man/set.Rd | 4 +++-
| 5 files changed, 32 insertions(+), 7 deletions(-)
* 2015-07-15(Tal Galili) Mention other names for the circlized dendrogram plot. |1d8a78b|
| R/circlize.R | 3 +++
| man/circlize_dendrogram.Rd | 3 +++
| 2 files changed, 6 insertions(+)
* 2015-07-15(Tal Galili) switch URL order |7bac0fe|
| DESCRIPTION | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2015-07-15(Tal Galili) explain proper citation of circlize function. |636c15f|
| R/circlize.R | 3 ++-
| man/circlize_dendrogram.Rd | 3 ++-
| 2 files changed, 4 insertions(+), 2 deletions(-)
* 2015-07-14(Tal Galili) as.ggdend.dendrogram - fix "Error in FUN(X[[i]], ...) : subscript out of bounds" problem for some trees. |418cc2c|
| DESCRIPTION | 2 +-
| NEWS | 5 ++++-
| R/ggdend.R | 2 +-
| 3 files changed, 6 insertions(+), 3 deletions(-)
* 2015-07-11(Tal Galili) seealso linking |4b0d157|
| R/color_branches.R | 3 ++-
| man/color_branches.Rd | 3 ++-
| 2 files changed, 4 insertions(+), 2 deletions(-)
* 2015-07-11(Tal Galili) Another SO question |07abbc3|
| vignettes/FAQ.Rmd | 34 ++++++++++++++++++++++++++++++++++
| 1 file changed, 34 insertions(+)
* 2015-07-11(Tal Galili) fix "graphical parameter "mfrow" has the wrong length" |edb9613|
| vignettes/introduction.Rmd | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-07-11(Tal Galili) inte-linking and misc |fe50082|
| R/attr_access.R | 2 +-
| R/labels_colors.R | 2 +-
| man/get_leaves_branches_col.Rd | 2 +-
| man/labels_colors.Rd | 2 +-
| 4 files changed, 4 insertions(+), 4 deletions(-)
* 2015-07-11(Tal Galili) Fix "Error: Vignette 'FAQ.Rmd' is non-ASCII but has no declared encoding" (thanks to Duncan Murdoch :) ) |22c9e44|
| R/zzz.R | 3 +++
| vignettes/FAQ.Rmd | 4 ++--
| 2 files changed, 5 insertions(+), 2 deletions(-)
* 2015-07-11(Tal Galili) Added 2 new SO questions to FAQ |7f9a3ae|
| vignettes/FAQ.Rmd | 56 +++++++++++++++++++++++++++++++++++++++++++-
| vignettes/introduction.Rmd | 1 +
| 2 files changed, 56 insertions(+), 1 deletion(-)
* 2015-07-11(Tal Galili) more links |84ae6d0|
| R/color_branches.R | 3 ++-
| R/labels_colors.R | 3 +++
| man/color_labels.Rd | 3 ++-
| man/labels_colors.Rd | 5 +++++
| 4 files changed, 12 insertions(+), 2 deletions(-)
* 2015-07-10(Tal Galili) circlize_dendrogram - a function for creating radial dendrogram plots! (based on the circlize package) |8b080d7|
| DESCRIPTION | 8 ++-
| NAMESPACE | 1 +
| NEWS | 1 +
| R/circlize.R | 141 +++++++++++++++++++++++++++++++++++++++++++
| README.md | 9 +++
| man/circlize_dendrogram.Rd | 79 ++++++++++++++++++++++++
| vignettes/FAQ.Rmd | 29 +++++++++
| vignettes/introduction.Rmd | 54 +++++++++++++++++
| 8 files changed, 320 insertions(+), 2 deletions(-)
* 2015-07-10(Tal Galili) Added labels_cex |da35752|
| NAMESPACE | 2 ++
| NEWS | 1 +
| R/labels_colors.R | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
| man/labels_cex.Rd | 42 ++++++++++++++++++++++++++++++++++++++++++
| 4 files changed, 95 insertions(+)
* 2015-07-10(Tal Galili) Added labels_col as an alias of labels_colors |01ba9e6|
| NAMESPACE | 1 +
| NEWS | 8 +++++++-
| R/labels_colors.R | 6 +++++-
| man/labels_colors.Rd | 3 +++
| 4 files changed, 16 insertions(+), 2 deletions(-)
* 2015-07-05(Tal Galili) assign_values_to_nodes_nodePar - can now handle NA with a character string vector in value. Fixes #10 |9ceadb1|
| DESCRIPTION | 4 ++--
| NEWS | 7 +++++++
| R/attr_access.R | 9 ++++++++-
| man/assign_values_to_nodes_nodePar.Rd | 7 +++++++
| vignettes/introduction.Rmd | 2 +-
| 5 files changed, 25 insertions(+), 4 deletions(-)
* 2015-06-28(Tal Galili) update DESCRIPTION to 1.0.2 |64bc90f|
| DESCRIPTION | 2 +-
| NEWS | 4 ++++
| 2 files changed, 5 insertions(+), 1 deletion(-)
* 2015-06-28(Tal Galili) A new minimal quick introduction vignette |7ee0812|
| vignettes/Quick_Introduction.Rmd | 127 +++++++++++++++++++++++++++++++++++++
| 1 file changed, 127 insertions(+)
* 2015-06-28(Tal Galili) fix typo |ffc2c00|
| DESCRIPTION | 2 +-
| vignettes/FAQ.Rmd | 4 ++--
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2015-06-28(Tal Galili) ggplot.ggdend - added offset_labels |578e70f|
| NEWS | 7 +++++++
| R/ggdend.R | 9 +++++++--
| man/ggdend.Rd | 5 ++++-
| 3 files changed, 18 insertions(+), 3 deletions(-)
* 2015-06-28(Tal Galili) Added import to NAMESPACE: graphics, grDevices |0148a92|
| DESCRIPTION | 9 +++++----
| NAMESPACE | 2 ++
| NEWS | 8 ++++++++
| R/dendextend-package.R | 2 ++
| 4 files changed, 17 insertions(+), 4 deletions(-)
* 2015-06-27(Tal Galili) misc |f6890d6|
| ChangeLog | 19 +++++++++++++++++++
| 1 file changed, 19 insertions(+)
* 2015-06-27(Tal Galili) fix url |6b6bafd|
| inst/ignored/Introduction to dendextend.html | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-06-27(Tal Galili) fix dpi to get smaller vignettes |f53c729|
| vignettes/Cluster_Analysis.Rmd | 2 +-
| vignettes/introduction.Rmd | 4 ++--
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2015-06-27(Tal Galili) fix: prune.hclust: no visible binding for global variable 'x' unbranch.hclust: no visible binding for global variable 'x' |30804af|
| R/prune.R | 2 +-
| R/unbranch.R | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2015-06-27(Tal Galili) updated for 1.0.0. |69c26b4|
| ChangeLog | 316 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 18 +++-
| 2 files changed, 333 insertions(+), 1 deletion(-)
* 2015-06-27(Tal Galili) update date |a85432c|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-06-27(Tal Galili) object -> dend for: shuffle |ec62d71|
| NEWS | 2 +-
| R/untangle.R | 30 +++++++++++++++---------------
| man/shuffle.Rd | 12 ++++++------
| 3 files changed, 22 insertions(+), 22 deletions(-)
* 2015-06-27(Tal Galili) x -> dend for: unbranch |541d5ef|
| NEWS | 2 +-
| R/unbranch.R | 26 +++++++++++++-------------
| man/unbranch.Rd | 10 +++++-----
| 3 files changed, 19 insertions(+), 19 deletions(-)
* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2 for: tanglegram |5517d9b|
| NEWS | 2 +-
| R/tanglegram.R | 136 ++++++++++++++++++++++++++--------------------------
| man/tanglegram.Rd | 14 +++---
| 3 files changed, 76 insertions(+), 76 deletions(-)
* 2015-06-27(Tal Galili) x -> dend for: prune |8660626|
| NEWS | 2 +-
| R/prune.R | 94 ++++++++++++++++++++++++++---------------------------
| man/prune.Rd | 12 +++----
| man/prune_leaf.Rd | 4 +--
| 4 files changed, 56 insertions(+), 56 deletions(-)
* 2015-06-27(Tal Galili) intersect_trees x1/x2 -> dend1/dend2 |e87987d|
| NEWS | 3 +--
| R/prune.R | 22 +++++++++++-----------
| man/intersect_trees.Rd | 6 +++---
| 3 files changed, 15 insertions(+), 16 deletions(-)
* 2015-06-27(Tal Galili) object -> dend for: labels_colors |a306bb1|
| NEWS | 1 +
| R/labels_colors.R | 28 ++++++++++++++--------------
| man/labels_colors.Rd | 6 +++---
| 3 files changed, 18 insertions(+), 17 deletions(-)
* 2015-06-27(Tal Galili) x -> dend for: get_nodes_xy |3f50252|
| NEWS | 2 +-
| R/get_nodes_xy.R | 6 ++++--
| man/get_nodes_xy.Rd | 4 ++--
| 3 files changed, 7 insertions(+), 5 deletions(-)
* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2 for: untangle_random_search |9fa317f|
| NEWS | 2 +-
| R/untangle.R | 32 ++++++++++++++++----------------
| man/untangle_random_search.Rd | 6 +++---
| 3 files changed, 20 insertions(+), 20 deletions(-)
* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2 for: entanglement |5610519|
| NEWS | 2 +-
| R/entanglement.R | 88 +++++++++++++++++++++++++--------------------------
| man/entanglement.Rd | 14 ++++----
| 3 files changed, 52 insertions(+), 52 deletions(-)
* 2015-06-27(Tal Galili) y to dend2 |2e653c5|
| R/distinct_edges.R | 34 +++++++++++++++++-----------------
| man/dend_diff.Rd | 4 ++--
| man/distinct_edges.Rd | 6 +++---
| man/highlight_distinct_edges.Rd | 4 ++--
| 4 files changed, 24 insertions(+), 24 deletions(-)
* 2015-06-27(Tal Galili) x -> dend for: dend_diff, dist.dendlist, distinct_edges, highlight_distinct_edges, partition_leaves |1da678e|
| NEWS | 2 +-
| R/distinct_edges.R | 94 +++++++++++++++++++--------------------
| man/dend_diff.Rd | 8 ++--
| man/dist.dendlist.Rd | 4 +-
| man/distinct_edges.Rd | 6 +--
| man/highlight_distinct_edges.Rd | 10 ++---
| man/partition_leaves.Rd | 4 +-
| 7 files changed, 64 insertions(+), 64 deletions(-)
* 2015-06-27(Tal Galili) tree -> dend for: cutree_1h.dendrogram, cutree_1k.dendrogram, heights_per_k.dendrogram |7ec15a4|
| NEWS | 2 +-
| R/cutree.dendrogram.R | 95 ++++++++++++++++++++-------------------
| man/cutree_1h.dendrogram.Rd | 6 +--
| man/cutree_1k.dendrogram.Rd | 4 +-
| man/heights_per_k.dendrogram.Rd | 4 +-
| 5 files changed, 57 insertions(+), 54 deletions(-)
* 2015-06-27(Tal Galili) tree -> dend for: dendextend_cut_lower_fun |d13b9c6|
| NEWS | 2 +-
| R/cut_lower_fun.R | 24 ++++++++++++------------
| man/cut_lower_fun.Rd | 10 +++++-----
| 3 files changed, 18 insertions(+), 18 deletions(-)
* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2 for: cor_cophenetic |4c987d3|
| NEWS | 2 +-
| R/cor_cophenetic.R | 40 ++++++++++++++++++++--------------------
| man/cor_cophenetic.Rd | 10 +++++-----
| 3 files changed, 26 insertions(+), 26 deletions(-)
* 2015-06-27(Tal Galili) cor_bakers_gamma: tree1/2 -> dend1/2 |9641738|
| NEWS | 2 +-
| R/cor_bakers_gamma.R | 76 ++++++++++++++++++------------------
| man/bakers_gamma_for_2_k_matrix.Rd | 6 +--
| man/cor_bakers_gamma.Rd | 12 +++---
| 4 files changed, 48 insertions(+), 48 deletions(-)
* 2015-06-27(Tal Galili) * x -> dend for: cor.dendlist * tree1/tree2 -> dend1/dend2 for: cor_FM_index, cor_common_nodes |b62be29|
| NEWS | 2 ++
| R/cor.dendlist.R | 38 +++++++++++++++++++-------------------
| man/cor.dendlist.Rd | 6 +++---
| man/cor_FM_index.Rd | 6 +++---
| man/cor_common_nodes.Rd | 6 +++---
| 5 files changed, 30 insertions(+), 28 deletions(-)
* 2015-06-27(Tal Galili) bug fix (renaming object to dend) |952667f|
| R/branches_attr_by.R | 2 +-
| R/distinct_edges.R | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2015-06-27(Tal Galili) tree -> dend for: color_branches, color_labels_by_labels, color_labels, get_branches_heights, dendextend_get_branches_heights |7fd2a2c|
| NEWS | 2 +
| R/attr_access.R | 16 +++----
| R/color_branches.R | 100 ++++++++++++++++++++---------------------
| R/set.dendrogram.R | 6 +--
| man/color_branches.Rd | 10 ++---
| man/color_labels.Rd | 6 +--
| man/get_branches_heights.Rd | 4 +-
| man/rank_order.dendrogram.Rd | 2 +-
| 8 files changed, 74 insertions(+), 72 deletions(-)
* 2015-06-27(Tal Galili) object -> dend for: |95856ed|
| NEWS | 13 +-
| R/ape.R | 1 +
| R/attr_access.R | 194 ++++++++++++++---------------
| inst/tests/test-attr_access.R | 2 +-
| man/assign_values_to_branches_edgePar.Rd | 12 +-
| man/assign_values_to_leaves_edgePar.Rd | 10 +-
| man/assign_values_to_leaves_nodePar.Rd | 6 +-
| man/assign_values_to_nodes_nodePar.Rd | 4 +-
| man/get_leaves_attr.Rd | 4 +-
| man/get_leaves_branches_attr.Rd | 4 +-
| man/get_leaves_branches_col.Rd | 4 +-
| man/get_leaves_edgePar.Rd | 4 +-
| man/get_leaves_nodePar.Rd | 4 +-
| man/get_nodes_attr.Rd | 4 +-
| man/remove_branches_edgePar.Rd | 4 +-
| man/remove_leaves_nodePar.Rd | 4 +-
| man/remove_nodes_nodePar.Rd | 4 +-
| 17 files changed, 145 insertions(+), 133 deletions(-)
* 2015-06-27(Tal Galili) roxygen 4.1.1 |b1723fe|
| NAMESPACE | 2 +-
| man/Bk.Rd | 2 +-
| man/Bk_permutations.Rd | 2 +-
| man/Bk_plot.Rd | 2 +-
| man/DendSer.dendrogram.Rd | 2 +-
| man/FM_index.Rd | 2 +-
| man/FM_index_R.Rd | 2 +-
| man/FM_index_permutation.Rd | 2 +-
| man/FM_index_profdpm.Rd | 2 +-
| man/all.equal.dendrogram.Rd | 2 +-
| man/all_couple_rotations_at_k.Rd | 2 +-
| man/all_unique.Rd | 2 +-
| man/as.dendlist.Rd | 2 +-
| man/as.phylo.dendrogram.Rd | 2 +-
| man/as_hclust_fixed.Rd | 2 +-
| man/assign_dendextend_options.Rd | 2 +-
| man/assign_values_to_branches_edgePar.Rd | 2 +-
| man/assign_values_to_leaves_edgePar.Rd | 2 +-
| man/assign_values_to_leaves_nodePar.Rd | 2 +-
| man/assign_values_to_nodes_nodePar.Rd | 2 +-
| man/bakers_gamma_for_2_k_matrix.Rd | 2 +-
| man/branches_attr_by_clusters.Rd | 2 +-
| man/branches_attr_by_labels.Rd | 2 +-
| man/click_rotate.Rd | 2 +-
| man/collapse_branch.Rd | 2 +-
| man/color_branches.Rd | 2 +-
| man/color_labels.Rd | 2 +-
| man/colored_bars.Rd | 2 +-
| man/common_subtrees_clusters.Rd | 2 +-
| man/cor.dendlist.Rd | 2 +-
| man/cor_FM_index.Rd | 2 +-
| man/cor_bakers_gamma.Rd | 2 +-
| man/cor_common_nodes.Rd | 2 +-
| man/cor_cophenetic.Rd | 2 +-
| man/count_terminal_nodes.Rd | 2 +-
| man/cut_lower_fun.Rd | 2 +-
| man/cutree-methods.Rd | 2 +-
| man/cutree_1h.dendrogram.Rd | 2 +-
| man/cutree_1k.dendrogram.Rd | 2 +-
| man/d3dendro_options.Rd | 2 +-
| man/d3dendrogram.Rd | 2 +-
| man/dend_diff.Rd | 2 +-
| man/dendextend-package.Rd | 2 +-
| man/dendextend_labels.dendrogram.Rd | 2 +-
| man/dendextend_options.Rd | 2 +-
| man/dendlist.Rd | 2 +-
| man/dist.dendlist.Rd | 2 +-
| man/dist_long.Rd | 2 +-
| man/distinct_edges.Rd | 2 +-
| man/duplicate_leaf.Rd | 2 +-
| man/entanglement.Rd | 2 +-
| man/fac2num.Rd | 2 +-
| man/fix_members_attr.dendrogram.Rd | 2 +-
| man/flatten.dendrogram.Rd | 2 +-
| man/flip_leaves.Rd | 2 +-
| man/get_branches_heights.Rd | 2 +-
| man/get_childrens_heights.Rd | 2 +-
| man/get_leaves_attr.Rd | 2 +-
| man/get_leaves_branches_attr.Rd | 2 +-
| man/get_leaves_branches_col.Rd | 2 +-
| man/get_leaves_edgePar.Rd | 2 +-
| man/get_leaves_nodePar.Rd | 2 +-
| man/get_nodes_attr.Rd | 2 +-
| man/get_nodes_xy.Rd | 2 +-
| man/get_root_branches_attr.Rd | 2 +-
| man/ggdend.Rd | 2 +-
| man/hang.dendrogram.Rd | 2 +-
| man/heights_per_k.dendrogram.Rd | 2 +-
| man/highlight_distinct_edges.Rd | 2 +-
| man/identify.dendrogram.Rd | 2 +-
| man/intersect_trees.Rd | 2 +-
| man/is.dendlist.Rd | 2 +-
| man/is.dendrogram.Rd | 2 +-
| man/is.hclust.Rd | 2 +-
| man/is.natural.number.Rd | 2 +-
| man/is.phylo.Rd | 2 +-
| man/is_null_list.Rd | 2 +-
| man/khan.Rd | 2 +-
| man/labels-assign.Rd | 2 +-
| man/labels_colors.Rd | 2 +-
| man/ladderize.Rd | 2 +-
| man/leaf_Colors.Rd | 2 +-
| man/lowest_common_branch.Rd | 2 +-
| man/match_order_by_labels.Rd | 2 +-
| man/match_order_dendrogram_by_old_order.Rd | 2 +-
| man/na_locf.Rd | 2 +-
| man/nleaves.Rd | 2 +-
| man/nnodes.Rd | 2 +-
| man/noded_with_condition.Rd | 2 +-
| man/order.dendrogram-assign.Rd | 2 +-
| man/order.hclust.Rd | 2 +-
| man/partition_leaves.Rd | 2 +-
| man/pipe.Rd | 2 +-
| man/plot_horiz.dendrogram.Rd | 2 +-
| man/prune.Rd | 2 +-
| man/prune_common_subtrees.dendlist.Rd | 2 +-
| man/prune_leaf.Rd | 2 +-
| man/pvclust_show_signif.Rd | 2 +-
| man/pvclust_show_signif_gradient.Rd | 2 +-
| man/raise.dendrogram.Rd | 2 +-
| man/rank_branches.Rd | 2 +-
| man/rank_order.dendrogram.Rd | 2 +-
| man/rank_values_with_clusters.Rd | 2 +-
| man/rect.dendrogram.Rd | 2 +-
| man/remove_branches_edgePar.Rd | 2 +-
| man/remove_leaves_nodePar.Rd | 2 +-
| man/remove_nodes_nodePar.Rd | 2 +-
| man/rllply.Rd | 2 +-
| man/rotate.Rd | 2 +-
| man/rotate_DendSer.Rd | 2 +-
| man/sample.dendrogram.Rd | 2 +-
| man/shuffle.Rd | 2 +-
| man/sort_2_clusters_vectors.Rd | 2 +-
| man/sort_dist_mat.Rd | 2 +-
| man/sort_levels_values.Rd | 2 +-
| man/tanglegram.Rd | 2 +-
| man/theme_dendro.Rd | 2 +-
| man/unbranch.Rd | 2 +-
| man/unclass_dend.Rd | 2 +-
| man/untangle.Rd | 2 +-
| man/untangle_DendSer.Rd | 2 +-
| man/untangle_random_search.Rd | 2 +-
| man/untangle_step_rotate_1side.Rd | 2 +-
| man/untangle_step_rotate_2side.Rd | 2 +-
| man/which_leaf.Rd | 2 +-
| man/which_node.Rd | 2 +-
| 126 files changed, 126 insertions(+), 126 deletions(-)
* 2015-06-27(Tal Galili) object -> dend |8a2f94a|
| R/set.dendrogram.R | 80 ++++++++++++++++++++++++++--------------------------
| man/set.Rd | 16 +++++------
| 2 files changed, 48 insertions(+), 48 deletions(-)
* 2015-06-24(Tal Galili) Added d3heatmap example to vignette + as suggests to DESCRIPTION |f8a4926|
| DESCRIPTION | 1 +
| vignettes/introduction.Rmd | 33 ++++++++++++++++++++++++++++++++-
| 2 files changed, 33 insertions(+), 1 deletion(-)
* 2015-06-23(Tal Galili) moved assign_dendextend_options to ".onLoad" - this now allows the use of dendextend::some_func |bf35c68|
| DESCRIPTION | 2 +-
| NEWS | 3 ++-
| R/dendextend_options.R | 45 +++++++++++++++++++++++++++++++++++++++++++--
| R/zzz.R | 17 ++++++++++++++---
| vignettes/FAQ.Rmd | 13 +++++++++++++
| 5 files changed, 73 insertions(+), 7 deletions(-)
* 2015-06-07(Tal Galili) Added VignetteIndexEntry information (and Sys.Date) |5adda4c|
| vignettes/Cluster_Analysis.Rmd | 6 +++++-
| vignettes/FAQ.Rmd | 5 +++++
| vignettes/introduction.Rmd | 1 +
| 3 files changed, 11 insertions(+), 1 deletion(-)
* 2015-06-07(Tal Galili) Update instructions on viewing the vignette |4ca1df8|
| R/zzz.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-06-06(Tal Galili) Better format. |89a8aee|
| README.md | 2 +-
| inst/ignored/Introduction to dendextend.html | 1218 ++++++++++++++++++++++++
| inst/ignored/introduction.html | 1218 ------------------------
| vignettes/introduction.Rmd | 4 +-
| 4 files changed, 1221 insertions(+), 1221 deletions(-)
* 2015-06-06(Tal Galili) misc |b8c68cd|
| ChangeLog | 892 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 14 +-
| 2 files changed, 900 insertions(+), 6 deletions(-)
* 2015-06-06(Tal Galili) Fix "CRAN URL not in canonical form" |59b2397|
| DESCRIPTION | 2 +-
| R/bk_method.R | 2 +-
| R/colored_bars.R | 2 +-
| R/distinct_edges.R | 2 +-
| R/ggdendro.R | 2 +-
| R/magrittr.R | 4 ++--
| R/pvclust.R | 2 +-
| README.md | 2 +-
| inst/ignored/introduction.html | 12 ++++++------
| man/colored_bars.Rd | 2 +-
| vignettes/introduction.Rmd | 12 ++++++------
| 11 files changed, 22 insertions(+), 22 deletions(-)
* 2015-06-06(Tal Galili) Fix " \usage lines wider than 90 characters:" |36a9a84|
| R/cor_cophenetic.R | 4 +++-
| man/cor_cophenetic.Rd | 4 +++-
| 2 files changed, 6 insertions(+), 2 deletions(-)
* 2015-06-06(Tal Galili) Fix doc problems in cor_cophenetic |f2cd040|
| R/cor_cophenetic.R | 4 ++--
| man/cor_cophenetic.Rd | 4 ++--
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2015-06-06(Tal Galili) Fix cor_cophenetic.dendlist method |35ce2ce|
| R/cor_cophenetic.R | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2015-06-06(Tal Galili) Updated html with the khan analysis |19ca6e7|
| ...ts - enhanced with the dendextend package.html | 80 +++++++++++++++++++--
| 1 file changed, 76 insertions(+), 4 deletions(-)
* 2015-06-06(Tal Galili) Added the "khan" dataset analysis. |02db42c|
| NEWS | 2 +-
| vignettes/Cluster_Analysis.Rmd | 128 +++++++++++++++++++++++++++++++++++++++
| 2 files changed, 129 insertions(+), 1 deletion(-)
* 2015-06-06(Tal Galili) Added nleaves.dendlist |5ef24b1|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/nleaves.R | 13 ++++++++++++-
| man/nleaves.Rd | 5 ++++-
| 4 files changed, 18 insertions(+), 2 deletions(-)
* 2015-06-06(Tal Galili) added - prune_common_subtrees.dendlist - Prune trees to their common subtrees |86b8eb9|
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/prune.R | 33 +++++++++++++++++++++++++++++++++
| man/prune_common_subtrees.dendlist.Rd | 27 +++++++++++++++++++++++++++
| 4 files changed, 62 insertions(+), 1 deletion(-)
* 2015-06-06(Tal Galili) cor_cophenetic - changed method to method_coef (so it could be updated when using cor.dendlist) |f2bd51b|
| NEWS | 2 +-
| R/cor_cophenetic.R | 10 +++++-----
| man/cor_cophenetic.Rd | 2 +-
| 3 files changed, 7 insertions(+), 7 deletions(-)
* 2015-06-06(Tal Galili) untangle now has a new "labels" method, and it is now the default. |712bcd6|
| NEWS | 1 +
| R/untangle.R | 21 ++++++++++++++++-----
| man/untangle.Rd | 4 ++--
| 3 files changed, 19 insertions(+), 7 deletions(-)
* 2015-06-06(Tal Galili) clean code a bit from comments |becc43e|
| R/untangle.R | 557 ++++++++++++++++++++++++++++-----------------------------
| 1 file changed, 273 insertions(+), 284 deletions(-)
* 2015-06-06(Tal Galili) Adding Bk_plot to see also of Bk |674a498|
| R/bk_method.R | 2 +-
| man/Bk.Rd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2015-06-06(Tal Galili) Generated by roxygen2 (4.1.1.9000) |7acec1b|
| NAMESPACE | 2 +-
| man/Bk.Rd | 2 +-
| man/Bk_permutations.Rd | 2 +-
| man/Bk_plot.Rd | 2 +-
| man/DendSer.dendrogram.Rd | 2 +-
| man/FM_index.Rd | 2 +-
| man/FM_index_R.Rd | 2 +-
| man/FM_index_permutation.Rd | 2 +-
| man/FM_index_profdpm.Rd | 2 +-
| man/all.equal.dendrogram.Rd | 2 +-
| man/all_couple_rotations_at_k.Rd | 2 +-
| man/all_unique.Rd | 2 +-
| man/as.dendlist.Rd | 2 +-
| man/as.phylo.dendrogram.Rd | 2 +-
| man/as_hclust_fixed.Rd | 2 +-
| man/assign_dendextend_options.Rd | 2 +-
| man/assign_values_to_branches_edgePar.Rd | 2 +-
| man/assign_values_to_leaves_edgePar.Rd | 2 +-
| man/assign_values_to_leaves_nodePar.Rd | 2 +-
| man/assign_values_to_nodes_nodePar.Rd | 2 +-
| man/bakers_gamma_for_2_k_matrix.Rd | 2 +-
| man/branches_attr_by_clusters.Rd | 2 +-
| man/branches_attr_by_labels.Rd | 2 +-
| man/click_rotate.Rd | 2 +-
| man/collapse_branch.Rd | 2 +-
| man/color_branches.Rd | 2 +-
| man/color_labels.Rd | 2 +-
| man/colored_bars.Rd | 2 +-
| man/common_subtrees_clusters.Rd | 2 +-
| man/cor.dendlist.Rd | 2 +-
| man/cor_FM_index.Rd | 2 +-
| man/cor_bakers_gamma.Rd | 2 +-
| man/cor_common_nodes.Rd | 2 +-
| man/cor_cophenetic.Rd | 2 +-
| man/count_terminal_nodes.Rd | 2 +-
| man/cut_lower_fun.Rd | 2 +-
| man/cutree-methods.Rd | 2 +-
| man/cutree_1h.dendrogram.Rd | 2 +-
| man/cutree_1k.dendrogram.Rd | 2 +-
| man/d3dendro_options.Rd | 2 +-
| man/d3dendrogram.Rd | 2 +-
| man/dend_diff.Rd | 2 +-
| man/dendextend-package.Rd | 2 +-
| man/dendextend_labels.dendrogram.Rd | 2 +-
| man/dendextend_options.Rd | 2 +-
| man/dendlist.Rd | 2 +-
| man/dist.dendlist.Rd | 2 +-
| man/dist_long.Rd | 2 +-
| man/distinct_edges.Rd | 2 +-
| man/duplicate_leaf.Rd | 2 +-
| man/entanglement.Rd | 2 +-
| man/fac2num.Rd | 2 +-
| man/fix_members_attr.dendrogram.Rd | 2 +-
| man/flatten.dendrogram.Rd | 2 +-
| man/flip_leaves.Rd | 2 +-
| man/get_branches_heights.Rd | 2 +-
| man/get_childrens_heights.Rd | 2 +-
| man/get_leaves_attr.Rd | 2 +-
| man/get_leaves_branches_attr.Rd | 2 +-
| man/get_leaves_branches_col.Rd | 2 +-
| man/get_leaves_edgePar.Rd | 2 +-
| man/get_leaves_nodePar.Rd | 2 +-
| man/get_nodes_attr.Rd | 2 +-
| man/get_nodes_xy.Rd | 2 +-
| man/get_root_branches_attr.Rd | 2 +-
| man/ggdend.Rd | 2 +-
| man/hang.dendrogram.Rd | 2 +-
| man/heights_per_k.dendrogram.Rd | 2 +-
| man/highlight_distinct_edges.Rd | 2 +-
| man/identify.dendrogram.Rd | 2 +-
| man/intersect_trees.Rd | 2 +-
| man/is.dendlist.Rd | 2 +-
| man/is.dendrogram.Rd | 2 +-
| man/is.hclust.Rd | 2 +-
| man/is.natural.number.Rd | 2 +-
| man/is.phylo.Rd | 2 +-
| man/is_null_list.Rd | 2 +-
| man/labels-assign.Rd | 2 +-
| man/labels_colors.Rd | 2 +-
| man/ladderize.Rd | 2 +-
| man/leaf_Colors.Rd | 2 +-
| man/lowest_common_branch.Rd | 2 +-
| man/match_order_by_labels.Rd | 2 +-
| man/match_order_dendrogram_by_old_order.Rd | 2 +-
| man/na_locf.Rd | 2 +-
| man/nleaves.Rd | 2 +-
| man/nnodes.Rd | 2 +-
| man/noded_with_condition.Rd | 2 +-
| man/order.dendrogram-assign.Rd | 2 +-
| man/order.hclust.Rd | 2 +-
| man/partition_leaves.Rd | 2 +-
| man/pipe.Rd | 2 +-
| man/plot_horiz.dendrogram.Rd | 2 +-
| man/prune.Rd | 2 +-
| man/prune_leaf.Rd | 2 +-
| man/pvclust_show_signif.Rd | 2 +-
| man/pvclust_show_signif_gradient.Rd | 2 +-
| man/raise.dendrogram.Rd | 2 +-
| man/rank_branches.Rd | 2 +-
| man/rank_order.dendrogram.Rd | 2 +-
| man/rank_values_with_clusters.Rd | 2 +-
| man/rect.dendrogram.Rd | 2 +-
| man/remove_branches_edgePar.Rd | 2 +-
| man/remove_leaves_nodePar.Rd | 2 +-
| man/remove_nodes_nodePar.Rd | 2 +-
| man/rllply.Rd | 2 +-
| man/rotate.Rd | 2 +-
| man/rotate_DendSer.Rd | 2 +-
| man/sample.dendrogram.Rd | 2 +-
| man/set.Rd | 2 +-
| man/shuffle.Rd | 2 +-
| man/sort_2_clusters_vectors.Rd | 2 +-
| man/sort_dist_mat.Rd | 2 +-
| man/sort_levels_values.Rd | 2 +-
| man/tanglegram.Rd | 2 +-
| man/theme_dendro.Rd | 2 +-
| man/unbranch.Rd | 2 +-
| man/unclass_dend.Rd | 2 +-
| man/untangle.Rd | 2 +-
| man/untangle_DendSer.Rd | 2 +-
| man/untangle_random_search.Rd | 2 +-
| man/untangle_step_rotate_1side.Rd | 2 +-
| man/untangle_step_rotate_2side.Rd | 2 +-
| man/which_leaf.Rd | 2 +-
| man/which_node.Rd | 2 +-
| 125 files changed, 125 insertions(+), 125 deletions(-)
* 2015-06-06(Tal Galili) Adding the khan dataset to the package. |56baf12|
| DESCRIPTION | 3 +-
| NEWS | 6 ++--
| R/data.R | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| data/khan.rda | Bin 0 -> 114677 bytes
| man/khan.Rd | 80 +++++++++++++++++++++++++++++++++++++++++++
| 5 files changed, 189 insertions(+), 4 deletions(-)
* 2015-06-06(Tal Galili) more links |e14dc3a|
| README.md | 6 ++----
| 1 file changed, 2 insertions(+), 4 deletions(-)
* 2015-06-06(Tal Galili) update links to the newer vignettes |b56e833|
| README.md | 6 ++++--
| vignettes/Cluster_Analysis.Rmd | 14 ++++++++++++++
| 2 files changed, 18 insertions(+), 2 deletions(-)
* 2015-06-06(Tal Galili) got "codecov.io" to work. |a4e4443|
| README.md | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-06-05(Tal Galili) adding covr (to try to get some code coverage) |112fca3|
| DESCRIPTION | 3 ++-
| 1 file changed, 2 insertions(+), 1 deletion(-)
* 2015-06-05(Tal Galili) update travis.yml - Change lang to r (and some more things), and see if it still works. |21e5d93|
| .travis.yml | 31 ++++++-------------------------
| 1 file changed, 6 insertions(+), 25 deletions(-)
* 2015-05-24(Tal Galili) Date |e9dfd54|
| DESCRIPTION | 2 +-
| NEWS | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2015-05-24(Tal Galili) Update news since version 0.18.3 |424cd2b|
| NEWS.md | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 105 insertions(+)
* 2015-05-24(Tal Galili) fix typos |7cb02c6|
| vignettes/introduction.Rmd | 12 ++++++------
| 1 file changed, 6 insertions(+), 6 deletions(-)
* 2015-05-24(Tal Galili) updated vignettes to have smaller dpi (so that the file sizes will be more reasonable) |39e3c21|
| vignettes/Cluster_Analysis.Rmd | 6 +++---
| vignettes/FAQ.Rmd | 15 +++++++++++++++
| vignettes/introduction.Rmd | 8 ++++----
| 3 files changed, 22 insertions(+), 7 deletions(-)
* 2015-05-24(Tal Galili) html versions of the vignettes |a2204c5|
| inst/ignored/Frequantly asked questions.html | 325 +++++++++++
| ...ts - enhanced with the dendextend package.html | 574 ++++++++++++++++++++
| inst/ignored/introduction.html | 412 ++++----------
| 3 files changed, 1014 insertions(+), 297 deletions(-)
* 2015-05-24(Tal Galili) misc |4718cb5|
| vignettes/Cluster_Analysis.Rmd | 1 +
| 1 file changed, 1 insertion(+)
* 2015-05-24(Tal Galili) Fix typos |6334236|
| vignettes/Cluster_Analysis.Rmd | 24 ++++++++++++------------
| 1 file changed, 12 insertions(+), 12 deletions(-)
* 2015-05-24(Tal Galili) Added "animals - Attributes of Animals" section to cluster_analysis.Rmd |5dd94fc|
| NEWS | 1 +
| vignettes/Cluster_Analysis.Rmd | 115 +++++++++++++++++++++++++++++++++++++++
| 2 files changed, 116 insertions(+)
* 2015-05-24(Tal Galili) cor_FM_index - Correlation of FM_index for some k (similar to Bk actually). This is added to cor.dendlist |58eeedc|
| NAMESPACE | 1 +
| NEWS | 3 +++
| R/cor.dendlist.R | 59 +++++++++++++++++++++++++++++++++++++++++++++------
| man/cor.dendlist.Rd | 10 +++++----
| man/cor_FM_index.Rd | 39 ++++++++++++++++++++++++++++++++++
| 5 files changed, 101 insertions(+), 11 deletions(-)
* 2015-05-24(Tal Galili) added "cluster" as suggest |b6b1d35|
| DESCRIPTION | 3 ++-
| 1 file changed, 2 insertions(+), 1 deletion(-)
* 2015-05-24(Tal Galili) Vignette - added the votes.repub analysis (Votes for Republican Candidate in Presidential Elections) |9ddce80|
| vignettes/Cluster_Analysis.Rmd | 205 ++++++++++++++++++++++++++++++++++++++-
| 1 file changed, 200 insertions(+), 5 deletions(-)
* 2015-05-24(Tal Galili) exclude any cache folder in vignette or git |fbd747b|
| .Rbuildignore | 1 +
| .gitignore | 2 +-
| 2 files changed, 2 insertions(+), 1 deletion(-)
* 2015-05-24(Tal Galili) remove un-needed new line (cat("\n")) |062c9c4|
| inst/tests/test-distinct_edges.R | 2 +-
| inst/tests/test-entanglement.R | 2 +-
| inst/tests/test-ggdend.R | 2 +-
| 3 files changed, 3 insertions(+), 3 deletions(-)
* 2015-05-24(Tal Galili) added a link to cor_common_nodes from cor.dendlist |4844174|
| R/cor.dendlist.R | 3 ++-
| man/cor.dendlist.Rd | 3 ++-
| 2 files changed, 4 insertions(+), 2 deletions(-)
* 2015-05-24(Tal Galili) untangle_random_search/untangle_step_rotate_2side/untangle_best_k_to_rotate_by_2side_backNforth - |c9129c6|
| NEWS | 3 ++-
| R/untangle.R | 6 +++---
| 2 files changed, 5 insertions(+), 4 deletions(-)
* 2015-05-24(Tal Galili) Added Iris analysis to cluster_analysis.Rmd |e444b56|
| vignettes/Cluster_Analysis.Rmd | 293 ++++++++++++++++++++++++++++++++++-----
| 1 file changed, 261 insertions(+), 32 deletions(-)
* 2015-05-24(Tal Galili) misc |e404aa9|
| R/color_branches.R | 4 +++-
| R/tanglegram.R | 1 +
| R/zzz.R | 3 +++
| man/tanglegram.Rd | 3 ++-
| 4 files changed, 9 insertions(+), 2 deletions(-)
* 2015-05-24(Tal Galili) a warning for a common bug that happened. |6a16ace|
| R/branches_attr_by.R | 4 ++++
| 1 file changed, 4 insertions(+)
* 2015-05-24(Tal Galili) cor_common_nodes - a new correlation measure between dendrograms. |4b2410a|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/cor.dendlist.R | 60 +++++++++++++++++++++++++++++++++++++++++++----
| man/cor.dendlist.Rd | 6 ++---
| man/cor_common_nodes.Rd | 43 +++++++++++++++++++++++++++++++++
| 5 files changed, 104 insertions(+), 7 deletions(-)
* 2015-05-24(Tal Galili) Moved FAQ from introduction.Rmd to FAQ.Rmd |f20096a|
| NEWS | 2 +-
| vignettes/FAQ.Rmd | 818 +++++++++++++++++++++++++++++++++++++++++++
| vignettes/introduction.Rmd | 809 ------------------------------------------
| 3 files changed, 819 insertions(+), 810 deletions(-)
* 2015-05-24(Tal Galili) set - added "rank_branches" |33e838c|
| NEWS | 2 ++
| R/set.dendrogram.R | 3 +++
| man/set.Rd | 1 +
| 3 files changed, 6 insertions(+)
* 2015-05-24(Tal Galili) tanglegram - new parameter: faster. |728deab|
| NEWS | 4 +++-
| R/tanglegram.R | 10 ++++++++++
| man/tanglegram.Rd | 4 ++++
| 3 files changed, 17 insertions(+), 1 deletion(-)
* 2015-05-24(Tal Galili) moved lines to their right place. |085aff4|
| NEWS | 12 ++++++------
| 1 file changed, 6 insertions(+), 6 deletions(-)
* 2015-05-24(Tal Galili) move a line around. |aba3dfb|
| R/tanglegram.R | 5 ++++-
| 1 file changed, 4 insertions(+), 1 deletion(-)
* 2015-05-24(Tal Galili) untangle.dendlist - now preserve the names in the dendlist |cf5a1ae|
| NEWS | 4 +++-
| R/untangle.R | 4 ++++
| 2 files changed, 7 insertions(+), 1 deletion(-)
* 2015-05-24(Tal Galili) Added MASS (for using parcoord in the examples) |6f34c1a|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-05-24(Tal Galili) dendlist - added the `which` parameter (for indicating which elements in the dendlist to pick out) |f6edbbc|
| NEWS | 1 +
| R/dendlist.R | 18 +++++++++++++++---
| man/dendlist.Rd | 11 +++++++----
| 3 files changed, 23 insertions(+), 7 deletions(-)
* 2015-05-24(Tal Galili) untangle.dendlist - can now return a dendlist with more than two elements. |9fe8e48|
| NEWS | 1 +
| R/untangle.R | 13 ++++++++++++-
| man/untangle.Rd | 3 +++
| 3 files changed, 16 insertions(+), 1 deletion(-)
* 2015-05-24(Tal Galili) ladderize - added the `which` parameter (for indicating which elements in the dendlist to ladderize) |4f93598|
| NEWS | 1 +
| R/rotate.R | 14 ++++++++++----
| man/ladderize.Rd | 6 +++++-
| 3 files changed, 16 insertions(+), 5 deletions(-)
* 2015-05-24(Tal Galili) remove the warning when creating an empty dendlist |532fb37|
| NEWS | 2 +-
| R/dendlist.R | 2 +-
| inst/tests/test-dendlist.R | 25 ++++++++++++++-----------
| 3 files changed, 16 insertions(+), 13 deletions(-)
* 2015-05-23(Tal Galili) Rename file to be "cluster analysis" |aa156c6|
| vignettes/Cluster_Analysis.Rmd | 103 +++++++++++++++++++++++++++++++++++++++
| vignettes/Iris_Analysis.Rmd | 88 ---------------------------------
| 2 files changed, 103 insertions(+), 88 deletions(-)
* 2015-05-23(Tal Galili) Moved the "Iris analysis" from the introduction vignette to a seperate Rmd file. |25ed06f|
| vignettes/Iris_Analysis.Rmd | 88 +++++++++++++++++++++++++++++++++++++++++++
| vignettes/introduction.Rmd | 83 ----------------------------------------
| 2 files changed, 88 insertions(+), 83 deletions(-)
* 2015-05-23(Tal Galili) Added some explenations of the tanglegram when used with the coloring of the branches and lines. |8c639f4|
| vignettes/introduction.Rmd | 54 ++++++++++++++++++++++++++++++++++++++------
| 1 file changed, 47 insertions(+), 7 deletions(-)
* 2015-05-23(Tal Galili) Added tests for rank_values_with_clusters |b6660a5|
| NEWS | 2 +-
| inst/tests/test-common_subtrees.R | 49 +++++++++++++++++++++++++++++++++++++
| 2 files changed, 50 insertions(+), 1 deletion(-)
* 2015-05-23(Tal Galili) added context |0e3ae60|
| inst/tests/test-dendlist.R | 3 +++
| 1 file changed, 3 insertions(+)
* 2015-05-23(Tal Galili) Decided this will be version 1.0.0 and not 0.19.0 |25c19e1|
| DESCRIPTION | 4 ++--
| NEWS | 2 +-
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2015-05-23(Tal Galili) Fix "common_subtrees_color_branches" to make sure everyone are using the same colors. |36f22d3|
| R/tanglegram.R | 75 ++++++++++++++++++++++++++++++++++-------------------
| man/tanglegram.Rd | 10 ++++---
| 2 files changed, 55 insertions(+), 30 deletions(-)
* 2015-05-23(Tal Galili) color_branches - now uses branches_attr_by_clusters with "all" labels needing to fit a group for the branches to be colors. |9e27f28|
| R/color_branches.R | 3 ++-
| 1 file changed, 2 insertions(+), 1 deletion(-)
* 2015-05-23(Tal Galili) * branches_attr_by_clusters - * can now accept a vector of values with the length of the labels. * new parameter "branches_changed_have_which_labels" - allows the user the decide if the change in parameters will be for branches with all/any of the labels (useful for tanglegram - since we would like to color common subtrees with all of the labels, not just any.) |b2fd1d0|
| NEWS | 4 +++
| R/branches_attr_by.R | 70 ++++++++++++++++++++++++++++++++------
| man/branches_attr_by_clusters.Rd | 16 +++++++--
| 3 files changed, 77 insertions(+), 13 deletions(-)
* 2015-05-23(Tal Galili) Added rank_values_with_clusters - Rank a vector based on clusters (important for various functions.) |97787ac|
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/common_subtrees.R | 52 ++++++++++++++++++++++++++++++++++----
| man/rank_values_with_clusters.Rd | 37 +++++++++++++++++++++++++++
| 4 files changed, 86 insertions(+), 6 deletions(-)
* 2015-05-22(Tal Galili) Fix: ggplot.ggdend: no visible global function definition for |ff33554|
| R/ggdend.R | 1 +
| 1 file changed, 1 insertion(+)
* 2015-05-22(Tal Galili) Fix: Codoc mismatches from documentation object 'ggdend': |7161cd7|
| R/ggdend.R | 6 ++++--
| man/ggdend.Rd | 5 ++++-
| 2 files changed, 8 insertions(+), 3 deletions(-)
* 2015-05-22(Tal Galili) fix: \examples lines wider than 100 characters: |ca11269|
| R/attr_access.R | 4 +++-
| man/assign_values_to_branches_edgePar.Rd | 4 +++-
| 2 files changed, 6 insertions(+), 2 deletions(-)
* 2015-05-22(Tal Galili) added test for ggdend |d00f01a|
| inst/tests/test-ggdend.R | 50 ++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 50 insertions(+)
* 2015-05-22(Tal Galili) added get_nodes_attr test |788def3|
| inst/tests/test-attr_access.R | 13 +++++++++++++
| 1 file changed, 13 insertions(+)
* 2015-05-22(Tal Galili) plot.ggdend - added support to plot nodes |bd2e1a9|
| NEWS | 4 +++-
| R/ggdend.R | 28 +++++++++++++++++++++++++++-
| 2 files changed, 30 insertions(+), 2 deletions(-)
* 2015-05-22(Tal Galili) Fix ggdend to now deal with edgePar and nodePar being lists. (now the vignette doesn't crash) |d20f2d0|
| R/ggdend.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++---------
| 1 file changed, 48 insertions(+), 9 deletions(-)
* 2015-05-22(Tal Galili) Fix test to now account for edgePar and nodePar are lists. |2c608bf|
| inst/tests/test-attr_access.R | 4 +++-
| inst/tests/test-branches_attr_by.R | 10 ++++++++++
| inst/tests/test-set.dendrogram.R | 15 ++++++++-------
| 3 files changed, 21 insertions(+), 8 deletions(-)
* 2015-05-22(Tal Galili) made sure that the end of the vector in "dendextend_heights_per_k.dendrogram" will give the tree size (and not 0) as its name. |60cac76|
| R/cutree.dendrogram.R | 5 +++++
| inst/tests/test-cutree.dendrogram.R | 30 +++++++++++++++++++++++++++++-
| 2 files changed, 34 insertions(+), 1 deletion(-)
* 2015-05-22(Tal Galili) Date |f5ef241|
| NEWS | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-05-22(Tal Galili) Fix link |adeabab|
| vignettes/introduction.Rmd | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-05-22(Tal Galili) Date |5dbf21c|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-05-22(Tal Galili) Parameters are now stored as a list for (allows for branches to have colors/linetype/linewidth, some are numeric and some character): assign_values_to_branches_edgePar / assign_values_to_leaves_nodePar / assign_values_to_leaves_edgePar / assign_values_to_nodes_nodePar - the parameters are stored as a list in edgePar/nodePar (instead of a vector). Discovered thanks to Martin Maechler. Fixes: "Error in segments(x0, y0, x1, y1, col = col, lty = lty, lwd = lwd) : invalid line type: must be length 2, 4, 6 or 8" |4bf8f20|
| NEWS | 2 ++
| R/attr_access.R | 29 +++++++++++++++++++++--------
| inst/tests/test-branches_attr_by.R | 23 +++++++++++++++++------
| man/assign_values_to_branches_edgePar.Rd | 14 +++++++++++++-
| tests/test-all.R | 16 ++++++++++++----
| 5 files changed, 65 insertions(+), 19 deletions(-)
* 2015-05-22(Tal Galili) Added doc to common_subtrees_clusters |a6b4cb0|
| NAMESPACE | 1 +
| R/common_subtrees.R | 53 +++++++++++++++++++++++----------------
| man/common_subtrees_clusters.Rd | 44 ++++++++++++++++++++++++++++++++
| 3 files changed, 77 insertions(+), 21 deletions(-)
* 2015-05-22(Tal Galili) tanglegram - have doc match code. |d86f957|
| R/tanglegram.R | 7 ++++---
| man/tanglegram.Rd | 4 +++-
| 2 files changed, 7 insertions(+), 4 deletions(-)
* 2015-05-22(Tal Galili) Fix "color_branches: no visible binding for global variable 'cols'" |64a8bba|
| R/color_branches.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-05-22(Tal Galili) labels.dendrogram is now working through dendextend_options("labels.dendrogram"). The defualt is the new dendextend_labels.dendrogram (which is just stats:::labels.dendrogram), but this allows the package dendextendRcpp to change the function used by the package (without masking the function in base R) - thus making both me, and CRAN, happy :) |ae602a9|
| NAMESPACE | 1 +
| NEWS | 4 +++-
| R/dendextend_options.R | 1 +
| R/stats_imports.R | 35 +++++++++++++++++++++++++++++++++++
| R/zzz.R | 4 +++-
| man/dendextend_labels.dendrogram.Rd | 28 ++++++++++++++++++++++++++++
| 6 files changed, 71 insertions(+), 2 deletions(-)
* 2015-05-22(Tal Galili) rect.dendrogram - deals with the case we want to use k for which k+1 is not defined. |61eeded|
| NEWS | 3 ++-
| R/rect.dendrogram.R | 21 +++++++++++++++++++--
| inst/tests/test-rect.dendrogram.R | 26 ++++++++++++++++++++++++++
| man/rect.dendrogram.Rd | 8 ++++++++
| 4 files changed, 55 insertions(+), 3 deletions(-)
* 2015-05-19(Tal Galili) tanglegram - Added new parameters: common_subtrees_color_lines and common_subtrees_color_branches to color connecting-lines and/or the dendrograms themsleves, to help detect commonly shared subtrees. |7394cba|
| NEWS | 2 +-
| R/tanglegram.R | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++--
| man/tanglegram.Rd | 29 +++++++++++++++++++++
| 3 files changed, 100 insertions(+), 3 deletions(-)
* 2015-05-19(Tal Galili) common_subtrees_clusters - a (currently hidden) function to get clusters for labels of common subtrees between two trees. |22c3235|
| NEWS | 3 +
| R/common_subtrees.R | 175 ++++++++++++++++++++++++++++++++++++++++++++++++
| man/distinct_edges.Rd | 1 +
| tests/test-all.R | 2 -
| 4 files changed, 179 insertions(+), 2 deletions(-)
* 2015-05-18(Tal Galili) tanglegram - turned "highlight_distinct_edges = FALSE". This is due to a bug in R that causes plot.dendrogram to crash when trying to plot a tree with both lty and some character color for the branch. |cfebab3|
| NEWS | 2 +-
| R/tanglegram.R | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2015-05-18(Tal Galili) color_branches - gained a new "cluster" parameter to allow for easy uneven coloring of branches (using branches_attr_by_clusters). This is not a new feature, as it is an attempt to have the user access more options from one place (i.e.: color_branches). |5d601b0|
| DESCRIPTION | 2 +-
| NEWS | 6 ++-
| R/branches_attr_by.R | 2 +-
| R/color_branches.R | 81 ++++++++++++++++++++++++++++----------
| man/branches_attr_by_clusters.Rd | 2 +-
| man/color_branches.Rd | 20 +++++++++-
| 6 files changed, 87 insertions(+), 26 deletions(-)
* 2015-05-18(Tal Galili) roxygen2 (4.0.2) -> roxygen2 (4.1.1) |81c0709|
| NAMESPACE | 2 +-
| man/Bk.Rd | 3 ++-
| man/Bk_permutations.Rd | 3 ++-
| man/Bk_plot.Rd | 3 ++-
| man/DendSer.dendrogram.Rd | 3 ++-
| man/FM_index.Rd | 3 ++-
| man/FM_index_R.Rd | 3 ++-
| man/FM_index_permutation.Rd | 3 ++-
| man/FM_index_profdpm.Rd | 3 ++-
| man/all.equal.dendrogram.Rd | 3 ++-
| man/all_couple_rotations_at_k.Rd | 3 ++-
| man/all_unique.Rd | 3 ++-
| man/as.dendlist.Rd | 3 ++-
| man/as.phylo.dendrogram.Rd | 3 ++-
| man/as_hclust_fixed.Rd | 3 ++-
| man/assign_dendextend_options.Rd | 3 ++-
| man/assign_values_to_branches_edgePar.Rd | 3 ++-
| man/assign_values_to_leaves_edgePar.Rd | 3 ++-
| man/assign_values_to_leaves_nodePar.Rd | 3 ++-
| man/assign_values_to_nodes_nodePar.Rd | 3 ++-
| man/bakers_gamma_for_2_k_matrix.Rd | 3 ++-
| man/branches_attr_by_clusters.Rd | 3 ++-
| man/branches_attr_by_labels.Rd | 3 ++-
| man/click_rotate.Rd | 3 ++-
| man/collapse_branch.Rd | 3 ++-
| man/color_branches.Rd | 3 ++-
| man/color_labels.Rd | 3 ++-
| man/colored_bars.Rd | 3 ++-
| man/cor.dendlist.Rd | 3 ++-
| man/cor_bakers_gamma.Rd | 3 ++-
| man/cor_cophenetic.Rd | 3 ++-
| man/count_terminal_nodes.Rd | 3 ++-
| man/cut_lower_fun.Rd | 3 ++-
| man/cutree-methods.Rd | 3 ++-
| man/cutree_1h.dendrogram.Rd | 3 ++-
| man/cutree_1k.dendrogram.Rd | 3 ++-
| man/d3dendro_options.Rd | 3 ++-
| man/d3dendrogram.Rd | 3 ++-
| man/dend_diff.Rd | 3 ++-
| man/dendextend-package.Rd | 3 ++-
| man/dendextend_options.Rd | 3 ++-
| man/dendlist.Rd | 3 ++-
| man/dist.dendlist.Rd | 3 ++-
| man/dist_long.Rd | 3 ++-
| man/distinct_edges.Rd | 3 ++-
| man/duplicate_leaf.Rd | 3 ++-
| man/entanglement.Rd | 3 ++-
| man/fac2num.Rd | 3 ++-
| man/fix_members_attr.dendrogram.Rd | 3 ++-
| man/flatten.dendrogram.Rd | 3 ++-
| man/flip_leaves.Rd | 3 ++-
| man/get_branches_heights.Rd | 3 ++-
| man/get_childrens_heights.Rd | 3 ++-
| man/get_leaves_attr.Rd | 3 ++-
| man/get_leaves_branches_attr.Rd | 3 ++-
| man/get_leaves_branches_col.Rd | 3 ++-
| man/get_leaves_edgePar.Rd | 3 ++-
| man/get_leaves_nodePar.Rd | 3 ++-
| man/get_nodes_attr.Rd | 3 ++-
| man/get_nodes_xy.Rd | 3 ++-
| man/get_root_branches_attr.Rd | 3 ++-
| man/ggdend.Rd | 3 ++-
| man/hang.dendrogram.Rd | 3 ++-
| man/heights_per_k.dendrogram.Rd | 3 ++-
| man/highlight_distinct_edges.Rd | 3 ++-
| man/identify.dendrogram.Rd | 3 ++-
| man/intersect_trees.Rd | 3 ++-
| man/is.dendlist.Rd | 3 ++-
| man/is.dendrogram.Rd | 3 ++-
| man/is.hclust.Rd | 3 ++-
| man/is.natural.number.Rd | 3 ++-
| man/is.phylo.Rd | 3 ++-
| man/is_null_list.Rd | 3 ++-
| man/labels-assign.Rd | 3 ++-
| man/labels_colors.Rd | 3 ++-
| man/ladderize.Rd | 3 ++-
| man/leaf_Colors.Rd | 3 ++-
| man/lowest_common_branch.Rd | 3 ++-
| man/match_order_by_labels.Rd | 3 ++-
| man/match_order_dendrogram_by_old_order.Rd | 3 ++-
| man/na_locf.Rd | 3 ++-
| man/nleaves.Rd | 3 ++-
| man/nnodes.Rd | 3 ++-
| man/noded_with_condition.Rd | 3 ++-
| man/order.dendrogram-assign.Rd | 3 ++-
| man/order.hclust.Rd | 3 ++-
| man/partition_leaves.Rd | 3 ++-
| man/pipe.Rd | 3 ++-
| man/plot_horiz.dendrogram.Rd | 3 ++-
| man/prune.Rd | 3 ++-
| man/prune_leaf.Rd | 3 ++-
| man/pvclust_show_signif.Rd | 3 ++-
| man/pvclust_show_signif_gradient.Rd | 3 ++-
| man/raise.dendrogram.Rd | 3 ++-
| man/rank_branches.Rd | 3 ++-
| man/rank_order.dendrogram.Rd | 3 ++-
| man/rect.dendrogram.Rd | 3 ++-
| man/remove_branches_edgePar.Rd | 3 ++-
| man/remove_leaves_nodePar.Rd | 3 ++-
| man/remove_nodes_nodePar.Rd | 3 ++-
| man/rllply.Rd | 3 ++-
| man/rotate.Rd | 3 ++-
| man/rotate_DendSer.Rd | 3 ++-
| man/sample.dendrogram.Rd | 3 ++-
| man/set.Rd | 3 ++-
| man/shuffle.Rd | 3 ++-
| man/sort_2_clusters_vectors.Rd | 3 ++-
| man/sort_dist_mat.Rd | 3 ++-
| man/sort_levels_values.Rd | 3 ++-
| man/tanglegram.Rd | 6 ++++--
| man/theme_dendro.Rd | 3 ++-
| man/unbranch.Rd | 3 ++-
| man/unclass_dend.Rd | 3 ++-
| man/untangle.Rd | 3 ++-
| man/untangle_DendSer.Rd | 3 ++-
| man/untangle_random_search.Rd | 3 ++-
| man/untangle_step_rotate_1side.Rd | 3 ++-
| man/untangle_step_rotate_2side.Rd | 3 ++-
| man/which_leaf.Rd | 3 ++-
| man/which_node.Rd | 3 ++-
| 120 files changed, 241 insertions(+), 121 deletions(-)
* 2015-05-18(Tal Galili) tanglegram - tiny clarification about color_lines |3fe5dd9|
| R/tanglegram.R | 1 +
| 1 file changed, 1 insertion(+)
* 2015-05-18(Tal Galili) distinct_edges - a simpler R code |47975fb|
| R/distinct_edges.R | 6 ++++--
| 1 file changed, 4 insertions(+), 2 deletions(-)
* 2015-05-18(Tal Galili) Fix: as.hclust.pvclust: no visible binding for global variable ‘object’ |c3ada78|
| R/pvclust.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-05-17(Tal Galili) Fix coveralls badge |c5fcb1c|
| README.md | 4 +---
| 1 file changed, 1 insertion(+), 3 deletions(-)
* 2015-05-17(Tal Galili) Added coveralls and CRAN status |6948645|
| .travis.yml | 4 ++++
| NEWS | 2 ++
| README.md | 3 +++
| 3 files changed, 9 insertions(+)
* 2015-05-17(Tal Galili) Added Code of conduct |fd5a95a|
| .Rbuildignore | 3 ++-
| CONDUCT.md | 25 +++++++++++++++++++++++++
| NEWS | 5 +++++
| R/zzz.R | 11 +++++++++++
| README.md | 6 ++++++
| 5 files changed, 49 insertions(+), 1 deletion(-)
* 2015-05-17(Tal Galili) Fix "Objects in \usage without \alias in documentation object". For ‘prune.rpart’ and ‘sort.dendlist’. |872678a|
| NEWS | 1 +
| R/prune.R | 1 +
| R/rotate.R | 1 +
| man/prune.Rd | 1 +
| man/rotate.Rd | 1 +
| 5 files changed, 5 insertions(+)
* 2015-05-17(Tal Galili) as.hclust.pvclust - use "x" instead of "object", to avoid "checking S3 generic/method consistency ... WARNING" |12c1c08|
| NEWS | 1 +
| R/pvclust.R | 2 +-
| 2 files changed, 2 insertions(+), 1 deletion(-)
* 2015-05-17(Tal Galili) Fix "'::' or ':::' import not declared from: ‘rpart’" by adding rpart to DESCRIPTION. |e8a85e7|
| DESCRIPTION | 4 ++--
| NEWS | 8 ++++++++
| 2 files changed, 10 insertions(+), 2 deletions(-)
* 2015-05-17(Tal Galili) version bump 0.18.8 |ca2a085|
| DESCRIPTION | 2 +-
| NEWS | 2 +-
| README.md | 4 ++--
| 3 files changed, 4 insertions(+), 4 deletions(-)
* 2015-05-17(Tal Galili) identify.dendrogram - parameter horiz now works (fixes #4) |0cf59c3|
| NEWS | 3 +++
| R/rect.dendrogram.R | 16 +++++++++++++---
| man/identify.dendrogram.Rd | 6 +++++-
| 3 files changed, 21 insertions(+), 4 deletions(-)
* 2015-05-16(Tal Galili) tiny fix |117e2b2|
| README.md | 1 +
| 1 file changed, 1 insertion(+)
* 2015-05-16(Tal Galili) Another tweak to the install of packages |9afdd03|
| README.md | 10 ++++++----
| 1 file changed, 6 insertions(+), 4 deletions(-)
* 2015-05-16(Tal Galili) Simplafy github installation code a bit. |29215cb|
| README.md | 15 ++++-----------
| 1 file changed, 4 insertions(+), 11 deletions(-)
* 2015-05-16(Tal Galili) Added a Vectorize example (fixes #6) |df95472|
| R/rect.dendrogram.R | 2 ++
| man/rect.dendrogram.Rd | 2 ++
| 2 files changed, 4 insertions(+)
* 2015-05-16(Tal Galili) rect.dendrogram - make the heights of the rects be in the middle of the two clusters so that they would look nicer. Added prop_k_height to state which proportion of the height the rect should be (between k and k+1 heights). Also added upper_rect to allow the user to customize the exact height. (this closes issue #6) |4526d46|
| DESCRIPTION | 7 ++++---
| NEWS | 4 ++--
| R/rect.dendrogram.R | 16 +++++++++++++---
| man/rect.dendrogram.Rd | 7 ++++++-
| 4 files changed, 25 insertions(+), 9 deletions(-)
* 2015-05-15(Tal Galili) all.equal.dendrogram - suppress warning for a dend with only 1 item, when using dendextendRcpp. |fb8515c|
| NEWS | 1 +
| R/all.equal.R | 17 +++++++++++++++--
| inst/tests/test-cut_lower_fun.R | 14 ++++++++++----
| 3 files changed, 26 insertions(+), 6 deletions(-)
* 2015-05-15(Tal Galili) Fix comments' text |1d22f77|
| R/cutree.dendrogram.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-05-15(Tal Galili) all.equal.dendlist - can now compare two dendlist objects to one another, and not only the dendrograms inside one dendlist. (also added new tests that all.equal.dendlist works) |c581e1b|
| NEWS | 7 +++++++
| R/all.equal.R | 19 +++++++++++++++++++
| inst/tests/test-dendlist.R | 32 +++++++++++++++++++++++++++++++-
| man/all.equal.dendrogram.Rd | 5 +++++
| 4 files changed, 62 insertions(+), 1 deletion(-)
* 2015-05-15(Tal Galili) Test commit |6449eb7|
| tests/test-all.R | 3 +++
| 1 file changed, 3 insertions(+)
* 2015-05-06(Tal Galili) remove dependancy in VIGNETTE on DendSer (using require instead of library) - bump to 0.18.7 |49a073f|
| DESCRIPTION | 7 +++----
| NEWS | 2 ++
| vignettes/introduction.Rmd | 30 ++++++++++++++++++------------
| 3 files changed, 23 insertions(+), 16 deletions(-)
* 2015-05-06(Tal Galili) ladderize instead of rotate_DendSer - in the example |729903b|
| R/set.dendrogram.R | 4 ++--
| man/set.Rd | 4 ++--
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2015-05-06(Tal Galili) tanglegram.dendlist - fix it when names is null to have the default be "" |8dbea82|
| NEWS | 1 +
| R/tanglegram.R | 5 ++++-
| 2 files changed, 5 insertions(+), 1 deletion(-)
* 2015-05-06(Tal Galili) untangle - added method="ladderize" |0c04568|
| NEWS | 7 +++++++
| R/untangle.R | 11 ++++++-----
| man/untangle.Rd | 4 ++--
| 3 files changed, 15 insertions(+), 7 deletions(-)
* 2015-04-25(Tal Galili) library corrplot added to plot cor.dendlist results. Examples added to vignette and function's example. |aea94bc|
| DESCRIPTION | 3 ++-
| NEWS | 3 ++-
| R/cor.dendlist.R | 8 +++++++-
| man/cor.dendlist.Rd | 8 +++++++-
| vignettes/introduction.Rmd | 9 +++++++++
| 5 files changed, 27 insertions(+), 4 deletions(-)
* 2015-04-25(Tal Galili) tanglegram.dendlist - now gets main_left and main_right (if they are null) from the names in dendlist (if they exist) |7cc9037|
| NEWS | 3 +++
| R/tanglegram.R | 14 +++++++++++---
| man/tanglegram.Rd | 2 +-
| 3 files changed, 15 insertions(+), 4 deletions(-)
* 2015-04-25(Tal Galili) added example for using "get_leaves_branches_col" in "How to color the branches in heatmap.2?" |c30208f|
| NEWS | 3 +++
| vignettes/introduction.Rmd | 8 +++++++-
| 2 files changed, 10 insertions(+), 1 deletion(-)
* 2015-04-25(Tal Galili) Fix get_leaves_branches_attr and also make it simpler. |6017490|
| R/attr_access.R | 12 ++++--------
| 1 file changed, 4 insertions(+), 8 deletions(-)
* 2015-04-25(Tal Galili) NEW FUNCTIONS: (version 0.18.6) * get_leaves_edgePar - Get edgePar of dendrogram's leaves * get_leaves_branches_attr - Get an attribute of the branches of a dendrogram's leaves * get_leaves_branches_col - Get the colors of the branches of a dendrogram's leaves. This function is actually the point of the two other functions. It is meant to help match the color of the labels with that of the branches - after running color_branches. |139236d|
| DESCRIPTION | 4 +-
| NAMESPACE | 3 +
| NEWS | 8 +++
| R/attr_access.R | 141 ++++++++++++++++++++++++++++++++++++++
| man/get_leaves_branches_attr.Rd | 48 +++++++++++++
| man/get_leaves_branches_col.Rd | 44 ++++++++++++
| man/get_leaves_edgePar.Rd | 45 ++++++++++++
| man/get_leaves_nodePar.Rd | 1 +
| 8 files changed, 292 insertions(+), 2 deletions(-)
* 2015-04-22(Tal Galili) use color_branches instead of set (easier for people - I would guess) |ade1635|
| vignettes/introduction.Rmd | 6 ++++--
| 1 file changed, 4 insertions(+), 2 deletions(-)
* 2015-04-22(Tal Galili) VIGNETTE added: "How to color the branches in heatmap.2?" |6127035|
| DESCRIPTION | 4 +-
| NEWS | 7 +
| vignettes/introduction.Rmd | 632 +++++++++++++++++++++++++++++++++++++++++++
| 3 files changed, 641 insertions(+), 2 deletions(-)
* 2015-03-05(Tal Galili) s |17f6568|
| README.md | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-03-05(Tal Galili) Added TOC to readme.md |4d083c0|
| README.md | 12 +++++++++++-
| 1 file changed, 11 insertions(+), 1 deletion(-)
* 2015-02-14(Tal Galili) Update vignette on github |e0ecc5a|
| inst/ignored/introduction.html | 1875 ++++++++++++++++++--------------------
| 1 file changed, 866 insertions(+), 1009 deletions(-)
* 2015-02-14(Tal Galili) moved to knitr::docco_linear (and some fixes to figures height) |6de5e7b|
| vignettes/introduction.Rmd | 10 +++++-----
| 1 file changed, 5 insertions(+), 5 deletions(-)
* 2015-02-07(Tal Galili) as.hclust.pvclust |1c3ce5b|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/pvclust.R | 11 ++++++++++-
| 3 files changed, 12 insertions(+), 1 deletion(-)
* 2015-02-07(Tal Galili) Added sort.dendlist |e90a0cd|
| DESCRIPTION | 4 ++--
| NAMESPACE | 1 +
| NEWS | 1 +
| R/rotate.R | 11 +++++++++++
| man/rotate.Rd | 2 ++
| 5 files changed, 17 insertions(+), 2 deletions(-)
* 2015-02-07(Tal Galili) prune.rpart added |3ae7031|
| NAMESPACE | 1 +
| NEWS | 10 ++++++++++
| R/prune.R | 8 ++++++++
| man/prune.Rd | 2 ++
| 4 files changed, 21 insertions(+)
* 2015-01-31(Tal Galili) Bump to 0.18.3 |86adb2a|
| ChangeLog | 13 +++++++++++++
| R/zzz.R | 2 +-
| 2 files changed, 14 insertions(+), 1 deletion(-)
* 2015-01-31(Tal Galili) require -> requireNamespace |6dcc805|
| .Rbuildignore | 2 +-
| R/bk_method.R | 2 +-
| R/rainbow_fun.R | 2 +-
| 3 files changed, 3 insertions(+), 3 deletions(-)
* 2015-01-31(Tal Galili) update NEWS.md and changelog |e8b9e78|
| ChangeLog | 42 ++++++++++++++++++++++++++++++++++++++++++
| NEWS | 2 +-
| NEWS.md | 20 ++++++++++++++++++++
| R/zzz.R | 2 +-
| 4 files changed, 64 insertions(+), 2 deletions(-)
* 2015-01-31(Tal Galili) Fix "Please use :: or requireNamespace() instead." by commenting out all "library", since using "::" is enough! |fc73295|
| NEWS | 6 +
| R/DendSer.R | 2 +-
| R/ape.R | 8 +-
| R/cutree.dendrogram.R | 42 +++---
| R/ggdend.R | 4 +-
| R/ggdendro.R | 2 +-
| R/nleaves.R | 4 +-
| R/prune.R | 2 +-
| R/rotate.R | 4 +-
| R/set.dendrogram.R | 2 +-
| R/unbranch.R | 2 +-
| R/untangle.R | 358 ++++++++++++++++++++++++------------------------
| R/zzz.R | 2 +-
| 13 files changed, 222 insertions(+), 216 deletions(-)
* 2015-01-31(Tal Galili) Fix "title case" for the package's Title in the DESCRIPTION |ccf93c3|
| DESCRIPTION | 4 ++--
| NEWS | 5 +++++
| 2 files changed, 7 insertions(+), 2 deletions(-)
* 2015-01-31(Tal Galili) Fix "No package encoding and non-ASCII characters in the following R files" |bba4e4c|
| R/ggdend.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-01-31(Tal Galili) Minor doc fix for `collapse_branch` |2f3019b|
| DESCRIPTION | 2 +-
| NEWS | 9 +++++++++
| R/unbranch.R | 3 ++-
| man/collapse_branch.Rd | 3 ++-
| 4 files changed, 14 insertions(+), 3 deletions(-)
* 2015-01-31(Tal Galili) Update NEWS.md and changelog |e0ef4b5|
| ChangeLog | 39 +++++++++++++++++++++++++++++++++++++++
| NEWS.md | 29 +++++++++++++++++++++++++++++
| 2 files changed, 68 insertions(+)
* 2015-01-31(Tal Galili) collapse_branch to vignette |4cafe05|
| NEWS | 8 +++++++-
| vignettes/introduction.Rmd | 17 +++++++++++++++++
| 2 files changed, 24 insertions(+), 1 deletion(-)
* 2015-01-31(Tal Galili) Add ladderize to collapse_branch example |f7043c6|
| R/rotate.R | 2 +-
| R/unbranch.R | 8 +++++---
| man/collapse_branch.Rd | 7 ++++---
| man/rotate.Rd | 2 +-
| 4 files changed, 11 insertions(+), 8 deletions(-)
* 2015-01-31(Tal Galili) ###VIGNETTE - new sections! * Quick functions for FAQ * How to colour the labels of a dendrogram by an additional factor variable * How to color a dendrogram's branches/labels based on cluster (i.e.: cutree result) * Change dendrogram's labels * Larger font for leaves in a dendrogram * How to view attributes of a dendrogram * rotate - explain about sort * ggplot2 integration (!) * Comparing trees: * dend_diff * all.equal * dist.dendlist * cor.dendlist |84335e7|
| NEWS | 15 +++
| vignettes/introduction.Rmd | 305 +++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 320 insertions(+)
* 2015-01-31(Tal Galili) `ggplot.ggdend` - support theme = NULL |d94efb6|
| NEWS | 2 +-
| R/ggdend.R | 9 ++++++---
| man/ggdend.Rd | 5 +++--
| 3 files changed, 10 insertions(+), 6 deletions(-)
* 2015-01-31(Tal Galili) Minor .Rd fixes. |d69de40|
| R/ggdend.R | 4 ++--
| man/ggdend.Rd | 4 ++--
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2015-01-31(Tal Galili) `sort.dendrogram` - added a new parameter: type = c("labels", "nodes"), to use `ladderize` for sorting |2d4fe25|
| DESCRIPTION | 4 ++--
| NEWS | 8 ++++++++
| R/rotate.R | 17 +++++++++++++++--
| man/rotate.Rd | 11 ++++++++++-
| 4 files changed, 35 insertions(+), 5 deletions(-)
* 2015-01-30(Tal Galili) cheatsheet? |1f2c862|
| TODO | 5 +++++
| 1 file changed, 5 insertions(+)
* 2015-01-30(Tal Galili) Updated ChangeLog and NEWS.md |d3b1613|
| ChangeLog | 674 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
| NEWS.md | 102 +++++++++
| 2 files changed, 768 insertions(+), 8 deletions(-)
* 2015-01-30(Tal Galili) Fix package date. |10d25e2|
| DESCRIPTION | 2 +-
| NEWS | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2015-01-29(Tal Galili) Fix various doc errors. |369cce9|
| R/rotate.R | 19 ++++++++++---------
| man/ladderize.Rd | 6 +++---
| man/rotate.Rd | 8 ++++----
| 3 files changed, 17 insertions(+), 16 deletions(-)
* 2015-01-29(Tal Galili) Fix "ggplot.ggdend: no visible global function definition for ‘aes_string’" error |f5b34b7|
| R/ggdend.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-01-29(Tal Galili) `ladderize` - Ladderize a Tree (reorganizes the internal structure of the tree to get the ladderized effect when plotted) |9120507|
| NAMESPACE | 4 ++
| NEWS | 1 +
| R/rotate.R | 116 +++++++++++++++++++++++++++++++++++++++++++++++++++--
| man/ladderize.Rd | 47 ++++++++++++++++++++++
| man/rotate.Rd | 4 +-
| 5 files changed, 167 insertions(+), 5 deletions(-)
* 2015-01-29(Tal Galili) Use aes_string instead of aes! |70ab17c|
| R/ggdend.R | 13 ++++++++-----
| 1 file changed, 8 insertions(+), 5 deletions(-)
* 2015-01-29(Tal Galili) Fix as.ggdend - to get the col/cex of the labels correctly. |174e12f|
| R/ggdend.R | 7 +++++--
| 1 file changed, 5 insertions(+), 2 deletions(-)
* 2015-01-29(Tal Galili) Fix "Missing link or links in documentation object" error |e8713e5|
| R/ape.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-01-29(Tal Galili) Fix "lines wider than 100 characters:" error |a035228|
| R/distinct_edges.R | 4 +++-
| man/as.phylo.dendrogram.Rd | 2 +-
| man/highlight_distinct_edges.Rd | 4 +++-
| 3 files changed, 7 insertions(+), 3 deletions(-)
* 2015-01-29(Tal Galili) Fix many "no visible global function definition for ..." errors. |c028b06|
| R/ggdend.R | 42 ++++++++++++++++++++++++++++++++----------
| man/ggdend.Rd | 18 ++++++++++--------
| 2 files changed, 42 insertions(+), 18 deletions(-)
* 2015-01-29(Tal Galili) Fix theme_dendro: no visible global function definition for 'element_text' |4e30954|
| R/ggdendro.R | 5 ++++-
| 1 file changed, 4 insertions(+), 1 deletion(-)
* 2015-01-29(Tal Galili) fix collapse_branch: no visible binding for global variable ‘dend_node’ |c51c27e|
| R/unbranch.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-01-29(Tal Galili) Fix Codoc mismatches in prepare.ggdend |c87b7d8|
| R/ggdend.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-01-29(Tal Galili) ggplot.ggdend: leaf_labels -> labels |5f6e090|
| R/ggdend.R | 8 ++++----
| 1 file changed, 4 insertions(+), 4 deletions(-)
* 2015-01-29(Tal Galili) DESCRIPTION: Moved ape and ggplot2 to "Suggests" packages - so that I could refer to them in the vignette/help pages. |9f54d6a|
| DESCRIPTION | 7 ++++---
| 1 file changed, 4 insertions(+), 3 deletions(-)
* 2015-01-29(Tal Galili) Rename dist_fun.R to dist_long.R |6ed91cc|
| NEWS | 1 +
| R/dist_fun.R | 62 ---------------------------------------------------------
| R/dist_long.R | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| R/unbranch.R | 1 +
| 4 files changed, 64 insertions(+), 62 deletions(-)
* 2015-01-29(Tal Galili) `collapse_branch` - simplifies a tree with branches lower than some tollerance level |691c490|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/unbranch.R | 90 ++++++++++++++++++++++++++++++++++++++++++++++++
| man/collapse_branch.Rd | 38 ++++++++++++++++++++
| 4 files changed, 130 insertions(+)
* 2015-01-29(Tal Galili) Fix "Error in plot.xy(xy.coords(x, y), type = type, ...) : " when dend has graphical parameters. |480b0fc|
| R/ggdendro.R | 16 ++++++++++++++++
| 1 file changed, 16 insertions(+)
* 2015-01-29(Tal Galili) Fix: Error in eval(expr, envir, enclos) : object 'cex' not found In addition: Warning message: In is.na(data$labels$cex) : is.na() applied to non-(list or vector) of type 'NULL' |50ab05a|
| R/ggdend.R | 22 +++++++++++++++++-----
| 1 file changed, 17 insertions(+), 5 deletions(-)
* 2015-01-29(Tal Galili) `remove_nodes_nodePar` - as the name implies... |3584e7c|
| NAMESPACE | 1 +
| NEWS | 2 ++
| R/attr_access.R | 37 ++++++++++++++++++++++++++++++++++++-
| man/remove_nodes_nodePar.Rd | 33 +++++++++++++++++++++++++++++++++
| 4 files changed, 72 insertions(+), 1 deletion(-)
* 2015-01-28(Tal Galili) fix namespace issues (using S3 for a non-imported package is NOT wise, and results in the main function not seeing the new S3 function implemented...) |bc5c1ee|
| NAMESPACE | 4 ++--
| R/ggdend.R | 14 ++++++++------
| man/ggdend.Rd | 4 ++--
| 3 files changed, 12 insertions(+), 10 deletions(-)
* 2015-01-28(Tal Galili) Added theme_dendro as the default theme for ggplot.ggdend |0dfc218|
| R/ggdend.R | 16 +++++++---------
| man/ggdend.Rd | 4 +++-
| 2 files changed, 10 insertions(+), 10 deletions(-)
* 2015-01-28(Tal Galili) Organize NEWS |c41aeba|
| NEWS | 31 +++++++++++++++++--------------
| 1 file changed, 17 insertions(+), 14 deletions(-)
* 2015-01-28(Tal Galili) Importing `theme_dendro` from the ggdendro package |d4f6552|
| NAMESPACE | 1 +
| R/ggdend.R | 2 +-
| R/ggdendro.R | 32 ++++++++++++++++++++++++++++++++
| man/ggdend.Rd | 3 +++
| man/theme_dendro.Rd | 24 ++++++++++++++++++++++++
| 5 files changed, 61 insertions(+), 1 deletion(-)
* 2015-01-28(Tal Galili) Mention ggplot2 -> plot.ly in the ggdend doc. |5340107|
| R/ggdend.R | 22 ++++++++++++++++++++--
| man/ggdend.Rd | 22 ++++++++++++++++++++--
| 2 files changed, 40 insertions(+), 4 deletions(-)
* 2015-01-27(Tal Galili) `prepare.ggdend` - fills a ggdend object with various default values (to be later used when plotted) (this function was extrected from ggplot.ggdend) |5fffec4|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/ggdend.R | 82 +++++++++++++++++++++++++++++++++------------------------
| man/ggdend.Rd | 24 ++++++++++++-----
| 4 files changed, 67 insertions(+), 41 deletions(-)
* 2015-01-27(Tal Galili) Thanks to Andrie de Vries, dendextend now enhances ggplot2 :) |13647d4|
| DESCRIPTION | 7 +++++--
| 1 file changed, 5 insertions(+), 2 deletions(-)
* 2015-01-27(Tal Galili) Adding documentation to ggdend and friends! |64a21a9|
| NAMESPACE | 5 +++
| NEWS | 3 +-
| R/ggdend.R | 121 ++++++++++++++++++++++++++++++++++++++++++++++++++------
| man/ggdend.Rd | 99 ++++++++++++++++++++++++++++++++++++++++++++++
| 4 files changed, 216 insertions(+), 12 deletions(-)
* 2015-01-27(Tal Galili) Added a working (at least partially) version of ggplot.ggdend |e54200a|
| R/ggdend.R | 246 +++++++++++++++++++++++++++++++++++++++++++++++++----------
| 1 file changed, 205 insertions(+), 41 deletions(-)
* 2015-01-27(Tal Galili) `as.ggdend.dendrogram` - turns a dendrogram to the ggdend class, ready to be plotted with ggplot2. |9cc9761|
| NEWS | 2 +
| R/ggdend.R | 241 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 243 insertions(+)
* 2015-01-27(Tal Galili) `get_leaves_nodePar` - a new function that Get's the nodePar of dendrogram's leaves (designed to help with as.ggdend) |57192cd|
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/attr_access.R | 45 +++++++++++++++++++++++++++++++++++++++++
| inst/tests/test-attr_access.R | 22 ++++++++++++++++++++
| man/get_leaves_nodePar.Rd | 40 ++++++++++++++++++++++++++++++++++++
| 5 files changed, 109 insertions(+), 1 deletion(-)
* 2015-01-27(Tal Galili) Added the file ggdendro.R with the dendrogram_data function (imported from the ggdendro package) |08d69d6|
| NEWS | 3 ++
| R/ggdendro.R | 165 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 168 insertions(+)
* 2015-01-26(Tal Galili) renamed imports_stats.R to stats_imports.R |27068c4|
| NEWS | 1 +
| R/imports_stats.R | 285 ----------------------------------------------------
| R/stats_imports.R | 285 ++++++++++++++++++++++++++++++++++++++++++++++++++++
| 3 files changed, 286 insertions(+), 285 deletions(-)
* 2015-01-26(Tal Galili) cor.dendlist and dist.dendlist - their matrix now includes dend names in col/row names. |951968a|
| R/cor.dendlist.R | 4 +++-
| R/distinct_edges.R | 5 ++++-
| man/cor.dendlist.Rd | 2 +-
| man/dist.dendlist.Rd | 2 +-
| 4 files changed, 9 insertions(+), 4 deletions(-)
* 2015-01-26(Tal Galili) Add ggdendro example for creating a radial plot :) |efaf335|
| R/ape.R | 12 ++++++++++++
| man/as.phylo.dendrogram.Rd | 19 ++++++++++++++++++-
| 2 files changed, 30 insertions(+), 1 deletion(-)
* 2015-01-26(Tal Galili) export as.phylo.dendrogram in a way that actually works... |c8b69de|
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/ape.R | 47 +++++++++++++++++++++++++++++++++++++++++---
| R/noded_with_condition.R | 2 +-
| man/as.phylo.dendrogram.Rd | 35 +++++++++++++++++++++++++++++++++
| man/which_node.Rd | 1 +
| 6 files changed, 83 insertions(+), 5 deletions(-)
* 2015-01-26(Tal Galili) get_nodes_attr with id example |d2464f6|
| vignettes/introduction.Rmd | 1 +
| 1 file changed, 1 insertion(+)
* 2015-01-26(Tal Galili) Fix "Error in missing(id) : 'missing' can only be used for arguments" in get_nodes_attr |e912cc3|
| R/attr_access.R | 8 +++++---
| 1 file changed, 5 insertions(+), 3 deletions(-)
* 2015-01-26(Tal Galili) magrittr is imported there is no longer a need for "library(magrittr)" in examples. |8210261|
| R/branches_attr_by.R | 1 -
| R/dist_fun.R | 1 -
| R/get_nodes_xy.R | 1 -
| R/noded_with_condition.R | 2 --
| R/set.dendrogram.R | 1 -
| man/branches_attr_by_labels.Rd | 1 -
| man/dist_long.Rd | 1 -
| man/get_nodes_xy.Rd | 1 -
| man/noded_with_condition.Rd | 1 -
| man/set.Rd | 1 -
| man/which_leaf.Rd | 1 -
| 11 files changed, 12 deletions(-)
* 2015-01-26(Tal Galili) `which_node` - a new function which finds Which node is common to a group of labels |fbaef43|
| NAMESPACE | 1 +
| NEWS | 2 ++
| R/noded_with_condition.R | 46 ++++++++++++++++++++++++++++++++++++++++++++++
| man/which_node.Rd | 43 +++++++++++++++++++++++++++++++++++++++++++
| 4 files changed, 92 insertions(+)
* 2015-01-26(Tal Galili) update `get_nodes_attr` - added the "id" parameter (to get attributes of only a subset of id's) |de61889|
| NEWS | 1 +
| R/attr_access.R | 26 +++++++++++++++++++++++---
| inst/tests/test-attr_access.R | 5 +++++
| man/get_nodes_attr.Rd | 8 +++++++-
| 4 files changed, 36 insertions(+), 4 deletions(-)
* 2015-01-26(Tal Galili) Rename `get_branches_attr` to be `get_root_branches_attr` |3e38822|
| NAMESPACE | 2 +-
| NEWS | 2 +-
| R/attr_access.R | 4 ++--
| R/unbranch.R | 12 +++++-----
| inst/tests/test-unbranch.R | 6 ++---
| man/assign_values_to_branches_edgePar.Rd | 2 +-
| man/get_branches_attr.Rd | 38 ------------------------------
| man/get_root_branches_attr.Rd | 38 ++++++++++++++++++++++++++++++
| man/remove_branches_edgePar.Rd | 2 +-
| 9 files changed, 53 insertions(+), 53 deletions(-)
* 2015-01-26(Tal Galili) minor docs update and version bump |5ac4ac6|
| DESCRIPTION | 4 ++--
| R/distinct_edges.R | 1 -
| man/dend_diff.Rd | 2 ++
| man/highlight_distinct_edges.Rd | 1 -
| 4 files changed, 4 insertions(+), 4 deletions(-)
* 2015-01-26(Tal Galili) Made dend_diff work with dendlist |4fd37af|
| NAMESPACE | 2 ++
| NEWS | 2 +-
| R/distinct_edges.R | 46 ++++++++++++++++++++++++++++++++++++++++++----
| man/dend_diff.Rd | 19 +++++++++++++++----
| 4 files changed, 60 insertions(+), 9 deletions(-)
* 2015-01-26(Tal Galili) Made highlight_distinct_edges work with dendlist (and added a nice iris example) |edcae3a|
| NAMESPACE | 2 ++
| NEWS | 2 +-
| R/distinct_edges.R | 51 +++++++++++++++++++++++++++++++++++++--
| man/highlight_distinct_edges.Rd | 34 +++++++++++++++++++++++---
| 4 files changed, 82 insertions(+), 7 deletions(-)
* 2015-01-25(Tal Galili) `cutree_1h.dendrogram` and `cutree_1k.dendrogram` - will now create clusters as the number of items if k==nleaves(tree) or if h<0. This is both consistent with stats::hclust, but it also "makes sense" (since this is well defined for ANY tree) |7afd28e|
| NEWS | 1 +
| R/cutree.dendrogram.R | 21 ++++++++++++++++++++-
| inst/tests/test-cut_lower_fun.R | 9 +++++++++
| inst/tests/test-cutree.dendrogram.R | 33 ++++++++++++++++++++++++---------
| inst/tests/test-distinct_edges.R | 1 +
| 5 files changed, 55 insertions(+), 10 deletions(-)
* 2015-01-25(Tal Galili) `cutree` - now produces warnings if it returns 0's. i.e.: when it can't cut the tree based on the required parameter. (following isue #5 reported by grafab) |fce5319|
| NEWS | 2 +-
| R/cutree.dendrogram.R | 13 ++++++++++---
| inst/tests/test-cutree.dendrogram.R | 24 ++++++++++++++++++++++++
| man/cutree-methods.Rd | 7 ++++++-
| 4 files changed, 41 insertions(+), 5 deletions(-)
* 2015-01-25(Tal Galili) Various doc .Rd fixes. |45b21e0|
| NAMESPACE | 1 -
| R/ape.R | 2 +-
| R/distinct_edges.R | 12 ++++++------
| R/tanglegram.R | 1 +
| man/dend_diff.Rd | 2 +-
| man/distinct_edges.Rd | 2 +-
| man/highlight_distinct_edges.Rd | 6 +++---
| man/partition_leaves.Rd | 2 +-
| man/tanglegram.Rd | 1 +
| 9 files changed, 15 insertions(+), 14 deletions(-)
* 2015-01-25(Tal Galili) `tanglegram` - a new highlight_distinct_edges parameter (default is TRUE) |7a7e758|
| NEWS | 1 +
| R/tanglegram.R | 6 ++++++
| man/tanglegram.Rd | 2 ++
| 3 files changed, 9 insertions(+)
* 2015-01-25(Tal Galili) New function: all.equal.dendrogram/all.equal.dendlist - Global Comparison of two (or more) dendrograms |8edaa3b|
| NAMESPACE | 2 +
| NEWS | 1 +
| R/all.equal.R | 157 ++++++++++++++++++++++++++++++++++++++++++
| man/all.equal.dendrogram.Rd | 65 +++++++++++++++++
| 4 files changed, 225 insertions(+)
* 2015-01-25(Tal Galili) `labels<-.dendrogram` - no longer forces as.character conversion |6a6223b|
| NEWS | 1 +
| R/labels.R | 3 ++-
| inst/tests/test-set.dendrogram.R | 5 ++++-
| 3 files changed, 7 insertions(+), 2 deletions(-)
* 2015-01-25(Tal Galili) minor test fix |0b8b076|
| inst/tests/test-distinct_edges.R | 11 ++++++++---
| 1 file changed, 8 insertions(+), 3 deletions(-)
* 2015-01-25(Tal Galili) use ave instead of ward in hclust (make sure the change to ward.D will no longer cause issues) |a220126|
| inst/tests/test-unbranch.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2015-01-25(Tal Galili) New functions (with doc and tests): * partition_leaves - A list with labels for each subtree (edge) * distinct_edges - Finds the edges present in the first tree but not in the second * highlight_distinct_edges - Highlight distint edges in a tree (compared to another one) * dend_diff - Plots two trees side by side, highlighting edges unique to each tree in red. * dist.dendlist - Topological Distances Between Two dendrograms (currently only the Robinson-Foulds distance) |05b4ebc|
| NAMESPACE | 5 +
| NEWS | 17 ++-
| R/distinct_edges.R | 291 +++++++++++++++++++++++++++++++++++++
| inst/tests/test-distinct_edges.R | 39 +++++
| man/dend_diff.Rd | 42 ++++++
| man/dist.dendlist.Rd | 38 +++++
| man/distinct_edges.Rd | 36 +++++
| man/highlight_distinct_edges.Rd | 49 +++++++
| man/partition_leaves.Rd | 43 ++++++
| 9 files changed, 559 insertions(+), 1 deletion(-)
* 2015-01-25(Tal Galili) Small document update to assign_values_to_branches_edgePar |330ed91|
| R/attr_access.R | 3 ++-
| man/assign_values_to_branches_edgePar.Rd | 3 ++-
| 2 files changed, 4 insertions(+), 2 deletions(-)
* 2015-01-25(Tal Galili) cor.dendlist - Correlation matrix between a list of trees. |a3d8371|
| NAMESPACE | 1 +
| NEWS | 2 ++
| R/cor.dendlist.R | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++
| man/cor.dendlist.Rd | 43 ++++++++++++++++++++++++++++
| 4 files changed, 123 insertions(+)
* 2015-01-24(Tal Galili) A new phylo method for `labels` and `labels<-` |f51e36a|
| DESCRIPTION | 2 +-
| NAMESPACE | 2 ++
| NEWS | 7 ++++++-
| R/labels.R | 38 ++++++++++++++++++++++++++++++++++++++
| man/labels-assign.Rd | 6 ++++++
| 5 files changed, 53 insertions(+), 2 deletions(-)
* 2015-01-24(Tal Galili) `nleaves.phylo` - no longer require conversion to a dendrogram in order to compute. |8b5dad4|
| R/nleaves.R | 5 ++++-
| 1 file changed, 4 insertions(+), 1 deletion(-)
* 2015-01-21(Tal Galili) 1) new file ape.R - to which I moved `as.dendrogram.phylo` and `as.phylo.dendrogram` functions to. |e94bd9b|
| DESCRIPTION | 4 ++--
| NAMESPACE | 1 +
| NEWS | 7 +++++++
| R/ape.R | 42 ++++++++++++++++++++++++++++++++++++++++++
| R/nleaves.R | 22 ----------------------
| tests/test-all.R | 2 ++
| 6 files changed, 54 insertions(+), 24 deletions(-)
* 2014-12-08(Tal Galili) Bump to 0.17.6 |a4d0561|
| DESCRIPTION | 4 ++--
| NEWS | 8 ++++++++
| 2 files changed, 10 insertions(+), 2 deletions(-)
* 2014-12-08(Tal Galili) roxygen2 from 4.0.1 to 4.0.2 |b46267b|
| man/Bk.Rd | 2 +-
| man/Bk_permutations.Rd | 2 +-
| man/Bk_plot.Rd | 2 +-
| man/DendSer.dendrogram.Rd | 2 +-
| man/FM_index.Rd | 2 +-
| man/FM_index_R.Rd | 2 +-
| man/FM_index_permutation.Rd | 2 +-
| man/FM_index_profdpm.Rd | 2 +-
| man/all_couple_rotations_at_k.Rd | 2 +-
| man/all_unique.Rd | 2 +-
| man/as.dendlist.Rd | 2 +-
| man/as_hclust_fixed.Rd | 2 +-
| man/assign_dendextend_options.Rd | 2 +-
| man/assign_values_to_branches_edgePar.Rd | 2 +-
| man/assign_values_to_leaves_edgePar.Rd | 2 +-
| man/assign_values_to_leaves_nodePar.Rd | 2 +-
| man/assign_values_to_nodes_nodePar.Rd | 2 +-
| man/bakers_gamma_for_2_k_matrix.Rd | 2 +-
| man/branches_attr_by_clusters.Rd | 2 +-
| man/branches_attr_by_labels.Rd | 2 +-
| man/click_rotate.Rd | 6 +++---
| man/color_branches.Rd | 2 +-
| man/color_labels.Rd | 8 ++++----
| man/colored_bars.Rd | 2 +-
| man/cor_bakers_gamma.Rd | 6 +++---
| man/cor_cophenetic.Rd | 6 +++---
| man/count_terminal_nodes.Rd | 2 +-
| man/cut_lower_fun.Rd | 2 +-
| man/cutree-methods.Rd | 6 +++---
| man/cutree_1h.dendrogram.Rd | 10 +++++-----
| man/cutree_1k.dendrogram.Rd | 2 +-
| man/d3dendro_options.Rd | 2 +-
| man/d3dendrogram.Rd | 2 +-
| man/dendextend-package.Rd | 2 +-
| man/dendextend_options.Rd | 2 +-
| man/dendlist.Rd | 2 +-
| man/duplicate_leaf.Rd | 2 +-
| man/entanglement.Rd | 6 +++---
| man/fac2num.Rd | 2 +-
| man/fix_members_attr.dendrogram.Rd | 2 +-
| man/flatten.dendrogram.Rd | 2 +-
| man/flip_leaves.Rd | 2 +-
| man/get_branches_attr.Rd | 2 +-
| man/get_branches_heights.Rd | 2 +-
| man/get_childrens_heights.Rd | 2 +-
| man/get_leaves_attr.Rd | 2 +-
| man/get_nodes_attr.Rd | 2 +-
| man/get_nodes_xy.Rd | 2 +-
| man/hang.dendrogram.Rd | 2 +-
| man/heights_per_k.dendrogram.Rd | 2 +-
| man/identify.dendrogram.Rd | 2 +-
| man/intersect_trees.Rd | 2 +-
| man/is.dendlist.Rd | 2 +-
| man/is.dendrogram.Rd | 2 +-
| man/is.hclust.Rd | 2 +-
| man/is.natural.number.Rd | 2 +-
| man/is.phylo.Rd | 2 +-
| man/is_null_list.Rd | 2 +-
| man/labels-assign.Rd | 6 +++---
| man/labels_colors.Rd | 2 +-
| man/leaf_Colors.Rd | 2 +-
| man/lowest_common_branch.Rd | 2 +-
| man/match_order_by_labels.Rd | 2 +-
| man/match_order_dendrogram_by_old_order.Rd | 2 +-
| man/na_locf.Rd | 2 +-
| man/nleaves.Rd | 6 +++---
| man/nnodes.Rd | 2 +-
| man/noded_with_condition.Rd | 2 +-
| man/order.dendrogram-assign.Rd | 2 +-
| man/order.hclust.Rd | 2 +-
| man/pipe.Rd | 2 +-
| man/plot_horiz.dendrogram.Rd | 2 +-
| man/prune.Rd | 6 +++---
| man/prune_leaf.Rd | 2 +-
| man/pvclust_show_signif.Rd | 2 +-
| man/pvclust_show_signif_gradient.Rd | 2 +-
| man/raise.dendrogram.Rd | 2 +-
| man/rank_branches.Rd | 2 +-
| man/rank_order.dendrogram.Rd | 2 +-
| man/rect.dendrogram.Rd | 6 +++---
| man/remove_branches_edgePar.Rd | 2 +-
| man/remove_leaves_nodePar.Rd | 2 +-
| man/rllply.Rd | 2 +-
| man/rotate.Rd | 6 +++---
| man/rotate_DendSer.Rd | 2 +-
| man/sample.dendrogram.Rd | 2 +-
| man/set.Rd | 6 +++---
| man/shuffle.Rd | 6 +++---
| man/sort_2_clusters_vectors.Rd | 2 +-
| man/sort_dist_mat.Rd | 2 +-
| man/sort_levels_values.Rd | 2 +-
| man/tanglegram.Rd | 6 +++---
| man/unbranch.Rd | 6 +++---
| man/unclass_dend.Rd | 2 +-
| man/untangle.Rd | 6 +++---
| man/untangle_DendSer.Rd | 2 +-
| man/untangle_random_search.Rd | 2 +-
| man/untangle_step_rotate_1side.Rd | 2 +-
| man/untangle_step_rotate_2side.Rd | 2 +-
| man/which_leaf.Rd | 2 +-
| 100 files changed, 137 insertions(+), 137 deletions(-)
* 2014-12-08(Tal Galili) dist_long - Turns a dist object to a "long" table. |a5fee75|
| NAMESPACE | 4 +++-
| R/dist_fun.R | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
| man/dist_long.Rd | 28 ++++++++++++++++++++++++
| 3 files changed, 94 insertions(+), 1 deletion(-)
* 2014-12-08(Tal Galili) Update text (per request by CRAN) |46697aa|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-12-08(Tal Galili) text editing |5afb4dd|
| vignettes/introduction.Rmd | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-10-04(Tal Galili) Ignore ^\.travis.yml$ when building the package. |45cba35|
| .Rbuildignore | 3 ++-
| 1 file changed, 2 insertions(+), 1 deletion(-)
* 2014-10-04(Tal Galili) Adding .travis.yml |6e17ba3|
| .travis.yml | 24 ++++++++++++++++++++++++
| README.md | 3 +++
| 2 files changed, 27 insertions(+)
* 2014-09-22(Tal Galili) VIGNETTE - fix several typos and grammatical mistakes. |7e41e50|
| NAMESPACE | 2 +-
| NEWS | 3 +++
| TODO | 61 ++++++++++++++++++++++++++++++++++++++++++++
| vignettes/introduction.Rmd | 26 +++++++++----------
| 4 files changed, 78 insertions(+), 14 deletions(-)
* 2014-09-22(Tal Galili) Fixing - \usage lines wider than 90 characters |fff3e9f|
| NEWS | 3 ++-
| R/cor_bakers_gamma.R | 6 ++++--
| man/cor_bakers_gamma.Rd | 6 ++++--
| 3 files changed, 10 insertions(+), 5 deletions(-)
* 2014-09-22(Tal Galili) Several bug fixes to the docs. |45bf641|
| NAMESPACE | 2 +-
| NEWS | 11 ++++++++
| R/cor_bakers_gamma.R | 18 ++++++++++++-
| R/dendlist.R | 64 +++++++++++++++++++++++++++++++----------------
| R/set.dendrogram.R | 1 +
| man/cor_bakers_gamma.Rd | 13 ++++++++--
| man/dendlist.Rd | 14 +++++++++++
| man/plot.dendlist.Rd | 34 -------------------------
| man/set.Rd | 1 +
| 9 files changed, 98 insertions(+), 60 deletions(-)
* 2014-09-22(Tal Galili) Fixing tests as well. (with as.hclust for sub dends. |bf0fd2b|
| NEWS | 2 +-
| inst/tests/test-cutree.dendrogram.R | 86 +++++++++++++++++------------------
| inst/tests/test-labels-assign.R | 3 +-
| 3 files changed, 46 insertions(+), 45 deletions(-)
* 2014-09-22(Tal Galili) `order.dendrogram<-` - commenting off an example which (as of R 3.1.1-patched) produces an error (as it should). |4a672fa|
| DESCRIPTION | 4 ++--
| NEWS | 10 ++++++++++
| R/labels.R | 4 ++--
| R/zzz.R | 1 +
| man/order.dendrogram-assign.Rd | 4 ++--
| 5 files changed, 17 insertions(+), 6 deletions(-)
* 2014-09-20(Tal Galili) Added set.data.table - informs the user of the conflict in "set" between dendextend and data.table. |e167228|
| DESCRIPTION | 5 +++--
| NAMESPACE | 1 +
| NEWS | 2 ++
| R/set.dendrogram.R | 10 ++++++++++
| man/set.Rd | 2 ++
| 5 files changed, 18 insertions(+), 2 deletions(-)
* 2014-09-20(Tal Galili) added sessionInfo to VIGNETTE |f34c02a|
| NEWS | 8 ++++++++
| vignettes/introduction.Rmd | 8 ++++++++
| 2 files changed, 16 insertions(+)
* 2014-08-26(Tal Galili) full name credit. |16ee14d|
| NEWS | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-08-26(Tal Galili) link to the bug report, and thanked varmara. |0e10459|
| NEWS | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-08-26(Tal Galili) color_labels - now can handle the coloring of labels when the function is without k and h, but that it is not possible to cut the tree to nleaves items (due to several leaves with 0 height). This is done by not doing any cutting in such cases, and just directly using labels_colors. (added tests) |734fe99|
| DESCRIPTION | 4 ++--
| NEWS | 7 +++++++
| R/color_branches.R | 8 ++++++--
| inst/tests/test-labels_colors.R | 35 +++++++++++++++++++++++++++++++++++
| man/color_labels.Rd | 3 ---
| 5 files changed, 50 insertions(+), 7 deletions(-)
* 2014-08-25(Tal Galili) Version 0.17.2 (updated NEWS DESCRIPTION, etc) |fa1dba2|
| DESCRIPTION | 4 ++--
| NEWS | 7 +++++--
| NEWS.md | 19 +++++++++++++++++--
| TODO | 11 ++++++++++-
| 4 files changed, 34 insertions(+), 7 deletions(-)
* 2014-08-25(Tal Galili) Add to introduction.Rmd how to install the package from github. |0ecf3af|
| README.md | 6 +-----
| vignettes/introduction.Rmd | 40 ++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 41 insertions(+), 5 deletions(-)
* 2014-08-25(Tal Galili) Added the function assign_values_to_leaves_edgePar |8ff1d61|
| NAMESPACE | 1 +
| R/attr_access.R | 92 +++++++++++++++++++++++++++++++-
| man/assign_values_to_leaves_edgePar.Rd | 52 ++++++++++++++++++
| 3 files changed, 144 insertions(+), 1 deletion(-)
* 2014-08-23(Tal Galili) capitalize R Core Team |48b8f6d|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-08-23(Tal Galili) Added cor_bakers_gamma.dendlist |08e0276|
| NAMESPACE | 1 +
| NEWS | 6 +++++-
| R/cor_bakers_gamma.R | 7 +++++++
| TODO | 3 +++
| 4 files changed, 16 insertions(+), 1 deletion(-)
* 2014-08-23(Tal Galili) VIGNETTE Fix some typos and mistakes |33316b3|
| NEWS | 11 +++++++++--
| vignettes/introduction.Rmd | 8 ++++----
| 2 files changed, 13 insertions(+), 6 deletions(-)
* 2014-08-19(Tal Galili) more editing, and thanks. |d47c870|
| NEWS | 1 +
| R/zzz.R | 29 +++++++++++++++++------------
| 2 files changed, 18 insertions(+), 12 deletions(-)
* 2014-08-19(Tal Galili) compacted ‘dendextend-tutorial.pdf’ from 725Kb to 551Kb |5944f4e|
| DESCRIPTION | 2 +-
| NEWS | 15 +++++++++++++
| NEWS.md | 15 +++++++++++++
| R/zzz.R | 42 ++++++++++++++++++++++++++++++++++---
| inst/doc/dendextend-tutorial.pdf | Bin 754947 -> 564592 bytes
| 5 files changed, 70 insertions(+), 4 deletions(-)
* 2014-08-19(Tal Galili) updated |6c952e3|
| ChangeLog | 37 +++++++++++++++++++++++++++++++++++++
| NEWS.md | 4 ++++
| 2 files changed, 41 insertions(+)
* 2014-08-19(Tal Galili) Have the package build the vignette. |8653ed9|
| DESCRIPTION | 1 +
| NEWS | 1 +
| 2 files changed, 2 insertions(+)
* 2014-08-19(Tal Galili) Update the location of vignettes on github. |ec66fa0|
| README.md | 7 ++++---
| 1 file changed, 4 insertions(+), 3 deletions(-)
* 2014-08-19(Tal Galili) Fixed introduction.html to not overlap the bounderies of the code area. |7d47c9e|
| vignettes/introduction.Rmd | 37 ++++++++++++++++++++++++-------------
| 1 file changed, 24 insertions(+), 13 deletions(-)
* 2014-08-19(Tal Galili) Created a copy of "introduction.html" in inst/ignored (so people could see it on github) |0a1195a|
| .Rbuildignore | 7 +-
| NEWS | 2 +-
| inst/ignored/introduction.html | 1543 ++++++++++++++++++++++++++++++++++++++
| 3 files changed, 1549 insertions(+), 3 deletions(-)
* 2014-08-19(Tal Galili) Moved dendextend-tutorial.rnw to vignettes\disabled - so it is still there, but not compiled. Also moved dendextend-tutorial.pdf to inst\doc - so there is a copy of this older vignette, but without needed to run it with all the benchmarks... (it is also compressed) |5558f2c|
| NEWS | 3 +
| R/zzz.R | 7 +-
| inst/doc/dendextend-tutorial.pdf | Bin 0 -> 754947 bytes
| vignettes/dendextend-tutorial.pdf | 9793 --------------------------
| vignettes/dendextend-tutorial.rnw | 2024 ------
| vignettes/disabled/dendextend-tutorial.rnw | 2024 ++++++
| 6 files changed, 2031 insertions(+), 11820 deletions(-)
* 2014-08-19(Tal Galili) erased file |a97af45|
| R/dendlist - Copy.R | 275 --------------------------------------------------
| 1 file changed, 275 deletions(-)
* 2014-08-19(Tal Galili) Update NEWS.md and ChangeLog before CRAN release. for 0.17.0 |4e47159|
| ChangeLog | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 11 ++++++---
| 2 files changed, 82 insertions(+), 3 deletions(-)
* 2014-08-19(Tal Galili) Moved ggdendro, labeltodendro, dendroextras, ape to "Enhances:" in DESCRIPTION. (include fixing tests, and adding library - so to through errors in case the package is not available) |992d09d|
| DESCRIPTION | 11 ++++++-----
| NAMESPACE | 1 -
| NEWS | 2 +-
| R/DendSer.R | 2 +-
| R/bk_method.R | 2 +-
| R/dendextend-package.R | 2 +-
| R/nleaves.R | 6 +++---
| R/prune.R | 2 +-
| R/pvclust.R | 2 +-
| R/rotate.R | 2 +-
| R/unbranch.R | 2 +-
| inst/tests/test-rotate.R | 2 +-
| 12 files changed, 18 insertions(+), 18 deletions(-)
* 2014-08-19(Tal Galili) Added spaces to docs |d4ce41a|
| man/as.dendlist.Rd | 22 ----------------------
| 1 file changed, 22 deletions(-)
* 2014-08-19(Tal Galili) new function: `rainbow_fun` - uses rainbow_hcl, or rainbow (if colorspace is not available) |f71d025|
| DESCRIPTION | 2 +-
| NEWS | 9 +-
| R/branches_attr_by.R | 4 +-
| R/color_branches.R | 14 +--
| R/colored_bars.R | 1 +
| R/dendlist - Copy.R | 275 +++++++++++++++++++++++++++++++++++++++++++++++++
| R/labels_colors.R | 4 +-
| R/rainbow_fun.R | 33 ++++++
| man/as.dendlist.Rd | 22 ++++
| man/colored_bars.Rd | 1 +
| 10 files changed, 345 insertions(+), 20 deletions(-)
* 2014-08-19(Tal Galili) Break lines which were too long. |fd1f130|
| R/pvclust.R | 8 ++++++--
| man/pvclust_show_signif.Rd | 4 +++-
| man/pvclust_show_signif_gradient.Rd | 4 +++-
| 3 files changed, 12 insertions(+), 4 deletions(-)
* 2014-08-19(Tal Galili) Added warn = dendextend_options("warn") to docs |94bd5f4|
| R/cutree.dendrogram.R | 5 +++--
| man/cutree-methods.Rd | 5 +++--
| 2 files changed, 6 insertions(+), 4 deletions(-)
* 2014-08-19(Tal Galili) edgeText is not needed here. |9a4441e|
| R/get_nodes_xy.R | 8 ++++----
| 1 file changed, 4 insertions(+), 4 deletions(-)
* 2014-08-19(Tal Galili) laply -> lapply , and some tree to dend fixes. |4167e7b|
| R/untangle.R | 10 +++++-----
| 1 file changed, 5 insertions(+), 5 deletions(-)
* 2014-08-18(Tal Galili) paramters to parameters |b4097c8|
| DESCRIPTION | 2 +-
| vignettes/introduction.Rmd | 8 ++++----
| 2 files changed, 5 insertions(+), 5 deletions(-)
* 2014-08-18(Tal Galili) The following files are already in R: 'jss.bst', 'jss.cls' and I remove them from the package. |954508e|
| .Rbuildignore | 2 ++
| 1 file changed, 2 insertions(+)
* 2014-08-18(Tal Galili) all.unique to all_unique in the example. |a100582|
| R/color_branches.R | 10 +++++-----
| man/all_unique.Rd | 10 +++++-----
| 2 files changed, 10 insertions(+), 10 deletions(-)
* 2014-08-18(Tal Galili) Update various files |6bc8a22|
| .Rbuildignore | 5 +-
| ChangeLog | 404 +++++++++++++++++++++++++++++++++++++++++++++++++
| DESCRIPTION | 2 +-
| NEWS.md | 52 +++++++
| TODO | 8 +
| vignettes/.gitignore | 3 +-
| 6 files changed, 470 insertions(+), 4 deletions(-)
* 2014-08-18(Tal Galili) cutree.hclust - added a dummy parameter |786c408|
| R/cutree.dendrogram.R | 1 +
| 1 file changed, 1 insertion(+)
* 2014-08-18(Tal Galili) Added a dendextendRcpp section. (and removed the not-working ggdendro section) |3d381da|
| vignettes/introduction.Rmd | 38 ++++++--------------------------------
| 1 file changed, 6 insertions(+), 32 deletions(-)
* 2014-08-18(Tal Galili) `cutree.dendrogram` - added a parameter (NA_to_0L) to control it. Also, make `Bk` work with cutree(NA_to_0L = FALSE) |b33a2a7|
| NEWS | 3 ++-
| R/bk_method.R | 4 ++--
| R/cutree.dendrogram.R | 6 +++++-
| man/cutree-methods.Rd | 4 ++++
| 4 files changed, 13 insertions(+), 4 deletions(-)
* 2014-08-18(Tal Galili) vignettes: Cophenetic correlation and Bk plots. |9cdc2d5|
| vignettes/introduction.Rmd | 133 ++++++++++++++++++++++++++++++++++++++++++-
| 1 file changed, 131 insertions(+), 2 deletions(-)
* 2014-08-18(Tal Galili) vignettes: Correlation measures - Baker's Gamma Index |b12f2df|
| vignettes/introduction.Rmd | 68 ++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 68 insertions(+)
* 2014-08-18(Tal Galili) vignettes: tanglegram |6666a97|
| vignettes/introduction.Rmd | 139 +++++++++++++++++++++++++++++++++++++++++--
| 1 file changed, 135 insertions(+), 4 deletions(-)
* 2014-08-18(Tal Galili) Fixing how the tests are printed by adding cat("\n") |6d5169c|
| inst/tests/test-entanglement.R | 3 +++
| 1 file changed, 3 insertions(+)
* 2014-08-18(Tal Galili) Test in set.dendrogram needed - dendextend_options("warn", TRUE) |576f951|
| inst/tests/test-set.dendrogram.R | 23 ++++++++++++++++++-----
| 1 file changed, 18 insertions(+), 5 deletions(-)
* 2014-08-18(Tal Galili) Test for Color recycling needed - dendextend_options("warn", TRUE) |006168a|
| inst/tests/test-labels_colors.R | 2 ++
| 1 file changed, 2 insertions(+)
* 2014-08-18(Tal Galili) Rename all.unique to all_unique |3411cc2|
| NAMESPACE | 3 ++-
| NEWS | 4 ++--
| R/color_branches.R | 27 ++++++++++++++++++++-------
| inst/tests/test-general.R | 9 +++++----
| man/all.unique.Rd | 32 --------------------------------
| man/all_unique.Rd | 32 ++++++++++++++++++++++++++++++++
| 6 files changed, 61 insertions(+), 46 deletions(-)
* 2014-08-18(Tal Galili) `cutree.dendrogram` - replaces NA values with 0L - adjust the tests. |49a4bd8|
| NEWS | 2 +-
| inst/tests/test-cutree.dendrogram.R | 8 ++++----
| 2 files changed, 5 insertions(+), 5 deletions(-)
* 2014-08-18(Tal Galili) * `untangle_step_rotate_1side` - added "leaves_matching_method" parameter. * `entanglement.dendrogram` - changed the default of "leaves_matching_method" to be "labels" (slower, but safer for the user...) |f77b4b6|
| NEWS | 2 ++
| R/entanglement.R | 7 ++++---
| R/untangle.R | 37 ++++++++++++++++++++++++++++++-------
| man/entanglement.Rd | 7 ++++---
| man/untangle_random_search.Rd | 4 ++--
| man/untangle_step_rotate_1side.Rd | 19 ++++++++++++++++++-
| 6 files changed, 60 insertions(+), 16 deletions(-)
* 2014-08-18(Tal Galili) tanglegram: Changed the deafult in cex_main to 2 |d02bd09|
| R/tanglegram.R | 4 ++--
| man/tanglegram.Rd | 2 +-
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2014-08-18(Tal Galili) `untangle` - has a default to method (DendSet) |424b02d|
| NEWS | 1 +
| R/untangle.R | 9 +++++++--
| man/untangle.Rd | 4 +++-
| 3 files changed, 11 insertions(+), 3 deletions(-)
* 2014-08-18(Tal Galili) `set.dendrogram` - added a "labels_to_char" option. |6f6f0cf|
| NEWS | 1 +
| R/set.dendrogram.R | 4 ++++
| man/set.Rd | 2 ++
| 3 files changed, 7 insertions(+)
* 2014-08-18(Tal Galili) vignettes: pvclust, and dendlist sections. |fe7206c|
| vignettes/introduction.Rmd | 72 ++++++++++++++++++++++++++++++++++++--------
| 1 file changed, 60 insertions(+), 12 deletions(-)
* 2014-08-18(Tal Galili) New function: `head.dendlist` |bd03014|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/dendlist.R | 15 +++++++++++++++
| 3 files changed, 17 insertions(+)
* 2014-08-18(Tal Galili) update pvrect2 - if we'd ever want one with adjustable lower rects... |07866e2|
| R/pvclust.R | 15 ++++++++++++---
| 1 file changed, 12 insertions(+), 3 deletions(-)
* 2014-08-18(Tal Galili) Added pvrect2 - a copy of pvrect |185e6bf|
| R/pvclust.R | 109 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 109 insertions(+)
* 2014-08-18(Tal Galili) vignettes: "Enhancing other packages" examples for DendSer, gplots and dynamicTreeCut |69d0a52|
| vignettes/introduction.Rmd | 92 ++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 92 insertions(+)
* 2014-08-18(Tal Galili) Added is.infinite2 and used it so to avoid endless warnings over type coercion... |b778982|
| R/attr_access.R | 22 +++++++++++++++++-----
| R/dendlist.R | 2 +-
| 2 files changed, 18 insertions(+), 6 deletions(-)
* 2014-08-18(Tal Galili) `assign_values_to_branches_edgePar`, `assign_values_to_nodes_nodePar`, `assign_values_to_leaves_nodePar` - now ignores "Inf" also when it is a character by adding as.numeric (and not only if it is numeric!) (this might be a problem if someone would try to update a label with the name "Inf"). |a6a2a78|
| NEWS | 4 ++++
| R/attr_access.R | 11 ++++++++---
| R/branches_attr_by.R | 2 +-
| man/branches_attr_by_clusters.Rd | 2 +-
| 4 files changed, 14 insertions(+), 5 deletions(-)
* 2014-08-18(Tal Galili) A new test for `assign_values_to_branches_edgePar` - make sure it deals with Inf and "Inf". |9036ac1|
| inst/tests/test-branches_attr_by.R | 76 ++++++++++++++++++++++++++++++++++++
| 1 file changed, 76 insertions(+)
* 2014-08-17(Tal Galili) Made sure "rotate_DendSer" shows in the docs. |1409976|
| R/DendSer.R | 6 +++---
| man/DendSer.dendrogram.Rd | 2 +-
| man/dendlist.Rd | 2 +-
| man/rotate_DendSer.Rd | 2 +-
| man/untangle_DendSer.Rd | 2 +-
| 5 files changed, 7 insertions(+), 7 deletions(-)
* 2014-08-17(Tal Galili) Adding DendSer.R (moving functions into it) |c9f589b|
| NEWS | 1 +
| R/DendSer.R | 130 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| R/untangle.R | 110 ------------------------------------------------
| 3 files changed, 131 insertions(+), 110 deletions(-)
* 2014-08-17(Tal Galili) vignettes: Adding extra bars and rectangles |9040574|
| vignettes/introduction.Rmd | 66 ++++++++++++++++++++++++++++++++++++++++++--
| 1 file changed, 64 insertions(+), 2 deletions(-)
* 2014-08-17(Tal Galili) `colored_bars` - fix for multiple bars to work. +have scale default be better for multiple bars. |2feadad|
| NEWS | 3 ++-
| R/colored_bars.R | 28 ++++++++++++++++++++--------
| man/colored_bars.Rd | 13 +++++++++----
| 3 files changed, 31 insertions(+), 13 deletions(-)
* 2014-08-16(Tal Galili) `rect.dendrogram` - Made sure the heights are working properly! |636a223|
| NEWS | 1 +
| R/rect.dendrogram.R | 22 +++++++++++++++-------
| 2 files changed, 16 insertions(+), 7 deletions(-)
* 2014-08-16(Tal Galili) rect.dendrogram - fix a bug with the location of the rect's (using "tree" and not "dend") |792929f|
| NEWS | 2 +-
| R/rect.dendrogram.R | 4 ++--
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2014-08-16(Tal Galili) `intersect_trees` - now returns a dendlist. |b2fa915|
| NEWS | 1 +
| R/prune.R | 4 ++--
| man/intersect_trees.Rd | 2 +-
| 3 files changed, 4 insertions(+), 3 deletions(-)
* 2014-08-16(Tal Galili) Rename files: trim.R -> prune.R |83f6388|
| NEWS | 1 +
| R/prune.R | 253 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| R/trim.R | 253 ------------------------------------------------------------
| 3 files changed, 254 insertions(+), 253 deletions(-)
* 2014-08-15(Tal Galili) Use "set" in order to not confuse the reader... |6e048d2|
| vignettes/introduction.Rmd | 30 ++++++++++++++++++++++--------
| 1 file changed, 22 insertions(+), 8 deletions(-)
* 2014-08-14(Tal Galili) Vignettes: Writing "Changing a dendrogram’s structure" |197d1fd|
| vignettes/introduction.Rmd | 64 ++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 64 insertions(+)
* 2014-08-14(Tal Galili) color_branches - warn of missing k only if warn=TRUE |f8677ba|
| R/color_branches.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-08-14(Tal Galili) vignettes: moved to dend15 and dend13. Wrote: * Setting a dendrogram's nodes/leaves (points) * Setting a dendrogram's branches |ffb1aaf|
| vignettes/introduction.Rmd | 226 +++++++++++++++++++++++++++++++------------
| 1 file changed, 164 insertions(+), 62 deletions(-)
* 2014-08-14(Tal Galili) `branches_attr_by_labels` now uses `dendextend_options("warn")` to decide if to print that labels were coerced into character. |a4fd3ef|
| NEWS | 1 +
| R/branches_attr_by.R | 2 +-
| 2 files changed, 2 insertions(+), 1 deletion(-)
* 2014-08-14(Tal Galili) Fix headers. |a3e5f79|
| NEWS | 13 ++++++++-----
| 1 file changed, 8 insertions(+), 5 deletions(-)
* 2014-08-14(Tal Galili) `branches_attr_by_clusters` and `branches_attr_by_labels` - moved from using NA to Inf. |2f3f5df|
| NEWS | 1 +
| R/branches_attr_by.R | 16 ++++++++--------
| man/branches_attr_by_labels.Rd | 4 ++--
| 3 files changed, 11 insertions(+), 10 deletions(-)
* 2014-08-14(Tal Galili) Move the function branches_attr_by_labels between two files |1e65ab0|
| NEWS | 2 +-
| R/branches_attr_by.R | 113 +++++++++++++++++++++++++++++++++++++++++++++
| R/noded_with_condition.R | 101 ----------------------------------------
| 3 files changed, 114 insertions(+), 102 deletions(-)
* 2014-08-14(Tal Galili) Simplify the introduction, and use if for DESCRIPTION |4142dd9|
| DESCRIPTION | 8 ++++++--
| NEWS | 2 +-
| vignettes/introduction.Rmd | 8 ++++----
| 3 files changed, 11 insertions(+), 7 deletions(-)
* 2014-08-14(Tal Galili) `colored_bars` - added defaults to make the bars be plotted bellow the labels (+allow the order of the bars to be based on the labels' order) |dc0b710|
| NEWS | 1 +
| R/colored_bars.R | 28 ++++++++++++++++++++++++++--
| man/colored_bars.Rd | 14 +++++++++++---
| 3 files changed, 38 insertions(+), 5 deletions(-)
* 2014-08-14(Tal Galili) `color_branches` - can now work when the labels of the tree are not unique (feature request by Heather Turner - thanks Heather :) ) |5722bcc|
| NEWS | 5 +++--
| R/color_branches.R | 13 +++++++++++++
| 2 files changed, 16 insertions(+), 2 deletions(-)
* 2014-08-14(Tal Galili) all.unique - check if all elements in a vector are unique (including tests) |0eb8327|
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/color_branches.R | 33 +++++++++++++++++++++++++++++++++
| inst/tests/test-general.R | 14 ++++++++++++++
| man/all.unique.Rd | 32 ++++++++++++++++++++++++++++++++
| 5 files changed, 81 insertions(+), 1 deletion(-)
* 2014-08-14(Tal Galili) vignettes: Explaining depth-first search |b77bded|
| vignettes/introduction.Rmd | 153 ++++++++++++++++++++++++++++++++-----------
| 1 file changed, 115 insertions(+), 38 deletions(-)
* 2014-08-11(Tal Galili) Fix lower_rect in rect.dendrogram to work with horiz=TRUE |ac6e2f7|
| R/rect.dendrogram.R | 5 ++++-
| man/rect.dendrogram.Rd | 5 ++++-
| 2 files changed, 8 insertions(+), 2 deletions(-)
* 2014-08-11(Tal Galili) moving the date. |6d7eb14|
| DESCRIPTION | 2 +-
| NEWS | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2014-08-11(Tal Galili) `rect.dendrogram` - a new xpd and lower_rect parameters - to control how low the rect will be (for example, below or above the labels). The default is below the labels. |f7e58f6|
| NEWS | 2 +-
| R/rect.dendrogram.R | 32 ++++++++++++++++++++++++++++----
| man/rect.dendrogram.Rd | 19 ++++++++++++++++---
| 3 files changed, 45 insertions(+), 8 deletions(-)
* 2014-08-10(Tal Galili) Dealing with a missing/junk attribute |12f3566|
| R/attr_access.R | 5 +----
| inst/tests/test-attr_access.R | 3 +++
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2014-08-10(Tal Galili) `get_nodes_attr` - can now return an array or a list for attributes which include a more complex structure (such as nodePar), by working with lists and adding a "simplify" parameter. |f264362|
| NEWS | 1 +
| R/attr_access.R | 19 +++++++++++++++++--
| inst/tests/test-attr_access.R | 8 +++++++-
| man/get_nodes_attr.Rd | 6 +++++-
| 4 files changed, 30 insertions(+), 4 deletions(-)
* 2014-08-10(Tal Galili) vignettes introduction: added a first draft of explaining depth first |a99955f|
| vignettes/introduction.Rmd | 36 +++++++++++++++++++++++++++++++++---
| 1 file changed, 33 insertions(+), 3 deletions(-)
* 2014-08-10(Tal Galili) get_nodes_xy - Get the x-y coordiantes of a dendrogram's nodes |28b8205|
| DESCRIPTION | 4 +-
| NAMESPACE | 1 +
| NEWS | 5 +
| R/get_nodes_xy.R | 253 ++++++++++++++++++++++++++++++++++++++++++++++++++
| man/get_nodes_xy.Rd | 72 ++++++++++++++
| 5 files changed, 333 insertions(+), 2 deletions(-)
* 2014-08-09(Tal Galili) Changing a dendrogram’s labels |1c2c9d5|
| vignettes/introduction.Rmd | 108 +++++++++++++++++++++++++++++++++++++++----
| 1 file changed, 99 insertions(+), 9 deletions(-)
* 2014-08-09(Tal Galili) set.dendrogram - if "what" is missing, return the object as is. |27836ee|
| NEWS | 3 ++-
| R/set.dendrogram.R | 5 +++++
| 2 files changed, 7 insertions(+), 1 deletion(-)
* 2014-08-09(Tal Galili) set.dendrogram - changed from using `labels_colors<-` to `color_labels` for "labels_colors" (this will now work with using k...) |69c8bcf|
| NEWS | 1 +
| R/set.dendrogram.R | 3 ++-
| 2 files changed, 3 insertions(+), 1 deletion(-)
* 2014-08-09(Tal Galili) `labels<-.dendrogram` - if value is missing, returning the dendrogram as is (this also affects `set`) |0c9d5fb|
| NEWS | 2 ++
| R/labels.R | 6 ++++++
| 2 files changed, 8 insertions(+)
* 2014-08-09(Tal Galili) `labels_colors<-` - added if(dendextend_options("warn")) |0585aae|
| NEWS | 1 +
| R/labels_colors.R | 4 ++--
| 2 files changed, 3 insertions(+), 2 deletions(-)
* 2014-08-09(Tal Galili) set.dendrogram - added nodes_pch, nodes_cex and nodes_col - using `assign_values_to_nodes_nodePar` |c638422|
| NEWS | 1 +
| R/set.dendrogram.R | 12 ++++++++++++
| man/set.Rd | 6 ++++++
| 3 files changed, 19 insertions(+)
* 2014-08-08(Tal Galili) Moved Iris example to the end. And added explenation in the .Rd docs of the different possible options for "what" can get in set.dendrogram. |15c19b7|
| vignettes/introduction.Rmd | 160 +++++++++++++++++++++++++++----------------
| 1 file changed, 101 insertions(+), 59 deletions(-)
* 2014-08-08(Tal Galili) set.dendrogram - added explenation in the .Rd docs of the different possible options for "what" |8f65726|
| NEWS | 1 +
| R/set.dendrogram.R | 21 +++++++++++++++++++++
| man/set.Rd | 21 +++++++++++++++++++++
| 3 files changed, 43 insertions(+)
* 2014-08-08(Tal Galili) Added a d3 .Rd |1c70916|
| man/d3dendro_options.Rd | 40 ++++++++++++++++++++++++++++++++++++++++
| man/d3dendrogram.Rd | 47 +++++++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 87 insertions(+)
* 2014-08-08(Tal Galili) Introdution vignettes - wrote a decent: tl;dr and Prerequisites (acknowledgement, iris, chaining) |b46135b|
| DESCRIPTION | 29 +++++-----
| vignettes/introduction.Rmd | 131 +++++++++++++++++++++++++++++--------------
| 2 files changed, 104 insertions(+), 56 deletions(-)
* 2014-08-08(Tal Galili) `cutree.dendrogram` - now replaces NA values with 0L |2061c3e|
| NEWS | 1 +
| R/cutree.dendrogram.R | 3 ++-
| 2 files changed, 3 insertions(+), 1 deletion(-)
* 2014-08-08(Tal Galili) `color_branches` - now handles flat trees more gracefully. (returns them as they are) |b999388|
| NEWS | 2 +-
| R/color_branches.R | 17 ++++++++++++++++-
| man/color_branches.Rd | 12 +++++++++++-
| 3 files changed, 28 insertions(+), 3 deletions(-)
* 2014-08-08(Tal Galili) Include dendextend_options("warn", TRUE) in tests. |c2f7b68|
| R/cutree.dendrogram.R | 4 ++--
| inst/tests/test-cutree.dendrogram.R | 5 ++++-
| inst/tests/test-unbranch.R | 3 +++
| man/untangle_step_rotate_2side.Rd | 4 ++--
| 4 files changed, 11 insertions(+), 5 deletions(-)
* 2014-08-08(Tal Galili) untangle_step_rotate_2side` - print_times is now dendextend_options("warn"), |0da7c3f|
| NEWS | 4 +++-
| R/untangle.R | 2 +-
| 2 files changed, 4 insertions(+), 2 deletions(-)
* 2014-08-08(Tal Galili) Update .Rd docs, now that ALL `warn` paramteres are set to dendextend_options("warn") (which is FALSE) |6f4031f|
| man/Bk.Rd | 9 +++++----
| man/Bk_permutations.Rd | 7 +++++--
| man/Bk_plot.Rd | 10 ++++++----
| man/FM_index.Rd | 6 ++++--
| man/FM_index_R.Rd | 6 ++++--
| man/FM_index_permutation.Rd | 7 +++++--
| man/FM_index_profdpm.Rd | 6 ++++--
| man/assign_values_to_branches_edgePar.Rd | 10 ++++------
| man/assign_values_to_leaves_nodePar.Rd | 11 +++++------
| man/assign_values_to_nodes_nodePar.Rd | 10 ++++------
| man/color_labels.Rd | 7 +++++--
| man/cor_bakers_gamma.Rd | 6 ++++--
| man/cut_lower_fun.Rd | 8 +++++---
| man/cutree-methods.Rd | 6 ++++--
| man/cutree_1h.dendrogram.Rd | 6 ++++--
| man/cutree_1k.dendrogram.Rd | 8 +++++---
| man/dendextend_options.Rd | 6 ++++++
| man/get_branches_attr.Rd | 7 +++++--
| man/intersect_trees.Rd | 8 +++++---
| man/sort_2_clusters_vectors.Rd | 6 ++++--
| man/sort_levels_values.Rd | 8 +++++---
| man/tanglegram.Rd | 5 +++--
| 22 files changed, 101 insertions(+), 62 deletions(-)
* 2014-08-08(Tal Galili) ALL `warn` paramteres are no set to dendextend_options("warn") (which is FALSE) |bb759ff|
| NEWS | 6 ++++++
| R/attr_access.R | 30 ++++++++++++-----------------
| R/bk_method.R | 50 +++++++++++++++++++++++++++++++------------------
| R/color_branches.R | 10 ++++++----
| R/cor_bakers_gamma.R | 10 ++++++----
| R/cor_cophenetic.R | 2 +-
| R/cut_lower_fun.R | 10 ++++++----
| R/cutree.dendrogram.R | 36 +++++++++++++++++++++--------------
| R/tanglegram.R | 11 ++++++-----
| R/trim.R | 8 +++++---
| 10 files changed, 102 insertions(+), 71 deletions(-)
* 2014-08-08(Tal Galili) `get_branches_attr` - change "warning" to "warn", and it now works with is.dendrogram, and no longer changes the class of something which is not a dendrogram. |73e4ad0|
| R/unbranch.R | 14 ++++++++------
| 1 file changed, 8 insertions(+), 6 deletions(-)
* 2014-08-08(Tal Galili) A new "warn" dendextend_options parameter. logical (FALSE). Should warning be issued? |d491d43|
| R/dendextend_options.R | 8 ++++++++
| 1 file changed, 8 insertions(+)
* 2014-08-08(Tal Galili) dendextend_options.R - moved `dendextend_options` functions to it. |8e33740|
| NEWS | 8 ++++
| R/dendextend_options.R | 110 +++++++++++++++++++++++++++++++++++++++++++++++
| R/zzz.R | 88 -------------------------------------
| 3 files changed, 118 insertions(+), 88 deletions(-)
* 2014-08-07(Tal Galili) A new draft for introduction.Rmd Vignettes |ddc69d9|
| vignettes/introduction.Rmd | 187 +++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 187 insertions(+)
* 2014-08-06(Tal Galili) Added pvclust - bump to 0.16.4 |e4cca44|
| ChangeLog | 120 ++++++++++++++++++++++++
| DESCRIPTION | 5 +-
| NEWS.md | 297 +++++++++++++++++++++++++++++++++-------------------------
| 3 files changed, 290 insertions(+), 132 deletions(-)
* 2014-08-06(Tal Galili) NEW FUNCTIONS: * `as.dendrogram.pvclust` - extract the hclust from a pvclust object, and turns it into a dendrogram. * `hc2axes` - imported from pvclust, needed for text.pvclust * `text.pvclust` - imported from pvclust, adds text to a dend plot of a pvclust result * `pvclust_show_signif` - Shows the significant branches in a dendrogram, based on a pvclust object * `pvclust_show_signif_gradient` - Shows the gradient of significance of branches in a dendrogram, based on a pvclust object |5677850|
| NAMESPACE | 4 +
| NEWS | 16 ++
| R/pvclust.R | 281 ++++++++++++++++++++++++++++++++--
| man/pvclust_show_signif.Rd | 65 ++++++++
| man/pvclust_show_signif_gradient.Rd | 58 +++++++
| 5 files changed, 412 insertions(+), 12 deletions(-)
* 2014-08-06(Tal Galili) Move from is.finite to !is.infinite - so to be able to handle characters and not just numbers! |c00faa7|
| R/attr_access.R | 6 +++---
| 1 file changed, 3 insertions(+), 3 deletions(-)
* 2014-08-06(Tal Galili) `assign_values_to_leaves_nodePar`, `assign_values_to_nodes_nodePar`, `assign_values_to_branches_edgePar` - If the value has `Inf` (instead of NA!) then the value will not be changed. |d44661d|
| R/attr_access.R | 16 +++++++---------
| inst/tests/test-set.dendrogram.R | 8 ++++----
| man/assign_values_to_branches_edgePar.Rd | 4 +---
| man/assign_values_to_leaves_nodePar.Rd | 2 +-
| man/assign_values_to_nodes_nodePar.Rd | 6 +++---
| 5 files changed, 16 insertions(+), 20 deletions(-)
* 2014-08-06(Tal Galili) Version bump to 0.16.3 |91b0884|
| DESCRIPTION | 9 +++++----
| 1 file changed, 5 insertions(+), 4 deletions(-)
* 2014-08-06(Tal Galili) `assign_values_to_nodes_nodePar` - Assign values to nodePar of dendrogram's nodes |5dbfb56|
| NAMESPACE | 2 +-
| NEWS | 6 ++
| R/attr_access.R | 116 +++++++++++++++++++++++++++++--
| man/assign_values_to_leaves_nodePar.Rd | 6 +-
| man/assign_values_to_nodes_nodePar.Rd | 55 +++++++++++++++
| 5 files changed, 177 insertions(+), 8 deletions(-)
* 2014-08-06(Tal Galili) NEWS - updated to use header 2 and 3 instead of 1 and 2 for the markdown version. |a025624|
| NEWS | 271 +++++++++++++++++++++++++++++++++--------------------------------
| 1 file changed, 139 insertions(+), 132 deletions(-)
* 2014-08-06(mark) removed export directive |09030d7|
| R/d3dendrogram.R | 1 -
| 1 file changed, 1 deletion(-)
* 2014-08-06(mark) Added and documented global options |bfc2809|
| NAMESPACE | 1 +
| R/d3dendrogram.R | 96 ++++++++++++++++++++++++++++++++++++++++++------------
| R/zzz.R | 3 ++
| 3 files changed, 79 insertions(+), 21 deletions(-)
* 2014-08-06(mark) d3dendrogram accepts global options, e.g. node_fill |2d39826|
| R/d3dendrogram.R | 89 +++++++++++++++++++++++++++++++++++-------------------
| 1 file changed, 58 insertions(+), 31 deletions(-)
* 2014-08-06(mark) d3dendrogram now opens in (RStudio) viewer by default |10a64b3|
| R/d3dendrogram.R | 33 ++++++++++++++++++++++-----------
| 1 file changed, 22 insertions(+), 11 deletions(-)
* 2014-07-29(Tal Galili) require -> library (Thanks Yihui: http://yihui.name/en/2014/07/library-vs-require/) |e676951|
| DESCRIPTION | 4 +--
| NEWS | 8 ++++++
| R/as.dendrogram.randomForest.R | 2 +-
| R/attr_access.R | 6 ++---
| R/bk_method.R | 4 +--
| R/branches_attr_by.R | 8 +++---
| R/color_branches.R | 10 ++++----
| R/colored_bars.R | 6 ++---
| R/cor_bakers_gamma.R | 4 +--
| R/cor_cophenetic.R | 2 +-
| R/cut_lower_fun.R | 8 +++---
| R/cutree.dendrogram.R | 10 ++++----
| R/d3dendrogram.R | 6 ++---
| R/nleaves.R | 8 +++---
| R/noded_with_condition.R | 12 ++++-----
| R/pvclust.R | 4 +--
| R/rotate.R | 6 ++---
| R/set.dendrogram.R | 2 +-
| R/trim.R | 2 +-
| R/unbranch.R | 2 +-
| R/untangle.R | 20 +++++++--------
| R/zzz.R | 10 ++++----
| TODO | 4 +++
| demo/dendextend.R | 2 +-
| inst/tests/test-attr_access.R | 4 +--
| inst/tests/test-bk_method.R | 2 +-
| inst/tests/test-cor_bakers_gamma.R | 2 +-
| inst/tests/test-cor_cophenetic.R | 2 +-
| inst/tests/test-cut_lower_fun.R | 8 +++---
| inst/tests/test-cutree.dendrogram.R | 8 +++---
| inst/tests/test-dendlist.R | 2 +-
| inst/tests/test-entanglement.R | 4 +--
| inst/tests/test-labels-assign.R | 2 +-
| inst/tests/test-nleaves.R | 2 +-
| inst/tests/test-rotate.R | 4 +--
| inst/tests/test-set.dendrogram.R | 10 ++++----
| inst/tests/test-trim.R | 4 +--
| inst/tests/test-untangle.R | 4 +--
| man/DendSer.dendrogram.Rd | 2 +-
| man/FM_index.Rd | 2 +-
| man/FM_index_permutation.Rd | 2 +-
| man/branches_attr_by_clusters.Rd | 6 ++---
| man/branches_attr_by_labels.Rd | 4 +--
| man/color_branches.Rd | 6 ++---
| man/cor_bakers_gamma.Rd | 2 +-
| man/cor_cophenetic.Rd | 2 +-
| man/cut_lower_fun.Rd | 6 ++---
| man/cutree-methods.Rd | 2 +-
| man/cutree_1h.dendrogram.Rd | 2 +-
| man/cutree_1k.dendrogram.Rd | 2 +-
| man/get_branches_heights.Rd | 4 +--
| man/get_nodes_attr.Rd | 2 +-
| man/heights_per_k.dendrogram.Rd | 2 +-
| man/na_locf.Rd | 4 +--
| man/noded_with_condition.Rd | 4 +--
| man/rotate_DendSer.Rd | 2 +-
| man/set.Rd | 2 +-
| man/which_leaf.Rd | 4 +--
| vignettes/dendextend-tutorial.rnw | 48 +++++++++++++++++------------------
| 59 files changed, 165 insertions(+), 153 deletions(-)
* 2014-07-26(Tal Galili) ChangeLog |2257d2c|
| ChangeLog | 20 ++++++++++++++++++++
| 1 file changed, 20 insertions(+)
* 2014-07-26(Tal Galili) Comment out example code that won't run. |f39d69e|
| NEWS.md | 7 ++
| R/pvclust.R | 242 +++++++++++++++++++++++++++++-----------------------------
| 2 files changed, 128 insertions(+), 121 deletions(-)
* 2014-07-26(Tal Galili) Fix: \examples lines wider than 100 characters |051eab6|
| DESCRIPTION | 2 +-
| NEWS | 7 +++++++
| R/branches_attr_by.R | 3 ++-
| R/noded_with_condition.R | 30 ++++++++++++++++++++++--------
| man/branches_attr_by_clusters.Rd | 3 ++-
| man/branches_attr_by_labels.Rd | 24 ++++++++++++++++++------
| man/noded_with_condition.Rd | 4 +++-
| 7 files changed, 55 insertions(+), 18 deletions(-)
* 2014-07-26(Tal Galili) Update NEWS and ChangeLog |9cd933b|
| ChangeLog | 47 +++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 8 ++++++--
| 2 files changed, 53 insertions(+), 2 deletions(-)
* 2014-07-26(Tal Galili) added a pvclust example (using a condition on p-value, and heighlighting branches based on that with lwd/col.) |cbbaae3|
| NEWS | 2 +
| R/pvclust.R | 121 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| TODO | 1 -
| 3 files changed, 123 insertions(+), 1 deletion(-)
* 2014-07-26(Tal Galili) `na_locf` - Fill Last Observation Carried Forward |5e764d7|
| DESCRIPTION | 2 +-
| NAMESPACE | 1 +
| NEWS | 4 +--
| R/pvclust.R | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| man/na_locf.Rd | 57 +++++++++++++++++++++++++++++++++++
| 5 files changed, 153 insertions(+), 3 deletions(-)
* 2014-07-26(Tal Galili) `which_leaf` - a new function to tell us Which node is a leaf |3658216|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/noded_with_condition.R | 35 +++++++++++++++++++++++++++++++++++
| TODO | 1 +
| man/which_leaf.Rd | 40 ++++++++++++++++++++++++++++++++++++++++
| 5 files changed, 78 insertions(+)
* 2014-07-26(Tal Galili) `assign_values_to_branches_edgePar` - allow the option to skip leaves |9ec9e1d|
| NEWS | 1 +
| R/attr_access.R | 10 ++++++++--
| man/assign_values_to_branches_edgePar.Rd | 5 ++++-
| 3 files changed, 13 insertions(+), 3 deletions(-)
* 2014-07-26(Tal Galili) branches_attr_by_labels - if dend is not a dendrogram, we should stop and not warn! |591c3b9|
| R/noded_with_condition.R | 6 +++++-
| 1 file changed, 5 insertions(+), 1 deletion(-)
* 2014-07-25(Tal Galili) various doc updates. |a8863ab|
| ChangeLog | 203 +++++++++++++++++++++++++++++++++++++
| NEWS.md | 60 ++++++++++-
| R/branches_attr_by.R | 1 +
| TODO | 6 +-
| man/branches_attr_by_clusters.Rd | 1 +
| 5 files changed, 267 insertions(+), 4 deletions(-)
* 2014-07-25(Tal Galili) Added import for "whisker" for d3dendrogram. |426bd4a|
| DESCRIPTION | 1 +
| NAMESPACE | 1 +
| R/d3dendrogram.R | 3 ++-
| R/dendextend-package.R | 1 +
| 4 files changed, 5 insertions(+), 1 deletion(-)
* 2014-07-25(Tal Galili) Updated TODO :) |82524ce|
| TODO | 4 ----
| 1 file changed, 4 deletions(-)
* 2014-07-25(Tal Galili) Added ref to plotDendroAndColors |81e15ee|
| R/branches_attr_by.R | 3 ++-
| R/colored_bars.R | 4 ++--
| man/branches_attr_by_clusters.Rd | 3 ++-
| man/colored_bars.Rd | 3 ++-
| 4 files changed, 8 insertions(+), 5 deletions(-)
* 2014-07-25(Tal Galili) For now - version 0.16.0 |4c13ada|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-07-25(Tal Galili) branches_attr_by_clusters - modified the example in the docs a bit (using the original dist matrix for the cutreeDynamic). |04ffde4|
| R/branches_attr_by.R | 16 +++++++++-------
| man/branches_attr_by_clusters.Rd | 16 +++++++++-------
| 2 files changed, 18 insertions(+), 14 deletions(-)
* 2014-07-25(Tal Galili) `colored_bars` - update docs |6283ece|
| NEWS | 2 +-
| R/colored_bars.R | 9 +++++++--
| man/colored_bars.Rd | 3 +++
| 3 files changed, 11 insertions(+), 3 deletions(-)
* 2014-07-25(Tal Galili) `branches_attr_by_labels` - change the order of some parameters (based on how much I expect users to use each of them.) |efd8c42|
| NEWS | 1 +
| R/noded_with_condition.R | 11 ++++++-----
| man/branches_attr_by_labels.Rd | 16 +++++++++-------
| 3 files changed, 16 insertions(+), 12 deletions(-)
* 2014-07-25(Tal Galili) Added branches_attr_by_clusters - This function was designed to enable the manipulation (mainly coloring) of branches, based on the results from the cutreeDynamic function (from the {dynamicTreeCut} package). |cf18ef3|
| NAMESPACE | 1 +
| NEWS | 8 +-
| R/branches_attr_by.R | 182 +++++++++++++++++++++++++++++++++++++
| man/branches_attr_by_clusters.Rd | 111 ++++++++++++++++++++++
| 4 files changed, 300 insertions(+), 2 deletions(-)
* 2014-07-25(Tal Galili) colored_bars - change the order of colors and dend, and allowing for dend to be missing. |4e85359|
| NEWS | 4 ++++
| R/colored_bars.R | 19 ++++++++++++-------
| man/colored_bars.Rd | 7 ++++---
| 3 files changed, 20 insertions(+), 10 deletions(-)
* 2014-07-25(Tal Galili) assign_values_to_branches_edgePar - now can keep existing value, if gets NA. |0c29c7b|
| DESCRIPTION | 4 ++--
| NEWS | 8 ++++++++
| R/attr_access.R | 9 ++++++++-
| R/noded_with_condition.R | 8 ++++++--
| man/assign_values_to_branches_edgePar.Rd | 4 ++++
| man/branches_attr_by_labels.Rd | 5 +++--
| 6 files changed, 31 insertions(+), 7 deletions(-)
* 2014-07-24(talgalili) minor fixes |f0306e8|
| README.md | 6 ++++--
| 1 file changed, 4 insertions(+), 2 deletions(-)
* 2014-07-24(talgalili) Add options to the methods. |922befd|
| R/set.dendrogram.R | 3 +++
| man/set.Rd | 3 +++
| 2 files changed, 6 insertions(+)
* 2014-07-24(talgalili) In the docs: \dontrun { -> \dontrun{ |76e215f|
| R/noded_with_condition.R | 4 ++--
| man/branches_attr_by_labels.Rd | 2 +-
| man/noded_with_condition.Rd | 2 +-
| 3 files changed, 4 insertions(+), 4 deletions(-)
* 2014-07-24(talgalili) make package installation easier |859ad72|
| README.md | 14 ++++++++------
| 1 file changed, 8 insertions(+), 6 deletions(-)
* 2014-07-24(talgalili) Updated DESCRIPTION and NEWS to version 0.15.2 |069acdf|
| DESCRIPTION | 5 +++--
| NEWS | 11 ++++++++++-
| 2 files changed, 13 insertions(+), 3 deletions(-)
* 2014-07-24(talgalili) set.dendrogram - added new options: by_labels_branches_col, by_labels_branches_lwd, by_labels_branches_lty |0e4e414|
| R/set.dendrogram.R | 38 +++++++++++++++++++++++++++++++++++++-
| man/set.Rd | 31 ++++++++++++++++++++++++++++++-
| 2 files changed, 67 insertions(+), 2 deletions(-)
* 2014-07-24(talgalili) NEW FUNCTIONS: * `noded_with_condition` - Find which nodes satisfies a condition * `branches_attr_by_labels` - Change col/lwd/lty of branches matching labels condition |1c59527|
| NAMESPACE | 2 +
| R/noded_with_condition.R | 184 +++++++++++++++++++++++++++++++++++++++
| man/branches_attr_by_labels.Rd | 56 ++++++++++++
| man/noded_with_condition.Rd | 61 +++++++++++++
| 4 files changed, 303 insertions(+)
* 2014-07-24(talgalili) Minor fixes to get the package to work. Also added some credit, and a more robust installation code to README.md (so it would work on non-Windows OS better) |53046d2|
| DESCRIPTION | 3 ++-
| README.md | 6 ++++--
| dendextend.Rproj | 2 +-
| man/identify.dendrogram.Rd | 2 +-
| 4 files changed, 8 insertions(+), 5 deletions(-)
* 2014-07-24(talgalili) Fix malformed character. |5931a29|
| R/zzz.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-07-24(talgalili) Fix malformed character. |8126b0d|
| R/rect.dendrogram.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-07-19(Tal Galili) Added Mark van der Loo's first version of d3dendrogram |590e0d7|
| R/d3dendrogram.R | 198 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 198 insertions(+)
* 2014-07-19(Tal Galili) Added a heatmap.2 example to set.dendrogram |ce47f54|
| R/set.dendrogram.R | 28 ++++++++++++++++++++++++++++
| man/set.Rd | 28 ++++++++++++++++++++++++++++
| 2 files changed, 56 insertions(+)
* 2014-07-18(Tal Galili) `rect.dendrogram` - adding paramters for creating text under the clusters, as well as make it easier to plot lines on the rect (density = 7). props to skullkey for his help. |8706a7d|
| NEWS | 7 +++++++
| R/rect.dendrogram.R | 39 +++++++++++++++++++++++++++++++++++----
| TODO | 12 +++++++-----
| man/rect.dendrogram.Rd | 29 ++++++++++++++++++++++++++++-
| 4 files changed, 77 insertions(+), 10 deletions(-)
* 2014-07-16(Tal Galili) identify.dendrogram - function and docs added. (it might be a bit buggy...) |941521e|
| NAMESPACE | 1 +
| NEWS | 2 ++
| R/rect.dendrogram.R | 78 +++++++++++++++++++++++++++++++++++++++-----
| man/identify.dendrogram.Rd | 69 +++++++++++++++++++++++++++++++++++++++
| 4 files changed, 141 insertions(+), 9 deletions(-)
* 2014-07-16(Tal Galili) `rect.dendrogram` - just like `rect.hclust`, plus: works for dendrograms, passes `...` to rect for lwd lty etc, now has an horiz parameter! |b290b8b|
| NAMESPACE | 1 +
| NEWS | 11 ++--
| R/labels.R | 2 +-
| R/rect.dendrogram.R | 136 +++++++++++++++++++++++++++++++++++++++++++----
| man/rect.dendrogram.Rd | 70 ++++++++++++++++++++++++
| 5 files changed, 206 insertions(+), 14 deletions(-)
* 2014-07-16(Tal Galili) rect.dendrogram - started working on the function. (we start with rect.hclust, and move from there) |3c8aa38|
| R/rect.dendrogram.R | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 60 insertions(+)
* 2014-07-16(Tal Galili) order.hclust (new function) - Ordering of the Leaves in a hclust Dendrogram |224f9a0|
| NAMESPACE | 1 +
| NEWS | 3 +++
| R/dendextend.R | 1 -
| R/labels.R | 28 ++++++++++++++++++++++++++++
| man/order.hclust.Rd | 33 +++++++++++++++++++++++++++++++++
| 5 files changed, 65 insertions(+), 1 deletion(-)
* 2014-07-15(Tal Galili) Rename 2 file names from add->set (set.dendrogram.R and tests-set.dendrogram.R) |6b14d4b|
| DESCRIPTION | 4 +-
| NEWS | 10 ++
| R/add.dendrogram.R | 212 -------------------------------------
| R/set.dendrogram.R | 212 +++++++++++++++++++++++++++++++++++++
| inst/tests/test-add.dendrogram.R | 143 -------------------------
| inst/tests/test-set.dendrogram.R | 143 +++++++++++++++++++++++++
| 6 files changed, 367 insertions(+), 357 deletions(-)
* 2014-07-15(Tal Galili) Rename from "add" to "set"! |fb77b15|
| NAMESPACE | 6 +-
| R/add.dendrogram.R | 109 ++++++++++++++---------------
| inst/tests/test-add.dendrogram.R | 46 ++++++-------
| man/add.Rd | 137 -------------------------------------
| man/set.Rd | 137 +++++++++++++++++++++++++++++++++++++
| 5 files changed, 216 insertions(+), 219 deletions(-)
* 2014-07-15(Tal Galili) Rename files - from update to add |e08cccb|
| NEWS | 7 +-
| R/add.dendrogram.R | 215 ++++++++++++++++++++++++++++++++++
| R/update.dendrogram.R | 215 ----------------------------------
| inst/tests/test-add.dendrogram.R | 143 ++++++++++++++++++++++
| inst/tests/test-update.dendrogram.R | 143 ----------------------
| 5 files changed, 362 insertions(+), 361 deletions(-)
* 2014-07-15(Tal Galili) Changed "update" to be "add". To make it easier to read and write... |cd72d1e|
| NAMESPACE | 5 +-
| R/update.dendrogram.R | 118 ++++++++++++++++-------------
| R/zzz.R | 5 ++
| inst/tests/test-update.dendrogram.R | 46 ++++++------
| man/add.Rd | 137 ++++++++++++++++++++++++++++++++++
| man/update.dendrogram.Rd | 135 ---------------------------------
| 6 files changed, 233 insertions(+), 213 deletions(-)
* 2014-07-15(Tal Galili) update: change "with" to "value" (probably a better name for this parameter) |e9f44e6|
| R/update.dendrogram.R | 34 +++++++++++++++++-----------------
| man/update.dendrogram.Rd | 6 +++---
| 2 files changed, 20 insertions(+), 20 deletions(-)
* 2014-07-14(Tal Galili) is_null_list - making the example donotrun. Reason: I can run this only if I'd make is_null_list exported |d7cfcac|
| R/dendlist.R | 4 ++++
| TODO | 1 +
| man/is_null_list.Rd | 4 ++++
| 3 files changed, 9 insertions(+)
* 2014-07-14(Tal Galili) Updated some docs. |2b98871|
| ChangeLog | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| DESCRIPTION | 2 +-
| NEWS | 2 +-
| NEWS.md | 8 ++++--
| R/magrittr.R | 10 ++++++++
| R/zzz.R | 1 +
| TODO | 1 -
| 7 files changed, 96 insertions(+), 5 deletions(-)
* 2014-07-14(Tal Galili) Minor doc fixed for: cor_cophenetic, entanglement. as.phylo.dendrogram, untangle.dendlist, and labels.hclust (which required the use of @rdname) |30c5277|
| R/cor_cophenetic.R | 7 +++++--
| R/dendextend-package.R | 8 ++++++++
| R/entanglement.R | 6 +++---
| R/nleaves.R | 6 ++----
| R/untangle.R | 5 +++--
| man/cor_cophenetic.Rd | 4 +++-
| man/entanglement.Rd | 4 ++--
| man/labels-assign.Rd | 9 +++++++++
| man/labels.hclust.Rd | 11 -----------
| man/shuffle.Rd | 1 +
| man/untangle.Rd | 2 +-
| 11 files changed, 37 insertions(+), 26 deletions(-)
* 2014-07-14(Tal Galili) Added an internal function "zero_range" |58cf6bc|
| R/colored_bars.R | 19 +++++++++++++++++++
| 1 file changed, 19 insertions(+)
* 2014-07-14(Tal Galili) Change "" to `` when wrapping a function of style `fo<-`, so to have RStudio pick up on it. |bdca139|
| R/labels.R | 24 ++++++++++++++----------
| 1 file changed, 14 insertions(+), 10 deletions(-)
* 2014-07-14(Tal Galili) Moved {magrittr} to the "Imports" section in DESCRIPTION. And imported the %>% function from magrittr (using a trick from the dplyr package) |f2bb8be|
| DESCRIPTION | 4 ++--
| NAMESPACE | 3 ++-
| NEWS | 3 +++
| R/magrittr.R | 43 +++++++++++++++++++++++++++++++++++++++++++
| man/pipe.Rd | 32 ++++++++++++++++++++++++++++++++
| 5 files changed, 82 insertions(+), 3 deletions(-)
* 2014-07-14(Tal Galili) roxygen2 - Moved from using @S3method to @export (removed 45 warnings from check() ) |e036f50|
| NEWS | 3 ++-
| R/cor_bakers_gamma.R | 6 ++++--
| R/cutree.dendrogram.R | 4 ++--
| R/entanglement.R | 12 ++++++++----
| R/labels.R | 12 ++++++------
| R/nleaves.R | 27 +++++++++++++++++----------
| R/rotate.R | 18 ++++++++++++------
| R/tanglegram.R | 12 ++++++++----
| R/trim.R | 9 ++++++---
| R/unbranch.R | 9 ++++++---
| R/untangle.R | 18 ++++++++++++------
| R/update.dendrogram.R | 3 ++-
| R/zzz.R | 1 +
| TODO | 4 ++++
| man/labels.hclust.Rd | 11 +++++++++++
| 15 files changed, 101 insertions(+), 48 deletions(-)
* 2014-07-14(Tal Galili) untangle.dendrogram - fix doc, and add \n to massage |0f2afed|
| R/untangle.R | 4 ++--
| man/untangle_step_rotate_2side.Rd | 2 +-
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2014-07-14(Tal Galili) Replace expect_that with expect_equal |8a27370|
| inst/tests/test-labels-assign.R | 49 +++++++++++++++++++++------------------
| 1 file changed, 27 insertions(+), 22 deletions(-)
* 2014-07-14(Tal Galili) tests - add an option to stop the warnings (I know they are there, so really no point in them keep showing up...) |4862624|
| inst/tests/test-update.dendrogram.R | 7 +++++++
| 1 file changed, 7 insertions(+)
* 2014-07-14(Tal Galili) add ` to functions in NEWS |ece7863|
| NEWS | 36 ++++++++++++++++++------------------
| NEWS.md | 36 ++++++++++++++++++------------------
| 2 files changed, 36 insertions(+), 36 deletions(-)
* 2014-07-14(Tal Galili) Turn news to be more marked down... |b231b9b|
| NEWS | 230 +++++++++++++++++++++++++++++++-------------------------------
| NEWS.md | 230 +++++++++++++++++++++++++++++++-------------------------------
| 2 files changed, 230 insertions(+), 230 deletions(-)
* 2014-07-14(Tal Galili) update NEWS.md and changelog |5f206dd|
| ChangeLog | 232 ++++++++++++++++++++++++++++++++++++++++++++++++++++
| NEWS.md | 265 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-----
| R/zzz.R | 4 +-
| 3 files changed, 479 insertions(+), 22 deletions(-)
* 2014-07-14(Tal Galili) Updated the README a bit. |8d6bb95|
| README.md | 37 +++++++------------------------------
| 1 file changed, 7 insertions(+), 30 deletions(-)
* 2014-07-14(Tal Galili) add .gitignore to not keep the cache and figure folders |5a4028c|
| vignettes/.gitignore | 2 ++
| 1 file changed, 2 insertions(+)
* 2014-07-14(Tal Galili) update TODO and ChangeLog |99430e2|
| ChangeLog | 400 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| TODO | 25 ++++
| 2 files changed, 425 insertions(+)
* 2014-07-14(Tal Galili) Remove all extra doc files |8a3a863|
| inst/doc/2013-09-05_Boston-useR/.gitignore | 4 -
| .../precip_dend_plot_1.png | Bin 3665 -> 0 bytes
| .../precip_dend_plot_2.png | Bin 3715 -> 0 bytes
| .../precip_subset__hclust_single_plot.png | Bin 3900 -> 0 bytes
| .../precip_subset__hclust_single_plot_rect.png | Bin 3833 -> 0 bytes
| .../unnamed-chunk-17.png | Bin 5737 -> 0 bytes
| .../unnamed-chunk-19.png | Bin 7510 -> 0 bytes
| .../unnamed-chunk-21.png | Bin 3900 -> 0 bytes
| .../unnamed-chunk-5.png | Bin 11621 -> 0 bytes
| .../2013-09-05_Boston-useR_01_intro.R | 198 -
| .../2013-09-05_Boston-useR_01_intro.Rpres | 454 --
| .../2013-09-05_Boston-useR_01_intro.html | 1471 ----
| .../2013-09-05_Boston-useR_01_intro.md | 659 --
| .../dend_hang_tree_1.png | Bin 4731 -> 0 bytes
| .../dend_rotating_example_1.png | Bin 4759 -> 0 bytes
| .../dend_trimming_example_1.png | Bin 4139 -> 0 bytes
| .../dend_unbranching_example_1.png | Bin 4748 -> 0 bytes
| .../first_tanglegram.png | Bin 39575 -> 0 bytes
| .../first_tanglegram_with_code.png | Bin 40772 -> 0 bytes
| .../iris_colored_branches.png | Bin 16950 -> 0 bytes
| .../simple_tanglegram_1.png | Bin 3256 -> 0 bytes
| .../simple_tanglegram_1_worst_case.png | Bin 4577 -> 0 bytes
| .../simple_tanglegram_one_shuffle_1.png | Bin 3621 -> 0 bytes
| .../simple_tanglegram_random_search_1.png | Bin 2846 -> 0 bytes
| ...ple_tanglegram_step_rotate_1side_example_1.png | Bin 2822 -> 0 bytes
| .../tanglegram_iris_untangle_random.png | Bin 42100 -> 0 bytes
| .../unnamed-chunk-11.png | Bin 5869 -> 0 bytes
| .../unnamed-chunk-12.png | Bin 4755 -> 0 bytes
| .../unnamed-chunk-14.png | Bin 4755 -> 0 bytes
| .../unnamed-chunk-15.png | Bin 4755 -> 0 bytes
| .../unnamed-chunk-16.png | Bin 4759 -> 0 bytes
| .../unnamed-chunk-17.png | Bin 4748 -> 0 bytes
| .../unnamed-chunk-18.png | Bin 22344 -> 0 bytes
| .../unnamed-chunk-19.png | Bin 4759 -> 0 bytes
| .../unnamed-chunk-2.png | Bin 18023 -> 0 bytes
| .../unnamed-chunk-20.png | Bin 4748 -> 0 bytes
| .../unnamed-chunk-21.png | Bin 4139 -> 0 bytes
| .../unnamed-chunk-22.png | Bin 4748 -> 0 bytes
| .../unnamed-chunk-23.png | Bin 4139 -> 0 bytes
| .../unnamed-chunk-24.png | Bin 22344 -> 0 bytes
| .../unnamed-chunk-25.png | Bin 4139 -> 0 bytes
| .../unnamed-chunk-26.png | Bin 22344 -> 0 bytes
| .../unnamed-chunk-33.png | Bin 3740 -> 0 bytes
| .../unnamed-chunk-4.png | Bin 6132 -> 0 bytes
| .../unnamed-chunk-6.png | Bin 6132 -> 0 bytes
| .../unnamed-chunk-8.png | Bin 5869 -> 0 bytes
| .../unnamed-chunk-9.png | Bin 6132 -> 0 bytes
| .../2013-09-05_Boston-useR_02_dendextend.R | 432 --
| .../2013-09-05_Boston-useR_02_dendextend.Rpres | 676 --
| .../2013-09-05_Boston-useR_02_dendextend.html | 1666 -----
| .../2013-09-05_Boston-useR_02_dendextend.md | 876 ---
| .../first_tanglegram_with_2side_untangle.png | Bin 18166 -> 0 bytes
| .../first_tanglegram_with_2side_untangle_hang.png | Bin 26292 -> 0 bytes
| .../first_tanglegram_with_code.png | Bin 29397 -> 0 bytes
| .../first_tanglegram_with_random_untangle.png | Bin 23574 -> 0 bytes
| .../unnamed-chunk-4.png | Bin 23574 -> 0 bytes
| .../unnamed-chunk-7.png | Bin 18112 -> 0 bytes
| .../unnamed-chunk-9.png | Bin 18112 -> 0 bytes
| .../2013-09-05_Boston-useR_03_untangle_iris.R | 179 -
| .../2013-09-05_Boston-useR_03_untangle_iris.Rpres | 184 -
| .../2013-09-05_Boston-useR_03_untangle_iris.html | 1058 ---
| .../2013-09-05_Boston-useR_03_untangle_iris.md | 200 -
| .../__packages | 8 -
| ...ordered_ca9a216309a7a760068a06f608ab2ccd.RData | Bin 2844 -> 0 bytes
| ...m_ordered_ca9a216309a7a760068a06f608ab2ccd.rdb | Bin 1975 -> 0 bytes
| ...m_ordered_ca9a216309a7a760068a06f608ab2ccd.rdx | Bin 154 -> 0 bytes
| .../dend1_plot_1.png | Bin 3877 -> 0 bytes
| .../iris_tanglegram_ordered.png | Bin 18166 -> 0 bytes
| .../precip_dend5_plot_2.png | Bin 3334 -> 0 bytes
| .../tanglegram_dend12_1.png | Bin 4528 -> 0 bytes
| .../unnamed-chunk-10.png | Bin 7186 -> 0 bytes
| .../unnamed-chunk-11.png | Bin 2578 -> 0 bytes
| .../unnamed-chunk-12.png | Bin 2625 -> 0 bytes
| .../unnamed-chunk-5.png | Bin 4055 -> 0 bytes
| .../unnamed-chunk-6.png | Bin 6754 -> 0 bytes
| .../unnamed-chunk-7.png | Bin 6419 -> 0 bytes
| .../unnamed-chunk-9.png | Bin 2000 -> 0 bytes
| .../2013-09-05_Boston-useR_04_tree_inference.R | 125 -
| ...2013-09-05_Boston-useR_04_tree_inference.Rpres | 192 -
| .../2013-09-05_Boston-useR_04_tree_inference.html | 1100 ---
| .../2013-09-05_Boston-useR_04_tree_inference.md | 255 -
| inst/doc/dendextend-tutorial.pdf | Bin 569458 -> 0 bytes
| vignettes/.gitignore | 1 -
| vignettes/cache/__packages | 12 -
| ...hunk-40_72720aff4e60fb7daa0fc155de695631.RData | Bin 4201 -> 0 bytes
| ...-chunk-40_72720aff4e60fb7daa0fc155de695631.rdb | Bin 9497 -> 0 bytes
| ...-chunk-40_72720aff4e60fb7daa0fc155de695631.rdx | Bin 179 -> 0 bytes
| vignettes/dendextend-tutorial-concordance.tex | 14 -
| vignettes/dendextend-tutorial.blg | 5 -
| vignettes/dendextend-tutorial.log | 3070 --------
| vignettes/dendextend-tutorial.pdf | 7393 ++++++++++---------
| vignettes/dendextend-tutorial.rnw | 72 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 238204 -> 0 bytes
| vignettes/dendextend-tutorial.tex | 3434 ---------
| vignettes/figure/Bk_examples.pdf | Bin 20539 -> 0 bytes
| vignettes/figure/Bk_plot_for_dends_correct.pdf | Bin 20591 -> 0 bytes
| vignettes/figure/Bk_plot_for_hclust_WRONG.pdf | Bin 29264 -> 0 bytes
| vignettes/figure/FM_permutation_example_1.pdf | Bin 10674 -> 0 bytes
| vignettes/figure/FM_permutation_example_2.pdf | Bin 10392 -> 0 bytes
| vignettes/figure/FM_permutation_example_3.pdf | Bin 9977 -> 0 bytes
| vignettes/figure/cor_bakers_gamma_example_11.pdf | Bin 5053 -> 0 bytes
| vignettes/figure/cor_bakers_gamma_example_12.pdf | Bin 5082 -> 0 bytes
| vignettes/figure/cor_bakers_gamma_example_13.pdf | Bin 5054 -> 0 bytes
| vignettes/figure/cor_bakers_gamma_example_14.pdf | Bin 5057 -> 0 bytes
| .../figure/cor_bakers_gamma_simulation_1.pdf | Bin 7148 -> 0 bytes
| .../figure/cor_bakers_gamma_simulation_2.pdf | Bin 7609 -> 0 bytes
| .../figure/cor_bakers_gamma_simulation_3.pdf | Bin 7596 -> 0 bytes
| .../figure/cor_bakers_gamma_simulation_CI_41.pdf | Bin 5047 -> 0 bytes
| .../figure/cor_bakers_gamma_simulation_CI_42.pdf | Bin 4848 -> 0 bytes
| .../figure/cor_bakers_gamma_simulation_CI_43.pdf | Bin 7485 -> 0 bytes
| vignettes/figure/cor_cophenetic_simulation_2.pdf | Bin 7663 -> 0 bytes
| .../figure/cor_cophenetic_simulation_CI_3.pdf | Bin 7152 -> 0 bytes
| .../figure/cor_cophenetic_simulation_CI_4.pdf | Bin 7524 -> 0 bytes
| vignettes/figure/first_tanglegram.pdf | Bin 15816 -> 0 bytes
| vignettes/figure/first_tanglegram1.pdf | Bin 3450 -> 0 bytes
| vignettes/figure/first_tanglegram2.pdf | Bin 15825 -> 0 bytes
| vignettes/figure/iris_colored_branches.pdf | Bin 17747 -> 0 bytes
| vignettes/figure/iris_colored_pairs_plot.pdf | Bin 74472 -> 0 bytes
| vignettes/figure/unnamed-chunk-19.pdf | Bin 4578 -> 0 bytes
| vignettes/figure/unnamed-chunk-23.pdf | Bin 4921 -> 0 bytes
| vignettes/figure/unnamed-chunk-24.pdf | Bin 4576 -> 0 bytes
| vignettes/figure/unnamed-chunk-25.pdf | Bin 4925 -> 0 bytes
| vignettes/figure/unnamed-chunk-26.pdf | Bin 4564 -> 0 bytes
| vignettes/figure/unnamed-chunk-27.pdf | Bin 5273 -> 0 bytes
| vignettes/figure/unnamed-chunk-28.pdf | Bin 4694 -> 0 bytes
| vignettes/figure/unnamed-chunk-29.pdf | Bin 5655 -> 0 bytes
| vignettes/figure/unnamed-chunk-30.pdf | Bin 5374 -> 0 bytes
| vignettes/figure/unnamed-chunk-32.pdf | Bin 15728 -> 0 bytes
| vignettes/figure/unnamed-chunk-321.pdf | Bin 3448 -> 0 bytes
| vignettes/figure/unnamed-chunk-322.pdf | Bin 15508 -> 0 bytes
| vignettes/figure/unnamed-chunk-33.pdf | Bin 15779 -> 0 bytes
| vignettes/figure/unnamed-chunk-331.pdf | Bin 3448 -> 0 bytes
| vignettes/figure/unnamed-chunk-332.pdf | Bin 15665 -> 0 bytes
| vignettes/figure/unnamed-chunk-333.pdf | Bin 15739 -> 0 bytes
| vignettes/figure/unnamed-chunk-34.pdf | Bin 6850 -> 0 bytes
| vignettes/figure/unnamed-chunk-35.pdf | Bin 6847 -> 0 bytes
| vignettes/figure/unnamed-chunk-36.pdf | Bin 6824 -> 0 bytes
| vignettes/figure/unnamed-chunk-37.pdf | Bin 6832 -> 0 bytes
| vignettes/figure/unnamed-chunk-38.pdf | Bin 6815 -> 0 bytes
| vignettes/figure/unnamed-chunk-39.pdf | Bin 6961 -> 0 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 0 bytes
| vignettes/figure/unnamed-chunk-40.pdf | Bin 20539 -> 0 bytes
| .../untangle_step_rotate_2side_example1.pdf | Bin 6158 -> 0 bytes
| .../untangle_step_rotate_2side_example2.pdf | Bin 6137 -> 0 bytes
| .../untangle_step_rotate_2side_example3.pdf | Bin 6154 -> 0 bytes
| .../untangle_step_rotate_2side_example4.pdf | Bin 6141 -> 0 bytes
| .../untangle_step_rotate_2side_example5.pdf | Bin 5714 -> 0 bytes
| .../untangle_step_rotate_2side_example6.pdf | Bin 6163 -> 0 bytes
| 148 files changed, 3744 insertions(+), 19994 deletions(-)
* 2014-07-14(Tal Galili) Fix the docs of the functions in dendextend which relates to the newer dendextendRcpp (version 0.5.1): cut_lower_fun, get_branches_heights, heights_per_k.dendrogram |a0382df|
| NEWS | 6 +++---
| R/attr_access.R | 11 +++++------
| R/cut_lower_fun.R | 16 ++++++++--------
| R/cutree.dendrogram.R | 25 +++++++++++++------------
| man/cut_lower_fun.Rd | 16 ++++++++--------
| man/get_branches_heights.Rd | 11 +++++------
| man/heights_per_k.dendrogram.Rd | 23 ++++++++++++-----------
| 7 files changed, 54 insertions(+), 54 deletions(-)
* 2014-07-13(Tal Galili) Fix typos in vignettes - thank you Bob Muenchen! |96692d2|
| DESCRIPTION | 16 +++++----
| NEWS | 1 +
| vignettes/dendextend-tutorial.bib | 10 ++++++
| vignettes/dendextend-tutorial.rnw | 70 ++++++++++++++++++-------------------
| 4 files changed, 54 insertions(+), 43 deletions(-)
* 2014-07-13(Tal Galili) rotate_DendSer function added - and a bug was fixed in doing so. (also some credit corrections) |b045289|
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/untangle.R | 64 +++++++++++++++++++++++++++++++++++----------
| man/DendSer.dendrogram.Rd | 8 ++++--
| man/color_branches.Rd | 2 +-
| man/rotate_DendSer.Rd | 47 +++++++++++++++++++++++++++++++++
| man/tanglegram.Rd | 4 +--
| man/untangle_DendSer.Rd | 3 ++-
| 8 files changed, 110 insertions(+), 21 deletions(-)
* 2014-07-13(Tal Galili) Vignettes - fixing spelling mistakes. |cc792b7|
| vignettes/dendextend-tutorial.rnw | 48 ++++++++++++++++++-------------------
| 1 file changed, 24 insertions(+), 24 deletions(-)
* 2014-07-13(Tal Galili) Update credits. |184907e|
| DESCRIPTION | 8 +++++---
| R/color_branches.R | 2 +-
| R/tanglegram.R | 4 ++--
| 3 files changed, 8 insertions(+), 6 deletions(-)
* 2014-07-13(Tal Galili) Minor doc changes |210cf71|
| R/labels.R | 1 +
| man/color_branches.Rd | 1 +
| man/labels_colors.Rd | 4 ++++
| man/update.dendrogram.Rd | 2 +-
| 4 files changed, 7 insertions(+), 1 deletion(-)
* 2014-07-13(Tal Galili) Added tests for update.dendrogram! |ba435a1|
| inst/tests/test-update.dendrogram.R | 136 ++++++++++++++++++++++++++++++++++
| 1 file changed, 136 insertions(+)
* 2014-07-13(Tal Galili) update.dendrogram - added .Rd docs :) |208af7d|
| NAMESPACE | 1 +
| R/update.dendrogram.R | 297 ++++++++++++++++++++++-----------------------
| man/update.dendrogram.Rd | 135 +++++++++++++++++++++
| 3 files changed, 282 insertions(+), 151 deletions(-)
* 2014-07-13(Tal Galili) tanglegram - preserve and restore previous par options (will no longer have a tiny plot in the left corner, when using a simple plot after tanglegram) |982053b|
| NEWS | 4 +++-
| R/tanglegram.R | 5 ++++-
| 2 files changed, 7 insertions(+), 2 deletions(-)
* 2014-07-12(Tal Galili) colored_bars - added docs :) |08a7118|
| DESCRIPTION | 4 +-
| NAMESPACE | 2 +-
| NEWS | 2 +
| R/colored_bars.R | 243 +++++++++++++++++++++++++++++++-------------------
| man/colored_bars.Rd | 116 ++++++++++++++++++++++++
| 5 files changed, 271 insertions(+), 96 deletions(-)
* 2014-07-12(Tal Galili) color_bars - adding more parameters. Made sure it can now be placed on top of a plot(dend). |a3db1f1|
| NAMESPACE | 1 +
| NEWS | 2 +
| R/color_bars.R | 64 ----------------
| R/colored_bars.R | 216 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| 4 files changed, 219 insertions(+), 64 deletions(-)
* 2014-07-12(Tal Galili) color_bars - make sure to keep and reset the options |c13e95b|
| R/color_bars.R | 5 ++++-
| 1 file changed, 4 insertions(+), 1 deletion(-)
* 2014-07-12(Tal Galili) Rename plotHclustColors to color_bars - and made it work with dendrograms |61f854e|
| R/color_bars.R | 10 +++++++---
| 1 file changed, 7 insertions(+), 3 deletions(-)
* 2014-07-12(Tal Galili) plotHclustColors - first import into the package |5c5bec8|
| R/color_bars.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 57 insertions(+)
* 2014-07-11(Tal Galili) assign_values_to_branches_edgePar - value can now be different than 1 (it now also has a recycle option for the value) |fdc946e|
| NEWS | 5 ++++-
| R/attr_access.R | 24 +++++++++++++++++++++---
| man/assign_values_to_branches_edgePar.Rd | 8 +++++++-
| 3 files changed, 32 insertions(+), 5 deletions(-)
* 2014-07-11(Tal Galili) update.dendrogram added: branches_color, branches_k_color, branches_col, branches_lwd, branches_lty, clear_branches, clear_leaves |ee7d0c7|
| R/update.dendrogram.R | 68 ++++++++++++++++++++++++++++++++++++-------------
| 1 file changed, 50 insertions(+), 18 deletions(-)
* 2014-07-11(Tal Galili) `labels_colors<-` is more robust (for cases with partiel attr in nodePar). Also moved to using is.dendrogram more. |e774148|
| NEWS | 5 +++--
| R/attr_access.R | 4 ++--
| R/labels.R | 1 +
| R/labels_colors.R | 25 ++++++++++++++++++++-----
| 4 files changed, 26 insertions(+), 9 deletions(-)
* 2014-07-11(Tal Galili) Fix "is.dendlist" to use inherits instead of class |621dc3d|
| R/dendlist.R | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-07-11(Tal Galili) update.dendrogram - added options for: labels_colors, labels_cex, branches_color, hang, leaves_pch, leaves_cex, leaves_col |b29fa80|
| NEWS | 3 ++-
| R/attr_access.R | 8 ++++++-
| R/labels_colors.R | 2 ++
| R/update.dendrogram.R | 58 +++++++++++++++++++++++++++++++++++++++++++------
| 4 files changed, 62 insertions(+), 9 deletions(-)
* 2014-07-11(Tal Galili) plot.dendlist - a wrapper for tangelgram |05d2fc8|
| NAMESPACE | 3 +++
| NEWS | 1 +
| R/dendlist.R | 34 ++++++++++++++++++++++++++++++++++
| man/plot.dendlist.Rd | 34 ++++++++++++++++++++++++++++++++++
| 4 files changed, 72 insertions(+)
* 2014-07-11(Tal Galili) color_branches - now has a default behavior if k is missing. |f37929b|
| NEWS | 5 +++--
| R/color_branches.R | 31 ++++++++++++++++++-------------
| 2 files changed, 21 insertions(+), 15 deletions(-)
* 2014-07-11(Tal Galili) `labels_colors<-` now has a default behavior if value is missing. |928b499|
| NEWS | 1 +
| R/labels_colors.R | 11 ++++++++++-
| 2 files changed, 11 insertions(+), 1 deletion(-)
* 2014-07-11(Tal Galili) update.dendrogram - first draft of the function (implements only "labels") |7f76137|
| NAMESPACE | 1 +
| NEWS | 2 +
| R/update.dendrogram.R | 131 ++++++++++++++++++++++++++++++++++++++++++++++++
| 3 files changed, 134 insertions(+)
* 2014-07-10(Tal Galili) Added cor_cophenetic.dendlist with tests and docs. |3303e4a|
| NAMESPACE | 1 +
| R/cor_cophenetic.R | 26 ++++++++++++++++++---
| inst/tests/test-cor_bakers_gamma.R | 2 +-
| inst/tests/test-cor_cophenetic.R | 44 ++++++++++++++++++++++++++++++++++++
| man/cor_cophenetic.Rd | 19 ++++++++++++----
| 5 files changed, 83 insertions(+), 9 deletions(-)
* 2014-07-10(Tal Galili) Added entanglement.dendlist to the doc |6ae315a|
| R/entanglement.R | 1 +
| man/entanglement.Rd | 1 +
| 2 files changed, 2 insertions(+)
* 2014-07-10(Tal Galili) Added match.arg for Bk_plot, cor_cophenetic, entanglement, untangle_random_search, untangle_step_rotate_1side, and untangle_step_rotate_2side |ec129c1|
| NEWS | 1 +
| R/bk_method.R | 3 ++-
| R/cor_cophenetic.R | 7 ++++---
| R/entanglement.R | 3 ++-
| R/untangle.R | 8 +++++---
| man/cor_cophenetic.Rd | 3 ++-
| 6 files changed, 16 insertions(+), 9 deletions(-)
* 2014-07-10(Tal Galili) Fix untangle tests: untangle_step_rotate_1side now outputs a dendlist, so we needed to extract the first element so to get the same results as before. (also added piping) |75f99af|
| inst/tests/test-untangle.R | 18 +++++++++---------
| 1 file changed, 9 insertions(+), 9 deletions(-)
* 2014-07-10(Tal Galili) Piping %>% some examples |1691c78|
| R/attr_access.R | 10 +++++-----
| R/color_branches.R | 4 ++--
| R/entanglement.R | 4 ++--
| R/nleaves.R | 2 +-
| R/sample.dendrogram.R | 4 ++--
| R/tanglegram.R | 2 +-
| R/untangle.R | 12 ++++++------
| man/all_couple_rotations_at_k.Rd | 2 +-
| man/assign_values_to_branches_edgePar.Rd | 2 +-
| man/color_branches.Rd | 2 +-
| man/duplicate_leaf.Rd | 2 +-
| man/flip_leaves.Rd | 2 +-
| man/leaf_Colors.Rd | 2 +-
| man/match_order_by_labels.Rd | 2 +-
| man/match_order_dendrogram_by_old_order.Rd | 2 +-
| man/plot_horiz.dendrogram.Rd | 2 +-
| man/rank_branches.Rd | 2 +-
| man/rank_order.dendrogram.Rd | 2 +-
| man/remove_branches_edgePar.Rd | 2 +-
| man/remove_leaves_nodePar.Rd | 2 +-
| man/sample.dendrogram.Rd | 2 +-
| man/shuffle.Rd | 2 +-
| man/untangle_step_rotate_1side.Rd | 2 +-
| man/untangle_step_rotate_2side.Rd | 4 ++--
| 24 files changed, 37 insertions(+), 37 deletions(-)
* 2014-07-10(Tal Galili) Added a TODO file |0fbee3a|
| NEWS | 64 -----------------------------------------------------
| TODO | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 79 insertions(+), 64 deletions(-)
* 2014-07-10(Tal Galili) Fix some spaces around "<-" |c141009|
| R/color_branches.R | 18 +++++++++---------
| R/untangle.R | 4 ++--
| 2 files changed, 11 insertions(+), 11 deletions(-)
* 2014-07-10(Tal Galili) Rename back from .b to .R |c0fd282|
| R/as.dendrogram.randomForest.R | 54 +
| R/as.dendrogram.randomForest.b | 54 -
| R/attr_access.R | 814 ++++++++++++
| R/attr_access.b | 814 ------------
| R/bk_method.R | 1098 ++++++++++++++++
| R/bk_method.b | 1098 ----------------
| R/color_branches.R | 482 +++++++
| R/color_branches.b | 482 -------
| R/cor_bakers_gamma.R | 240 ++++
| R/cor_bakers_gamma.b | 240 ----
| R/cor_cophenetic.R | 187 +++
| R/cor_cophenetic.b | 187 ---
| R/cut_lower_fun.R | 104 ++
| R/cut_lower_fun.b | 104 --
| R/cutree.dendrogram.R | 952 ++++++++++++++
| R/cutree.dendrogram.b | 952 --------------
| R/dendextend-package.R | 30 +
| R/dendextend-package.b | 30 -
| R/dendextend.R | 70 +
| R/dendextend.b | 70 -
| R/dendlist.R | 222 ++++
| R/dendlist.b | 222 ----
| R/entanglement.R | 458 +++++++
| R/entanglement.b | 458 -------
| R/imports_stats.R | 285 +++++
| R/imports_stats.b | 285 -----
| R/labels.R | 369 ++++++
| R/labels.b | 369 ------
| R/labels_colors.R | 144 +++
| R/labels_colors.b | 144 ---
| R/nleaves.R | 316 +++++
| R/nleaves.b | 316 -----
| R/rotate.R | 337 +++++
| R/rotate.b | 337 -----
| R/sample.dendrogram.R | 267 ++++
| R/sample.dendrogram.b | 267 ----
| R/tanglegram.R | 815 ++++++++++++
| R/tanglegram.b | 815 ------------
| R/trim.R | 248 ++++
| R/trim.b | 248 ----
| R/unbranch.R | 246 ++++
| R/unbranch.b | 246 ----
| R/untangle.R | 1262 +++++++++++++++++++
| R/untangle.b | 1262 -------------------
| R/zzz.R | 360 ++++++
| R/zzz.b | 360 ------
| demo/dendextend.R | 23 +
| demo/dendextend.b | 23 -
| .../2013-09-05_Boston-useR_01_intro.R | 198 +++
| .../2013-09-05_Boston-useR_01_intro.b | 198 ---
| .../2013-09-05_Boston-useR_02_dendextend.R | 432 +++++++
| .../2013-09-05_Boston-useR_02_dendextend.b | 432 -------
| .../2013-09-05_Boston-useR_03_untangle_iris.R | 179 +++
| .../2013-09-05_Boston-useR_03_untangle_iris.b | 179 ---
| .../2013-09-05_Boston-useR_04_tree_inference.R | 125 ++
| .../2013-09-05_Boston-useR_04_tree_inference.b | 125 --
| inst/tests/test-attr_access.R | 181 +++
| inst/tests/test-attr_access.b | 181 ---
| inst/tests/test-bk_method.R | 286 +++++
| inst/tests/test-bk_method.b | 286 -----
| inst/tests/test-cor_bakers_gamma.R | 48 +
| inst/tests/test-cor_bakers_gamma.b | 48 -
| inst/tests/test-cut_lower_fun.R | 95 ++
| inst/tests/test-cut_lower_fun.b | 95 --
| inst/tests/test-cutree.dendrogram.R | 450 +++++++
| inst/tests/test-cutree.dendrogram.b | 450 -------
| inst/tests/test-dendlist.R | 61 +
| inst/tests/test-dendlist.b | 61 -
| inst/tests/test-entanglement.R | 139 ++
| inst/tests/test-entanglement.b | 139 --
| inst/tests/test-labels-assign.R | 193 +++
| inst/tests/test-labels-assign.b | 193 ---
| inst/tests/test-labels_colors.R | 81 ++
| inst/tests/test-labels_colors.b | 81 --
| inst/tests/test-nleaves.R | 68 +
| inst/tests/test-nleaves.b | 68 -
| inst/tests/test-rotate.R | 91 ++
| inst/tests/test-rotate.b | 91 --
| inst/tests/test-trim.R | 81 ++
| inst/tests/test-trim.b | 81 --
| inst/tests/test-unbranch.R | 45 +
| inst/tests/test-unbranch.b | 45 -
| inst/tests/test-untangle.R | 162 +++
| inst/tests/test-untangle.b | 162 ---
| tests/test-all.R | 13 +
| tests/test-all.b | 13 -
| 86 files changed, 12311 insertions(+), 12311 deletions(-)
* 2014-07-10(Tal Galili) rename all .r files to .b (so to allow the renaming from .r to .R on git on windows) |6145838|
| R/as.dendrogram.randomForest.b | 54 +
| R/as.dendrogram.randomForest.r | 54 -
| R/attr_access.b | 814 ++++++++++++
| R/attr_access.r | 814 ------------
| R/bk_method.b | 1098 ++++++++++++++++
| R/bk_method.r | 1098 ----------------
| R/color_branches.b | 482 +++++++
| R/color_branches.r | 482 -------
| R/cor_bakers_gamma.b | 240 ++++
| R/cor_bakers_gamma.r | 240 ----
| R/cor_cophenetic.b | 187 +++
| R/cor_cophenetic.r | 187 ---
| R/cut_lower_fun.b | 104 ++
| R/cut_lower_fun.r | 104 --
| R/cutree.dendrogram.b | 952 ++++++++++++++
| R/cutree.dendrogram.r | 952 --------------
| R/dendextend-package.b | 30 +
| R/dendextend-package.r | 30 -
| R/dendextend.b | 70 +
| R/dendextend.r | 70 -
| R/dendlist.R | 222 ----
| R/dendlist.b | 222 ++++
| R/entanglement.b | 458 +++++++
| R/entanglement.r | 458 -------
| R/imports_stats.b | 285 +++++
| R/imports_stats.r | 285 -----
| R/labels.b | 369 ++++++
| R/labels.r | 369 ------
| R/labels_colors.b | 144 +++
| R/labels_colors.r | 144 ---
| R/nleaves.b | 316 +++++
| R/nleaves.r | 316 -----
| R/rotate.b | 337 +++++
| R/rotate.r | 337 -----
| R/sample.dendrogram.b | 267 ++++
| R/sample.dendrogram.r | 267 ----
| R/tanglegram.b | 815 ++++++++++++
| R/tanglegram.r | 815 ------------
| R/trim.b | 248 ++++
| R/trim.r | 248 ----
| R/unbranch.b | 246 ++++
| R/unbranch.r | 246 ----
| R/untangle.b | 1262 +++++++++++++++++++
| R/untangle.r | 1262 -------------------
| R/zzz.b | 360 ++++++
| R/zzz.r | 360 ------
| demo/dendextend.b | 23 +
| demo/dendextend.r | 23 -
| .../2013-09-05_Boston-useR_01_intro.R | 198 ---
| .../2013-09-05_Boston-useR_01_intro.b | 198 +++
| .../2013-09-05_Boston-useR_02_dendextend.R | 432 -------
| .../2013-09-05_Boston-useR_02_dendextend.b | 432 +++++++
| .../2013-09-05_Boston-useR_03_untangle_iris.R | 179 ---
| .../2013-09-05_Boston-useR_03_untangle_iris.b | 179 +++
| .../2013-09-05_Boston-useR_04_tree_inference.R | 125 --
| .../2013-09-05_Boston-useR_04_tree_inference.b | 125 ++
| inst/tests/test-attr_access.b | 181 +++
| inst/tests/test-attr_access.r | 181 ---
| inst/tests/test-bk_method.b | 286 +++++
| inst/tests/test-bk_method.r | 286 -----
| inst/tests/test-cor_bakers_gamma.b | 48 +
| inst/tests/test-cor_bakers_gamma.r | 48 -
| inst/tests/test-cut_lower_fun.b | 95 ++
| inst/tests/test-cut_lower_fun.r | 95 --
| inst/tests/test-cutree.dendrogram.b | 450 +++++++
| inst/tests/test-cutree.dendrogram.r | 450 -------
| inst/tests/test-dendlist.R | 61 -
| inst/tests/test-dendlist.b | 61 +
| inst/tests/test-entanglement.b | 139 ++
| inst/tests/test-entanglement.r | 139 --
| inst/tests/test-labels-assign.b | 193 +++
| inst/tests/test-labels-assign.r | 193 ---
| inst/tests/test-labels_colors.b | 81 ++
| inst/tests/test-labels_colors.r | 81 --
| inst/tests/test-nleaves.b | 68 +
| inst/tests/test-nleaves.r | 68 -
| inst/tests/test-rotate.b | 91 ++
| inst/tests/test-rotate.r | 91 --
| inst/tests/test-trim.b | 81 ++
| inst/tests/test-trim.r | 81 --
| inst/tests/test-unbranch.b | 45 +
| inst/tests/test-unbranch.r | 45 -
| inst/tests/test-untangle.b | 162 +++
| inst/tests/test-untangle.r | 162 ---
| tests/test-all.b | 13 +
| tests/test-all.r | 13 -
| 86 files changed, 12311 insertions(+), 12311 deletions(-)
* 2014-07-08(Tal Galili) .Rd files commit |1fdac74|
| man/Bk.Rd | 65 ++++++------
| man/Bk_permutations.Rd | 69 ++++++------
| man/Bk_plot.Rd | 150 ++++++++++++---------------
| man/FM_index.Rd | 85 +++++++--------
| man/FM_index_R.Rd | 64 ++++++------
| man/FM_index_permutation.Rd | 36 +++----
| man/FM_index_profdpm.Rd | 81 +++++++--------
| man/all_couple_rotations_at_k.Rd | 29 +++---
| man/as_hclust_fixed.Rd | 18 ++--
| man/assign_dendextend_options.Rd | 1 +
| man/assign_values_to_branches_edgePar.Rd | 16 ++-
| man/assign_values_to_leaves_nodePar.Rd | 29 +++---
| man/bakers_gamma_for_2_k_matrix.Rd | 16 ++-
| man/click_rotate.Rd | 10 +-
| man/color_branches.Rd | 90 +++++++---------
| man/color_labels.Rd | 53 ++++------
| man/cor_bakers_gamma.Rd | 90 +++++++---------
| man/cor_cophenetic.Rd | 63 ++++++-----
| man/count_terminal_nodes.Rd | 26 ++---
| man/cut_lower_fun.Rd | 34 +++---
| man/cutree-methods.Rd | 142 ++++++++++++-------------
| man/cutree_1h.dendrogram.Rd | 35 +++----
| man/cutree_1k.dendrogram.Rd | 59 +++++------
| man/dendextend-package.Rd | 4 +-
| man/dendextend_options.Rd | 16 +--
| man/dendlist.Rd | 10 +-
| man/duplicate_leaf.Rd | 32 +++---
| man/entanglement.Rd | 93 +++++++++--------
| man/fac2num.Rd | 24 ++---
| man/fix_members_attr.dendrogram.Rd | 12 +--
| man/flatten.dendrogram.Rd | 19 ++--
| man/flip_leaves.Rd | 19 ++--
| man/get_branches_attr.Rd | 16 ++-
| man/get_branches_heights.Rd | 13 ++-
| man/get_childrens_heights.Rd | 5 +-
| man/get_leaves_attr.Rd | 23 ++--
| man/get_nodes_attr.Rd | 35 +++----
| man/hang.dendrogram.Rd | 32 +++---
| man/heights_per_k.dendrogram.Rd | 9 +-
| man/intersect_trees.Rd | 14 +--
| man/is.dendrogram.Rd | 3 +-
| man/is.hclust.Rd | 3 +-
| man/is.natural.number.Rd | 17 ++-
| man/is.phylo.Rd | 3 +-
| man/labels-assign.Rd | 39 +++----
| man/labels_colors.Rd | 27 +++--
| man/leaf_Colors.Rd | 9 +-
| man/lowest_common_branch.Rd | 20 ++--
| man/match_order_by_labels.Rd | 25 +++--
| man/match_order_dendrogram_by_old_order.Rd | 45 ++++----
| man/nleaves.Rd | 33 +++---
| man/nnodes.Rd | 16 ++-
| man/order.dendrogram-assign.Rd | 13 +--
| man/plot_horiz.dendrogram.Rd | 86 +++++++--------
| man/prune.Rd | 15 ++-
| man/prune_leaf.Rd | 8 +-
| man/raise.dendrogram.Rd | 8 +-
| man/rank_branches.Rd | 29 +++---
| man/rank_order.dendrogram.Rd | 11 +-
| man/remove_branches_edgePar.Rd | 11 +-
| man/remove_leaves_nodePar.Rd | 11 +-
| man/rllply.Rd | 27 +++--
| man/sample.dendrogram.Rd | 62 ++++++-----
| man/shuffle.Rd | 34 +++---
| man/sort_2_clusters_vectors.Rd | 31 +++---
| man/sort_dist_mat.Rd | 11 +-
| man/sort_levels_values.Rd | 49 ++++-----
| man/tanglegram.Rd | 23 ++--
| man/unbranch.Rd | 14 ++-
| man/unclass_dend.Rd | 5 +-
| man/untangle_random_search.Rd | 75 ++++++--------
| man/untangle_step_rotate_1side.Rd | 64 +++++-------
| man/untangle_step_rotate_2side.Rd | 57 +++++-----
| 73 files changed, 1170 insertions(+), 1351 deletions(-)
* 2014-07-08(Tal Galili) untangle_DendSer - a new untangle function (this time, only for dendlist), for leverging the serialization package for some more heuristics. |e6c4a48|
| ChangeLog | 35 ++++++++++++++++--
| NAMESPACE | 7 ++++
| NEWS | 1 +
| R/untangle.r | 87 +++++++++++++++++++++++++++++++++++++++++++--
| man/DendSer.dendrogram.Rd | 38 ++++++++++++++++++++
| man/as.dendlist.Rd | 33 +++++++++++++++++
| man/is.dendlist.Rd | 23 ++++++++++++
| man/is_null_list.Rd | 38 ++++++++++++++++++++
| man/untangle.Rd | 84 +++++++++++++++++++++++++++++++++++++++++++
| man/untangle_DendSer.Rd | 42 ++++++++++++++++++++++
| 10 files changed, 382 insertions(+), 6 deletions(-)
* 2014-07-08(Tal Galili) Added tests for empty dendlist |d128b2b|
| inst/tests/test-dendlist.R | 38 ++++++++++++++++++++++++++++++++++++++
| 1 file changed, 38 insertions(+)
* 2014-07-08(Tal Galili) Added "untangle" - a master function to control all untangle functions (making it much easier to navigate this feature, as well as use it through %>% piping) |f276111|
| NEWS | 4 ++
| R/untangle.r | 100 +++++++++++++++++++++++++++++++++++++++++++
| inst/tests/test-untangle.r | 35 +++++++++++++++
| 3 files changed, 139 insertions(+)
* 2014-07-08(Tal Galili) Make sure that the main untangle functions will return a dendlist (and also that untangle_step_rotate_2side will be able to work with the new untangle_step_rotate_1side output) |01d5312|
| R/untangle.r | 35 ++++++++++++++++++++---------------
| 1 file changed, 20 insertions(+), 15 deletions(-)
* 2014-07-08(Tal Galili) tanglegram - a minor fix to the doc |1470d5a|
| R/tanglegram.r | 3 ++-
| 1 file changed, 2 insertions(+), 1 deletion(-)
* 2014-07-08(Tal Galili) added the functions: * is.dendlist - to check that an object is a dendlist * as.dendlist - to turn a list to a dendlist * (hidden) is_null_list |780e851|
| NEWS | 2 ++
| R/dendlist.R | 103 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 105 insertions(+)
* 2014-07-08(Tal Galili) Added a S3 dendlist method to shuffle |0af1ac2|
| NAMESPACE | 2 ++
| R/untangle.r | 24 ++++++++++++++++++++++++
| inst/tests/test-untangle.r | 10 ++++++----
| 3 files changed, 32 insertions(+), 4 deletions(-)
* 2014-07-08(Tal Galili) Modify the changelog to a more compact view. |096a505|
| ChangeLog | 5373 +++++++++++++++++++++++++++++++++++------------------------
| R/zzz.r | 6 +
| 2 files changed, 3231 insertions(+), 2148 deletions(-)
* 2014-07-08(Tal Galili) Start creating "ChangeLog" file, based on my git commits :) |75ab7a8|
| ChangeLog | 2148 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| R/zzz.r | 32 +
| 2 files changed, 2180 insertions(+)
* 2014-07-08(Tal Galili) Added credit to Dylan Beaudette for his dueling.dendrograms function (the origin of the tanglegram plot) |2ff8718|
| R/tanglegram.r | 5 +++++
| 1 file changed, 5 insertions(+)
* 2014-07-08(Tal Galili) Add pipes to the untangle docs |6715788|
| R/untangle.r | 6 ++----
| 1 file changed, 2 insertions(+), 4 deletions(-)
* 2014-07-08(Tal Galili) Add tests for entenglement on dendlist |39fef73|
| inst/tests/test-entanglement.r | 10 ++++++++--
| 1 file changed, 8 insertions(+), 2 deletions(-)
* 2014-07-08(Tal Galili) tanglegram - making its output be a dendlist object |d9db482|
| R/tanglegram.r | 16 +++++++++-------
| 1 file changed, 9 insertions(+), 7 deletions(-)
* 2014-07-07(Tal Galili) Added entanglement.dendlist function |f7f8c83|
| NEWS | 2 ++
| R/entanglement.r | 33 +++++++++++++++++++++++++++------
| 2 files changed, 29 insertions(+), 6 deletions(-)
* 2014-07-07(Tal Galili) tanglegram.dendlist - bug fix for it to work + some minor fixes to the doc |acd20bb|
| R/tanglegram.r | 6 +++---
| 1 file changed, 3 insertions(+), 3 deletions(-)
* 2014-07-07(Tal Galili) Move magrittr to Depends, to make it easier to work with examples (this way it will always get the chain %>% operator to be available to all examples) |ec46e29|
| DESCRIPTION | 4 ++--
| NEWS | 4 ++--
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2014-07-07(Tal Galili) Added horiz and continue paramters to the click_rotate function |e19f738|
| R/rotate.r | 43 ++++++++++++++--------
| man/rotate.Rd | 110 +++++++++++++++++++++++++-------------------------------
| 2 files changed, 77 insertions(+), 76 deletions(-)
* 2014-07-06(Tal Galili) Check dendlist works (new tests) |c5866a8|
| DESCRIPTION | 1 +
| NEWS | 4 ++++
| inst/tests/test-dendlist.R | 23 +++++++++++++++++++++++
| 3 files changed, 28 insertions(+)
* 2014-07-06(Tal Galili) Updated DESCRIPTION and NEWS |1ce17d7|
| DESCRIPTION | 9 +++++----
| NEWS | 29 +++++++++++++++++++++++++++++
| 2 files changed, 34 insertions(+), 4 deletions(-)
* 2014-07-06(Tal Galili) Added the click_rotate function (thanks to Andrej-Nikolai Spiess) |c455d60|
| NAMESPACE | 2 ++
| R/rotate.r | 76 +++++++++++++++++++++++++++++++++++++++++++++++++++
| man/click_rotate.Rd | 47 +++++++++++++++++++++++++++++++
| 3 files changed, 125 insertions(+)
* 2014-07-05(Tal Galili) Added tanglegramm.dendlist S3 method |20e4c79|
| NAMESPACE | 1 +
| R/attr_access.r | 2 +-
| R/tanglegram.r | 20 +++++-
| man/tanglegram.Rd | 179 ++++++++++++++++++++++++----------------------------
| 4 files changed, 102 insertions(+), 100 deletions(-)
* 2014-07-05(Tal Galili) Make dendlist handle hclust and phylo |c74f06a|
| R/dendlist.R | 21 ++++++++++++++++++---
| 1 file changed, 18 insertions(+), 3 deletions(-)
* 2014-07-04(Tal Galili) dendlist - a function which creates a list of dendrogram of the new "dendlist" class. |2dec5f9|
| NAMESPACE | 3 ++
| R/dendlist.R | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
| man/dendlist.Rd | 38 ++++++++++++++++++++
| 3 files changed, 145 insertions(+)
* 2014-04-26(Tal Galili) Version 0.14.3 - minor changes to DESCRIPTION |70b93f9|
| DESCRIPTION | 4 ++--
| NEWS | 12 ++++++++++++
| 2 files changed, 14 insertions(+), 2 deletions(-)
* 2014-04-26(Tal Galili) minor fixes to examples |d7d3c86|
| R/color_branches.r | 1 +
| R/cutree.dendrogram.r | 2 +-
| 2 files changed, 2 insertions(+), 1 deletion(-)
* 2014-03-18(Tal Galili) Added dendextendRcpp (>= 0.5.0) to Suggests! |acd6f98|
| DESCRIPTION | 16 ++++++++--------
| 1 file changed, 8 insertions(+), 8 deletions(-)
* 2014-03-18(Tal Galili) Fixing spaces |b74e3ba|
| README.md | 3 +++
| 1 file changed, 3 insertions(+)
* 2014-03-18(Tal Galili) Fixing "jefferis" to full name |e2f9496|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2014-03-15(Tal Galili) Added dependency for R (>= 3.0.0) |25e3103|
| DESCRIPTION | 6 ++++--
| NEWS | 11 +++++++++++
| 2 files changed, 15 insertions(+), 2 deletions(-)
* 2014-03-15(Tal Galili) Note that the package will go on CRAN |8e92afb|
| DESCRIPTION | 1 -
| NEWS | 8 +++++++-
| 2 files changed, 7 insertions(+), 2 deletions(-)
* 2014-03-15(Tal Galili) Bumped to 0.14.1 |029e5a0|
| DESCRIPTION | 3 +--
| NEWS | 18 +++++++++++++++---
| 2 files changed, 16 insertions(+), 5 deletions(-)
* 2014-03-15(Tal Galili) Fix Undocumented arguments in documentation object 'dendextend_options' 'option' 'value' |a3d3520|
| R/zzz.r | 4 ++++
| man/dendextend_options.Rd | 7 +++++++
| 2 files changed, 11 insertions(+)
* 2014-03-15(Tal Galili) update test_rotate.r so it would make sure ape is loaded BEFORE dendextend. |067afc4|
| NEWS | 2 +-
| inst/tests/test-rotate.r | 14 ++++++++++++++
| 2 files changed, 15 insertions(+), 1 deletion(-)
* 2014-03-15(Tal Galili) dendextend_options (actually an enviornment + a function) - added |095861c|
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/zzz.r | 77 ++++++++++++++++++++++++++++-----------------
| man/dendextend_options.Rd | 27 ++++++++++++++++
| 4 files changed, 77 insertions(+), 30 deletions(-)
* 2014-03-15(Tal Galili) update tests to the new names in dendextendRcpp (dendextendRcpp_cut_lower_fun, dendextend_options) |d4c03b0|
| NEWS | 2 ++
| inst/tests/test-attr_access.r | 2 +-
| inst/tests/test-cut_lower_fun.r | 8 ++++----
| 3 files changed, 7 insertions(+), 5 deletions(-)
* 2014-03-15(Tal Galili) assign_dendextend_options - is now exported. |b0f1028|
| NAMESPACE | 1 +
| NEWS | 5 +++--
| R/zzz.r | 7 +++++++
| man/assign_dendextend_options.Rd | 10 ++++++++++
| 4 files changed, 21 insertions(+), 2 deletions(-)
* 2014-03-15(Tal Galili) Moved to passing the functions through "dendextend_options" instead of through "options" (Thanks to suggestions by Kurt Hornik and Uwe Ligges). |ce0c91b|
| DESCRIPTION | 9 +++++---
| NEWS | 14 +++++++++++++
| R/attr_access.r | 2 +-
| R/cut_lower_fun.r | 2 +-
| R/cutree.dendrogram.r | 2 +-
| R/zzz.r | 56 +++++++++++++++++++++++++++++++++++++++++++------
| 6 files changed, 73 insertions(+), 12 deletions(-)
* 2014-03-01(Tal Galili) Bump to version 0.13.0 |7c8c681|
| DESCRIPTION | 5 +++--
| NEWS | 26 ++++++++++++++++++++++++++
| README.md | 6 +++---
| 3 files changed, 32 insertions(+), 5 deletions(-)
* 2014-03-01(Tal Galili) Added a compressed version of the pdf tutorial. |68d7376|
| inst/doc/dendextend-tutorial.pdf | Bin 0 -> 569458 bytes
| 1 file changed, 0 insertions(+), 0 deletions(-)
* 2014-03-01(Tal Galili) assign_dendextend_options - we now pass all functions that have a Rcpp equivalent through "options". While this adds a bit of an overhead (sadly), it still gets a much faster speed gain, and without verious warnings that CRAN checks would not like. |4e47c40|
| NAMESPACE | 3 +++
| R/attr_access.r | 24 +++++++++++++++++++++++-
| R/cut_lower_fun.r | 15 ++++++++++++++-
| R/cutree.dendrogram.r | 28 +++++++++++++++++++++++++---
| R/dendextend-package.r | 2 +-
| R/zzz.r | 21 +++++++++++++++++++--
| man/cut_lower_fun.Rd | 1 +
| man/dendextend-package.Rd | 4 ++--
| man/get_branches_heights.Rd | 14 ++++++++++++++
| man/heights_per_k.dendrogram.Rd | 15 +++++++++++++++
| tests/test-all.r | 10 ++++++++--
| 11 files changed, 125 insertions(+), 12 deletions(-)
* 2014-03-01(Tal Galili) When comparing to dendextendRcpp - added condition to not make the check if the package is not loaded and in the search path (this way I could compare the tests with and without the dendextendRcpp package). |f7bad9b|
| inst/tests/test-cut_lower_fun.r | 148 +++++++++++++++++-----------------
| inst/tests/test-cutree.dendrogram.r | 6 +-
| 2 files changed, 79 insertions(+), 75 deletions(-)
* 2014-03-01(Tal Galili) added a minor test for dendextend_get_branches_heights - checking the function directly through the options. |523e604|
| inst/tests/test-attr_access.r | 4 +++-
| 1 file changed, 3 insertions(+), 1 deletion(-)
* 2014-02-03(Tal Galili) dendextend 0.12.2 is intended to be shipped to CRAN. |d86832f|
| NEWS | 27 ++++++++++++++++++++++++++-
| R/zzz.r | 29 ++++++++++++++++++++++++++++-
| 2 files changed, 54 insertions(+), 2 deletions(-)
* 2014-02-03(Tal Galili) Hidden "stats" functions have been added to a new file "imports_stats.r" with a new local copy for 'stats:::.memberDend' 'stats:::.midDend' 'stats:::midcache.dendrogram' 'stats:::plotNode' 'stats:::plotNodeLimit' with stats::: -> stats_ |62f874e|
| R/imports_stats.r | 285 ++++++++++++++++++++++++++++++++++++++++++++++++
| R/sample.dendrogram.r | 4 +-
| R/tanglegram.r | 16 +--
| R/trim.r | 2 +-
| R/unbranch.r | 2 +-
| 5 files changed, 297 insertions(+), 12 deletions(-)
* 2014-02-03(Tal Galili) dendextend:::cutree -> dendextend::cutree |c6db8e8|
| R/color_branches.r | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2014-02-03(Tal Galili) UPDATED DESCRIPTION: * Removed VignetteBuilder: knitr (until later) * Removed Suggests: dendextendRcpp, (until later) * fixed mis-spelled words: extanding (14:40) |b83bb5a|
| DESCRIPTION | 8 +++-----
| 1 file changed, 3 insertions(+), 5 deletions(-)
* 2014-02-03(Tal Galili) stats:::cutree -> stats::cutree |72eee44|
| R/cutree.dendrogram.r | 6 +++---
| inst/tests/test-cutree.dendrogram.r | 2 +-
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2014-02-02(Tal Galili) Fix "\examples lines wider than 100 characters:" in several places. |18a2420|
| NEWS | 1 +
| R/bk_method.r | 24 ++++++++++++++++--------
| R/color_branches.r | 6 ++++--
| R/cor_bakers_gamma.r | 3 ++-
| R/cutree.dendrogram.r | 7 ++++---
| R/nleaves.r | 15 ++++++++++-----
| R/trim.r | 10 ++++++++--
| man/Bk_plot.Rd | 3 ++-
| man/FM_index.Rd | 15 ++++++++++-----
| man/FM_index_profdpm.Rd | 6 ++++--
| man/color_branches.Rd | 6 ++++--
| man/cor_bakers_gamma.Rd | 3 ++-
| man/cutree_1k.dendrogram.Rd | 7 ++++---
| man/intersect_trees.Rd | 10 ++++++++--
| man/unclass_dend.Rd | 15 ++++++++++-----
| 15 files changed, 89 insertions(+), 42 deletions(-)
* 2014-02-02(Tal Galili) data(iris) -> data(iris, envir = environment()) |c5f56e4|
| NEWS | 2 ++
| R/as.dendrogram.randomForest.r | 2 +-
| R/color_branches.r | 6 +++---
| R/zzz.r | 8 ++++++++
| man/color_branches.Rd | 4 ++--
| 5 files changed, 16 insertions(+), 6 deletions(-)
* 2014-02-02(Tal Galili) Made sure to check dendextendRcpp is available before calling it. |c0b9bc0|
| DESCRIPTION | 6 ++---
| NEWS | 7 +++--
| inst/tests/test-bk_method.r | 32 +++++++++++-----------
| inst/tests/test-cor_bakers_gamma.r | 4 +--
| inst/tests/test-cut_lower_fun.r | 51 ++++++++++++++++++-----------------
| inst/tests/test-cutree.dendrogram.r | 20 ++++++++------
| inst/tests/test-entanglement.r | 4 +--
| tests/test-all.r | 2 +-
| 8 files changed, 68 insertions(+), 58 deletions(-)
* 2014-02-02(Tal Galili) Commented out manipulations on the search path and of assignInNamespace. (to avoid NOTES/warnings) |d40fc34|
| NEWS | 9 ++-
| R/attr_access.r | 4 +-
| R/cut_lower_fun.r | 6 +-
| R/cutree.dendrogram.r | 4 +-
| R/nleaves.r | 3 +-
| R/zzz.r | 160 +++++++++++++++++++-------------------
| man/cut_lower_fun.Rd | 1 -
| man/get_branches_heights.Rd | 1 -
| man/heights_per_k.dendrogram.Rd | 1 -
| 9 files changed, 99 insertions(+), 90 deletions(-)
* 2014-02-01(Tal Galili) Vignettes - getting the latest version. |6e073a7|
| ...xamples_4afbfd2a825a9cb1746e8a947dcd1ada.RData | Bin 3520 -> 0 bytes
| ..._examples_4afbfd2a825a9cb1746e8a947dcd1ada.rdb | Bin 9497 -> 0 bytes
| ..._examples_4afbfd2a825a9cb1746e8a947dcd1ada.rdx | Bin 179 -> 0 bytes
| ...correct_ba0710e2563b1d13774723d2f4cc3bdc.RData | Bin 2963 -> 0 bytes
| ...s_correct_ba0710e2563b1d13774723d2f4cc3bdc.rdb | 0
| ...s_correct_ba0710e2563b1d13774723d2f4cc3bdc.rdx | Bin 113 -> 0 bytes
| ...t_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.RData | Bin 3004 -> 0 bytes
| ...ust_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.rdb | 0
| ...ust_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.rdx | Bin 113 -> 0 bytes
| ...mples_1_029622319f287d8b49913a8360888f62.RData | Bin 3268 -> 0 bytes
| ...xamples_1_029622319f287d8b49913a8360888f62.rdb | Bin 4167 -> 0 bytes
| ...xamples_1_029622319f287d8b49913a8360888f62.rdx | Bin 153 -> 0 bytes
| ...ample_1_5611fd32e4958b7af1d3a861c0b0ac03.RData | Bin 3832 -> 0 bytes
| ...example_1_5611fd32e4958b7af1d3a861c0b0ac03.rdb | Bin 20576 -> 0 bytes
| ...example_1_5611fd32e4958b7af1d3a861c0b0ac03.rdx | Bin 266 -> 0 bytes
| ...ample_2_7b84c47fe53f8a70663ff1fa00920e54.RData | Bin 2924 -> 0 bytes
| ...example_2_7b84c47fe53f8a70663ff1fa00920e54.rdb | Bin 27124 -> 0 bytes
| ...example_2_7b84c47fe53f8a70663ff1fa00920e54.rdx | Bin 264 -> 0 bytes
| ...ample_3_7a56e3e58e6a7be600fce19c6856dc94.RData | Bin 2923 -> 0 bytes
| ...example_3_7a56e3e58e6a7be600fce19c6856dc94.rdb | Bin 16398 -> 0 bytes
| ...example_3_7a56e3e58e6a7be600fce19c6856dc94.rdx | Bin 265 -> 0 bytes
| ...wer_fun_11e6d15e4d39a2eca09990d42c1235c0.RData | Bin 3255 -> 0 bytes
| ...lower_fun_11e6d15e4d39a2eca09990d42c1235c0.rdb | Bin 2727 -> 0 bytes
| ...lower_fun_11e6d15e4d39a2eca09990d42c1235c0.rdx | Bin 136 -> 0 bytes
| ...heights_849ab68f2f2a2097dd7a0ed7aff83b86.RData | Bin 3252 -> 0 bytes
| ...s_heights_849ab68f2f2a2097dd7a0ed7aff83b86.rdb | Bin 2727 -> 0 bytes
| ...s_heights_849ab68f2f2a2097dd7a0ed7aff83b86.rdx | Bin 130 -> 0 bytes
| ...s_per_k_f9a2db4f130fcab9432e1d1577484543.RData | Bin 3248 -> 0 bytes
| ...hts_per_k_f9a2db4f130fcab9432e1d1577484543.rdb | Bin 2727 -> 0 bytes
| ...hts_per_k_f9a2db4f130fcab9432e1d1577484543.rdx | Bin 130 -> 0 bytes
| ...drogram_4e659e16709537f25caa621e291d2794.RData | Bin 3222 -> 0 bytes
| ...endrogram_4e659e16709537f25caa621e291d2794.rdb | Bin 2727 -> 0 bytes
| ...endrogram_4e659e16709537f25caa621e291d2794.rdx | Bin 130 -> 0 bytes
| ...ample_1_a6f852561e8ce9d553b9d2b27b424b22.RData | Bin 3823 -> 0 bytes
| ...example_1_a6f852561e8ce9d553b9d2b27b424b22.rdb | Bin 2409 -> 0 bytes
| ...example_1_a6f852561e8ce9d553b9d2b27b424b22.rdx | Bin 204 -> 0 bytes
| ...ation_1_dd930ca5c4802d808d8e1ff37bc0edef.RData | Bin 3502 -> 0 bytes
| ...ulation_1_dd930ca5c4802d808d8e1ff37bc0edef.rdb | Bin 7988 -> 0 bytes
| ...ulation_1_dd930ca5c4802d808d8e1ff37bc0edef.rdx | Bin 257 -> 0 bytes
| ...ation_2_a386542ebf46e61430ae6d546755ef8a.RData | Bin 3513 -> 0 bytes
| ...ulation_2_a386542ebf46e61430ae6d546755ef8a.rdb | Bin 8768 -> 0 bytes
| ...ulation_2_a386542ebf46e61430ae6d546755ef8a.rdx | Bin 259 -> 0 bytes
| ...ation_3_a2067a06e2dadc01a424503feeb67ad9.RData | Bin 3527 -> 0 bytes
| ...ulation_3_a2067a06e2dadc01a424503feeb67ad9.rdb | Bin 9118 -> 0 bytes
| ...ulation_3_a2067a06e2dadc01a424503feeb67ad9.rdx | Bin 269 -> 0 bytes
| ...on_CI_4_a4452373b91f83c32fa8ad187e0fa475.RData | Bin 3914 -> 0 bytes
| ...tion_CI_4_a4452373b91f83c32fa8ad187e0fa475.rdb | Bin 8375 -> 0 bytes
| ...tion_CI_4_a4452373b91f83c32fa8ad187e0fa475.rdx | Bin 310 -> 0 bytes
| ...ample_1_49438132f802c72c76330a0c6277e5c9.RData | Bin 3844 -> 0 bytes
| ...example_1_49438132f802c72c76330a0c6277e5c9.rdb | Bin 1636 -> 0 bytes
| ...example_1_49438132f802c72c76330a0c6277e5c9.rdx | Bin 174 -> 0 bytes
| ...ation_2_f52d3297030e8ccb9446f2dc58662c66.RData | Bin 3525 -> 0 bytes
| ...ulation_2_f52d3297030e8ccb9446f2dc58662c66.rdb | Bin 9947 -> 0 bytes
| ...ulation_2_f52d3297030e8ccb9446f2dc58662c66.rdx | Bin 264 -> 0 bytes
| ...on_CI_3_3243f384d2df989a75438b63f85f44f5.RData | Bin 3884 -> 0 bytes
| ...tion_CI_3_3243f384d2df989a75438b63f85f44f5.rdb | Bin 9380 -> 0 bytes
| ...tion_CI_3_3243f384d2df989a75438b63f85f44f5.rdx | Bin 308 -> 0 bytes
| ...on_CI_4_dd6497988cbed58310cbeaaabb6163b2.RData | Bin 3904 -> 0 bytes
| ...tion_CI_4_dd6497988cbed58310cbeaaabb6163b2.rdb | Bin 8389 -> 0 bytes
| ...tion_CI_4_dd6497988cbed58310cbeaaabb6163b2.rdx | Bin 308 -> 0 bytes
| ...glegram_4820b99e23c40b3df4be2cd55320490f.RData | Bin 3205 -> 0 bytes
| ...anglegram_4820b99e23c40b3df4be2cd55320490f.rdb | Bin 8590 -> 0 bytes
| ...anglegram_4820b99e23c40b3df4be2cd55320490f.rdx | Bin 170 -> 0 bytes
| ...ranches_df7b6dfc097a9c6cde2152189b405e32.RData | Bin 3828 -> 0 bytes
| ..._branches_df7b6dfc097a9c6cde2152189b405e32.rdb | Bin 51879 -> 0 bytes
| ..._branches_df7b6dfc097a9c6cde2152189b405e32.rdx | Bin 189 -> 0 bytes
| ...rs_plot_daac58f156bd023132ab44332d441f28.RData | Bin 3161 -> 0 bytes
| ...airs_plot_daac58f156bd023132ab44332d441f28.rdb | Bin 127 -> 0 bytes
| ...airs_plot_daac58f156bd023132ab44332d441f28.rdx | Bin 148 -> 0 bytes
| ...hunk-10_0854e43359590ce23429966d09b02815.RData | Bin 307 -> 0 bytes
| ...-chunk-10_0854e43359590ce23429966d09b02815.rdb | 0
| ...-chunk-10_0854e43359590ce23429966d09b02815.rdx | Bin 113 -> 0 bytes
| ...hunk-11_d0998d8fbc02d1b6575b886950562355.RData | Bin 327 -> 0 bytes
| ...-chunk-11_d0998d8fbc02d1b6575b886950562355.rdb | Bin 36 -> 0 bytes
| ...-chunk-11_d0998d8fbc02d1b6575b886950562355.rdx | Bin 130 -> 0 bytes
| ...hunk-12_ad4eab6c111317bd487ccce36f736a90.RData | Bin 368 -> 0 bytes
| ...-chunk-12_ad4eab6c111317bd487ccce36f736a90.rdb | Bin 67 -> 0 bytes
| ...-chunk-12_ad4eab6c111317bd487ccce36f736a90.rdx | Bin 130 -> 0 bytes
| ...hunk-13_a9b7eef6382ba74e22dd9268dc381f13.RData | Bin 311 -> 0 bytes
| ...-chunk-13_a9b7eef6382ba74e22dd9268dc381f13.rdb | Bin 67 -> 0 bytes
| ...-chunk-13_a9b7eef6382ba74e22dd9268dc381f13.rdx | Bin 130 -> 0 bytes
| ...hunk-14_8bdeda75791482f7fe0c15ca4add7f4d.RData | Bin 3006 -> 0 bytes
| ...-chunk-14_8bdeda75791482f7fe0c15ca4add7f4d.rdb | Bin 265 -> 0 bytes
| ...-chunk-14_8bdeda75791482f7fe0c15ca4add7f4d.rdx | Bin 128 -> 0 bytes
| ...hunk-15_bc3ceeeb91232d23574416482184aa73.RData | Bin 3092 -> 0 bytes
| ...-chunk-15_bc3ceeeb91232d23574416482184aa73.rdb | Bin 296 -> 0 bytes
| ...-chunk-15_bc3ceeeb91232d23574416482184aa73.rdx | Bin 131 -> 0 bytes
| ...hunk-16_4566da6efa80cf3df53d8a91be5f5cc3.RData | Bin 3194 -> 0 bytes
| ...-chunk-16_4566da6efa80cf3df53d8a91be5f5cc3.rdb | Bin 666 -> 0 bytes
| ...-chunk-16_4566da6efa80cf3df53d8a91be5f5cc3.rdx | Bin 163 -> 0 bytes
| ...hunk-17_180ef22b097680ce8849623318fc5899.RData | Bin 2860 -> 0 bytes
| ...-chunk-17_180ef22b097680ce8849623318fc5899.rdb | 0
| ...-chunk-17_180ef22b097680ce8849623318fc5899.rdx | Bin 113 -> 0 bytes
| ...hunk-18_718657d68309d4e0c45b4501ea8a9e83.RData | Bin 3131 -> 0 bytes
| ...-chunk-18_718657d68309d4e0c45b4501ea8a9e83.rdb | 0
| ...-chunk-18_718657d68309d4e0c45b4501ea8a9e83.rdx | Bin 113 -> 0 bytes
| ...hunk-19_d1af6f9960f0c005eccb931d7793bf6b.RData | Bin 3474 -> 0 bytes
| ...-chunk-19_d1af6f9960f0c005eccb931d7793bf6b.rdb | Bin 512 -> 0 bytes
| ...-chunk-19_d1af6f9960f0c005eccb931d7793bf6b.rdx | Bin 143 -> 0 bytes
| ...hunk-20_9f866b5b953b10f3b8d5b092eed33057.RData | Bin 2964 -> 0 bytes
| ...-chunk-20_9f866b5b953b10f3b8d5b092eed33057.rdb | Bin 519 -> 0 bytes
| ...-chunk-20_9f866b5b953b10f3b8d5b092eed33057.rdx | Bin 143 -> 0 bytes
| ...hunk-21_8a160c3dee2afef22ce093e3668819de.RData | Bin 3472 -> 0 bytes
| ...-chunk-21_8a160c3dee2afef22ce093e3668819de.rdb | Bin 761 -> 0 bytes
| ...-chunk-21_8a160c3dee2afef22ce093e3668819de.rdx | Bin 155 -> 0 bytes
| ...hunk-22_a00ca74792504d853d3e8938a2d4dc0f.RData | Bin 3164 -> 0 bytes
| ...-chunk-22_a00ca74792504d853d3e8938a2d4dc0f.rdb | 0
| ...-chunk-22_a00ca74792504d853d3e8938a2d4dc0f.rdx | Bin 113 -> 0 bytes
| ...hunk-23_32ab7758407c06a18f8c0738d91da189.RData | Bin 3266 -> 0 bytes
| ...-chunk-23_32ab7758407c06a18f8c0738d91da189.rdb | Bin 985 -> 0 bytes
| ...-chunk-23_32ab7758407c06a18f8c0738d91da189.rdx | Bin 169 -> 0 bytes
| ...hunk-24_e2fb976bd1c4ddd539d48664c820d3e8.RData | Bin 3092 -> 0 bytes
| ...-chunk-24_e2fb976bd1c4ddd539d48664c820d3e8.rdb | Bin 1028 -> 0 bytes
| ...-chunk-24_e2fb976bd1c4ddd539d48664c820d3e8.rdx | Bin 176 -> 0 bytes
| ...hunk-25_cebb76da215882e646d5949e7741bb6f.RData | Bin 3201 -> 0 bytes
| ...-chunk-25_cebb76da215882e646d5949e7741bb6f.rdb | Bin 1071 -> 0 bytes
| ...-chunk-25_cebb76da215882e646d5949e7741bb6f.rdx | Bin 172 -> 0 bytes
| ...hunk-26_565dc1be57a60e1f915586415a455837.RData | Bin 3458 -> 0 bytes
| ...-chunk-26_565dc1be57a60e1f915586415a455837.rdb | Bin 562 -> 0 bytes
| ...-chunk-26_565dc1be57a60e1f915586415a455837.rdx | Bin 141 -> 0 bytes
| ...hunk-27_2b1e0e0b0ed387ea5b59f6dde28cb372.RData | Bin 3288 -> 0 bytes
| ...-chunk-27_2b1e0e0b0ed387ea5b59f6dde28cb372.rdb | Bin 1952 -> 0 bytes
| ...-chunk-27_2b1e0e0b0ed387ea5b59f6dde28cb372.rdx | Bin 172 -> 0 bytes
| ...chunk-2_b4628ab5709db378bcab1727e34e1a30.RData | Bin 488 -> 0 bytes
| ...d-chunk-2_b4628ab5709db378bcab1727e34e1a30.rdb | 0
| ...d-chunk-2_b4628ab5709db378bcab1727e34e1a30.rdx | Bin 113 -> 0 bytes
| ...hunk-30_81ab30eb315472d1e8c00b2edf11b5d8.RData | Bin 3347 -> 0 bytes
| ...-chunk-30_81ab30eb315472d1e8c00b2edf11b5d8.rdb | Bin 760 -> 0 bytes
| ...-chunk-30_81ab30eb315472d1e8c00b2edf11b5d8.rdx | Bin 141 -> 0 bytes
| ...hunk-31_c0f390969f965340b112bb54614c5ea0.RData | Bin 4255 -> 0 bytes
| ...-chunk-31_c0f390969f965340b112bb54614c5ea0.rdb | Bin 954 -> 0 bytes
| ...-chunk-31_c0f390969f965340b112bb54614c5ea0.rdx | Bin 158 -> 0 bytes
| ...hunk-32_035887295a5884b323b1e65c8c65dd5a.RData | Bin 3314 -> 0 bytes
| ...-chunk-32_035887295a5884b323b1e65c8c65dd5a.rdb | Bin 9082 -> 0 bytes
| ...-chunk-32_035887295a5884b323b1e65c8c65dd5a.rdx | Bin 202 -> 0 bytes
| ...hunk-33_c9bfcda22efd46a0858e444c19ad4d39.RData | Bin 3165 -> 0 bytes
| ...-chunk-33_c9bfcda22efd46a0858e444c19ad4d39.rdb | Bin 8534 -> 0 bytes
| ...-chunk-33_c9bfcda22efd46a0858e444c19ad4d39.rdx | Bin 182 -> 0 bytes
| ...hunk-34_4cad004366f0784e24de81f2f1e1a5b1.RData | Bin 3372 -> 0 bytes
| ...-chunk-34_4cad004366f0784e24de81f2f1e1a5b1.rdb | Bin 3305 -> 0 bytes
| ...-chunk-34_4cad004366f0784e24de81f2f1e1a5b1.rdx | Bin 211 -> 0 bytes
| ...hunk-35_c84407e79fe989eb7f3fdc6fddcdb3b9.RData | Bin 3107 -> 0 bytes
| ...-chunk-35_c84407e79fe989eb7f3fdc6fddcdb3b9.rdb | Bin 1824 -> 0 bytes
| ...-chunk-35_c84407e79fe989eb7f3fdc6fddcdb3b9.rdx | Bin 136 -> 0 bytes
| ...hunk-36_69145b2450999a80e4893d8ba64db6dd.RData | Bin 3282 -> 0 bytes
| ...-chunk-36_69145b2450999a80e4893d8ba64db6dd.rdb | Bin 1339 -> 0 bytes
| ...-chunk-36_69145b2450999a80e4893d8ba64db6dd.rdx | Bin 164 -> 0 bytes
| ...hunk-37_b1ba3f3d9a8a8cc37716b304f0834850.RData | Bin 3130 -> 0 bytes
| ...-chunk-37_b1ba3f3d9a8a8cc37716b304f0834850.rdb | Bin 1017 -> 0 bytes
| ...-chunk-37_b1ba3f3d9a8a8cc37716b304f0834850.rdx | Bin 137 -> 0 bytes
| ...hunk-38_536de094e0e3e4ccc261c1918659f094.RData | Bin 3116 -> 0 bytes
| ...-chunk-38_536de094e0e3e4ccc261c1918659f094.rdb | Bin 1035 -> 0 bytes
| ...-chunk-38_536de094e0e3e4ccc261c1918659f094.rdx | Bin 136 -> 0 bytes
| ...hunk-39_6081bd526faf34d32cd6a13be83e6937.RData | Bin 3071 -> 0 bytes
| ...-chunk-39_6081bd526faf34d32cd6a13be83e6937.rdb | 0
| ...-chunk-39_6081bd526faf34d32cd6a13be83e6937.rdx | Bin 113 -> 0 bytes
| ...chunk-3_2b65de8658503fe47d1d10c4cb83073c.RData | Bin 514 -> 0 bytes
| ...d-chunk-3_2b65de8658503fe47d1d10c4cb83073c.rdb | Bin 1847 -> 0 bytes
| ...d-chunk-3_2b65de8658503fe47d1d10c4cb83073c.rdx | Bin 175 -> 0 bytes
| ...chunk-4_8d9acbb5d1f738b78a4e4d01a7c12331.RData | Bin 518 -> 0 bytes
| ...d-chunk-4_8d9acbb5d1f738b78a4e4d01a7c12331.rdb | 0
| ...d-chunk-4_8d9acbb5d1f738b78a4e4d01a7c12331.rdx | Bin 113 -> 0 bytes
| ...chunk-5_47af34f72262629ec1361d6f77945080.RData | Bin 463 -> 0 bytes
| ...d-chunk-5_47af34f72262629ec1361d6f77945080.rdb | Bin 38 -> 0 bytes
| ...d-chunk-5_47af34f72262629ec1361d6f77945080.rdx | Bin 135 -> 0 bytes
| ...chunk-6_9fd4890494b261cc7b5cb2c7169b4458.RData | Bin 473 -> 0 bytes
| ...d-chunk-6_9fd4890494b261cc7b5cb2c7169b4458.rdb | 0
| ...d-chunk-6_9fd4890494b261cc7b5cb2c7169b4458.rdx | Bin 113 -> 0 bytes
| ...chunk-7_1027ff91092bfb1b34b33071e7672401.RData | Bin 287 -> 0 bytes
| ...d-chunk-7_1027ff91092bfb1b34b33071e7672401.rdb | 0
| ...d-chunk-7_1027ff91092bfb1b34b33071e7672401.rdx | Bin 113 -> 0 bytes
| ...chunk-8_8fb95628a4ed34b21ac6737e13bd30fd.RData | Bin 456 -> 0 bytes
| ...d-chunk-8_8fb95628a4ed34b21ac6737e13bd30fd.rdb | Bin 1866 -> 0 bytes
| ...d-chunk-8_8fb95628a4ed34b21ac6737e13bd30fd.rdx | Bin 176 -> 0 bytes
| ...chunk-9_fa9394504afd6a07fa83f4d539ad4911.RData | Bin 270 -> 0 bytes
| ...d-chunk-9_fa9394504afd6a07fa83f4d539ad4911.rdb | 0
| ...d-chunk-9_fa9394504afd6a07fa83f4d539ad4911.rdx | Bin 113 -> 0 bytes
| ...example_802a64d3a4c0dd3e9bb0e2a4dee353da.RData | Bin 3699 -> 0 bytes
| ...e_example_802a64d3a4c0dd3e9bb0e2a4dee353da.rdb | Bin 6426 -> 0 bytes
| ...e_example_802a64d3a4c0dd3e9bb0e2a4dee353da.rdx | Bin 205 -> 0 bytes
| vignettes/dendextend-tutorial-concordance.tex | 14 +-
| vignettes/dendextend-tutorial.log | 1205 +--
| vignettes/dendextend-tutorial.pdf | 8003 ++++++++++---------
| vignettes/dendextend-tutorial.rnw | 21 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 240890 -> 238204 bytes
| vignettes/dendextend-tutorial.tex | 331 +-
| vignettes/figure/Bk_plot_for_dends_correct.pdf | Bin 20591 -> 20591 bytes
| vignettes/figure/Bk_plot_for_hclust_WRONG.pdf | Bin 29264 -> 29264 bytes
| vignettes/figure/FM_permutation_example_1.pdf | Bin 10674 -> 10674 bytes
| vignettes/figure/FM_permutation_example_2.pdf | Bin 10392 -> 10392 bytes
| vignettes/figure/FM_permutation_example_3.pdf | Bin 9977 -> 9977 bytes
| vignettes/figure/cor_bakers_gamma_example_11.pdf | Bin 5053 -> 5053 bytes
| vignettes/figure/cor_bakers_gamma_example_12.pdf | Bin 5082 -> 5082 bytes
| vignettes/figure/cor_bakers_gamma_example_13.pdf | Bin 5053 -> 5054 bytes
| vignettes/figure/cor_bakers_gamma_example_14.pdf | Bin 5056 -> 5057 bytes
| .../figure/cor_bakers_gamma_simulation_1.pdf | Bin 7148 -> 7148 bytes
| .../figure/cor_bakers_gamma_simulation_2.pdf | Bin 7609 -> 7609 bytes
| .../figure/cor_bakers_gamma_simulation_3.pdf | Bin 7596 -> 7596 bytes
| .../figure/cor_bakers_gamma_simulation_CI_41.pdf | Bin 5047 -> 5047 bytes
| .../figure/cor_bakers_gamma_simulation_CI_42.pdf | Bin 4848 -> 4848 bytes
| .../figure/cor_bakers_gamma_simulation_CI_43.pdf | Bin 7496 -> 7485 bytes
| vignettes/figure/cor_cophenetic_simulation_2.pdf | Bin 7663 -> 7663 bytes
| .../figure/cor_cophenetic_simulation_CI_3.pdf | Bin 7152 -> 7152 bytes
| .../figure/cor_cophenetic_simulation_CI_4.pdf | Bin 7524 -> 7524 bytes
| vignettes/figure/first_tanglegram.pdf | Bin 15798 -> 15816 bytes
| vignettes/figure/iris_colored_branches.pdf | Bin 17747 -> 17747 bytes
| vignettes/figure/iris_colored_pairs_plot.pdf | Bin 74472 -> 74472 bytes
| vignettes/figure/unnamed-chunk-19.pdf | Bin 4578 -> 4578 bytes
| vignettes/figure/unnamed-chunk-23.pdf | Bin 4921 -> 4921 bytes
| vignettes/figure/unnamed-chunk-24.pdf | Bin 4576 -> 4576 bytes
| vignettes/figure/unnamed-chunk-25.pdf | Bin 4925 -> 4925 bytes
| vignettes/figure/unnamed-chunk-26.pdf | Bin 4564 -> 4564 bytes
| vignettes/figure/unnamed-chunk-27.pdf | Bin 5273 -> 5273 bytes
| vignettes/figure/unnamed-chunk-28.pdf | Bin 4694 -> 4694 bytes
| vignettes/figure/unnamed-chunk-29.pdf | Bin 5655 -> 5655 bytes
| vignettes/figure/unnamed-chunk-30.pdf | Bin 5374 -> 5374 bytes
| vignettes/figure/unnamed-chunk-32.pdf | Bin 15665 -> 15728 bytes
| vignettes/figure/unnamed-chunk-33.pdf | Bin 15732 -> 15779 bytes
| vignettes/figure/unnamed-chunk-34.pdf | Bin 0 -> 6850 bytes
| vignettes/figure/unnamed-chunk-35.pdf | Bin 0 -> 6847 bytes
| vignettes/figure/unnamed-chunk-36.pdf | Bin 0 -> 6824 bytes
| vignettes/figure/unnamed-chunk-37.pdf | Bin 0 -> 6832 bytes
| vignettes/figure/unnamed-chunk-38.pdf | Bin 0 -> 6815 bytes
| vignettes/figure/unnamed-chunk-39.pdf | Bin 0 -> 6961 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| .../untangle_step_rotate_2side_example1.pdf | Bin 6158 -> 6158 bytes
| .../untangle_step_rotate_2side_example2.pdf | Bin 6137 -> 6137 bytes
| .../untangle_step_rotate_2side_example3.pdf | Bin 6154 -> 6154 bytes
| .../untangle_step_rotate_2side_example4.pdf | Bin 6141 -> 6141 bytes
| .../untangle_step_rotate_2side_example5.pdf | Bin 5714 -> 5714 bytes
| .../untangle_step_rotate_2side_example6.pdf | Bin 6163 -> 6163 bytes
| 231 files changed, 5284 insertions(+), 4290 deletions(-)
* 2014-02-01(Tal Galili) rotate - Remove the "flip" command in the example (after I noticed that "rev" does this just fine...) |4e2b110|
| NEWS | 2 ++
| R/rotate.r | 4 ++--
| man/rotate.Rd | 4 ++--
| 3 files changed, 6 insertions(+), 4 deletions(-)
* 2014-02-01(Tal Galili) Fixed the usage of person() in DESCRIPTION. (props goes to Uwe Ligges for his input) |28d84d8|
| DESCRIPTION | 15 ++++++++-------
| NEWS | 2 +-
| 2 files changed, 9 insertions(+), 8 deletions(-)
* 2014-02-01(Tal Galili) Fix "Argument items with no description in Rd object": 'plot_horiz.dendrogram', 'untangle_step_rotate_1side'. |6173ec9|
| NEWS | 2 +-
| R/tanglegram.r | 2 +-
| R/untangle.r | 2 +-
| man/plot_horiz.dendrogram.Rd | 3 ++-
| man/untangle_step_rotate_1side.Rd | 4 +++-
| 5 files changed, 8 insertions(+), 5 deletions(-)
* 2014-02-01(Tal Galili) Fix "Objects in \usage without \alias in documentation object 'shuffle'": 'shuffle.dendrogram' 'shuffle.hclust' 'shuffle.phylo' |87ec513|
| NEWS | 3 +++
| R/untangle.r | 4 +++-
| man/shuffle.Rd | 3 +++
| 3 files changed, 9 insertions(+), 1 deletion(-)
* 2014-02-01(Tal Galili) Fix "Undocumented arguments in documentation object" for: * 'bakers_gamma_for_2_k_matrix' * 'cor_bakers_gamma' * 'cut_lower_fun' |35bf958|
| NEWS | 4 ++++
| R/cor_bakers_gamma.r | 5 +++--
| R/cut_lower_fun.r | 1 +
| man/bakers_gamma_for_2_k_matrix.Rd | 4 ++--
| man/cor_bakers_gamma.Rd | 5 ++++-
| man/cut_lower_fun.Rd | 2 ++
| 6 files changed, 16 insertions(+), 5 deletions(-)
* 2014-02-01(Tal Galili) Fix "'library' or 'require' call not declared from: 'ape'" by commenting-off every "require(ape)" command in the code, since it is already mentioned in imports! (see: http://stackoverflow.com/questions/15648772/how-do-i-prevent-r-library-or-require-calls-not-declared-warnings-when-dev) The problem still persists because of .onLoad in zzz.r, but we'll look into this later... |651bd98|
| NEWS | 4 +++-
| R/nleaves.r | 7 +++----
| R/rotate.r | 6 +++---
| R/trim.r | 2 +-
| R/unbranch.r | 2 +-
| R/zzz.r | 7 +++++--
| man/rotate.Rd | 2 +-
| 7 files changed, 17 insertions(+), 13 deletions(-)
* 2014-02-01(Tal Galili) Fix "Argument names in code not in docs", for: edge.lwd dLeaf_left dLeaf_right main sub rank_branches hang match_order_by_labels cex_main cex_main_left cex_main_right cex_sub |1f58846|
| NEWS | 1 +
| R/tanglegram.r | 12 ++++++++++++
| man/tanglegram.Rd | 12 ++++++++++++
| 3 files changed, 25 insertions(+)
* 2014-02-01(Tal Galili) Fix "Mismatches in argument default values "tanglegram" |a4fe297|
| NEWS | 9 ++++++++-
| R/tanglegram.r | 6 +++---
| man/tanglegram.Rd | 6 +++---
| 3 files changed, 14 insertions(+), 7 deletions(-)
* 2014-02-01(Tal Galili) Fix "Codoc mismatches from documentation object 'rotate':" - by removing k and h (since I never got to implement them...) |12a24bf|
| NEWS | 1 +
| R/rotate.r | 15 +++++++++------
| man/rotate.Rd | 8 --------
| 3 files changed, 10 insertions(+), 14 deletions(-)
* 2014-02-01(Tal Galili) Fix Undocumented code objects: 'old_cut_lower_fun' 'old_get_branches_heights' 'old_heights_per_k.dendrogram'. By adding them as "#' @aliases" |13c28a1|
| NEWS | 2 ++
| R/attr_access.r | 2 ++
| R/cut_lower_fun.r | 2 ++
| R/cutree.dendrogram.r | 2 ++
| man/cut_lower_fun.Rd | 1 +
| man/get_branches_heights.Rd | 1 +
| man/heights_per_k.dendrogram.Rd | 1 +
| 7 files changed, 11 insertions(+)
* 2014-02-01(Tal Galili) Fix various "Missing link or links in documentation object" |cb607c6|
| NEWS | 8 +++++---
| NEWS.md | 2 +-
| R/color_branches.r | 2 +-
| R/cutree.dendrogram.r | 1 -
| R/entanglement.r | 8 ++++----
| R/tanglegram.r | 2 +-
| R/unbranch.r | 2 +-
| man/all_couple_rotations_at_k.Rd | 5 ++---
| man/cutree-methods.Rd | 1 -
| man/entanglement.Rd | 5 ++---
| man/flip_leaves.Rd | 4 ++--
| man/leaf_Colors.Rd | 2 +-
| man/match_order_by_labels.Rd | 2 +-
| man/match_order_dendrogram_by_old_order.Rd | 2 +-
| man/plot_horiz.dendrogram.Rd | 2 +-
| man/unbranch.Rd | 2 +-
| man/untangle_random_search.Rd | 4 ++--
| man/untangle_step_rotate_1side.Rd | 6 +++---
| man/untangle_step_rotate_2side.Rd | 6 +++---
| 19 files changed, 32 insertions(+), 34 deletions(-)
* 2014-02-01(Tal Galili) remove \link{untangle} from various .Rd (I never created this function...) |0d9c368|
| NEWS | 6 ++++--
| R/untangle.r | 10 +++++-----
| 2 files changed, 9 insertions(+), 7 deletions(-)
* 2014-02-01(Tal Galili) fix "Unknown package 'dendroextra' in Rd xrefs" in color_branches docs. |52b0ff4|
| NEWS | 4 ++++
| R/color_branches.r | 6 +++---
| R/tanglegram.r | 2 +-
| R/unbranch.r | 2 +-
| man/color_branches.Rd | 8 ++++----
| 5 files changed, 13 insertions(+), 9 deletions(-)
* 2014-02-01(Tal Galili) Add DESCRIPTION and NEWS to git. |e80c96f|
| DESCRIPTION | 40 ++++++++--------------------
| NEWS | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++---
| NEWS.md | 6 ++---
| R/zzz.r | 10 ++++---
| 4 files changed, 100 insertions(+), 39 deletions(-)
* 2014-02-01(Tal Galili) Return "as.phylo.dendrogram" by adding "ape" to "Imports" in DESCRIPTION and "import" to NAMESPACE. Also fixing consistancy (using x instead of object). |6706c68|
| NAMESPACE | 2 ++
| R/nleaves.r | 17 +++++++++++------
| 2 files changed, 13 insertions(+), 6 deletions(-)
* 2014-02-01(Tal Galili) Remove "as.phylo.dendrogram" so to not force the package to depend on "ape" |52f4780|
| NAMESPACE | 2 --
| R/dendextend.r | 15 +++++++++++++++
| R/nleaves.r | 18 +++++++++++-------
| 3 files changed, 26 insertions(+), 9 deletions(-)
* 2014-02-01(Tal Galili) Moved from ::: to :: (where possible with dendextendRcpp). |519cad5|
| NAMESPACE | 1 +
| R/cut_lower_fun.r | 2 +-
| R/cutree.dendrogram.r | 3 +--
| inst/tests/test-cut_lower_fun.r | 3 ++-
| inst/tests/test-cutree.dendrogram.r | 4 +++-
| man/cut_lower_fun.Rd | 2 +-
| vignettes/dendextend-tutorial.rnw | 8 ++++----
| 7 files changed, 13 insertions(+), 10 deletions(-)
* 2014-02-01(Tal Galili) Using 'talgalili/dendextend', in install_github |ec75abf|
| README.md | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2014-02-01(Tal Galili) Moved from ::: to :: (where possible). |f4cff30|
| R/rotate.r | 5 ++++-
| R/trim.r | 13 +++++++++----
| R/unbranch.r | 2 +-
| R/zzz.r | 12 +++++++++++-
| vignettes/dendextend-tutorial.rnw | 2 +-
| vignettes/dendextend-tutorial.tex | 2 +-
| 6 files changed, 27 insertions(+), 9 deletions(-)
* 2014-02-01(Tal Galili) cutree.dendrogram - turned into S3 (no longer exported) |20e1dae|
| man/cutree.dendrogram.Rd | 118 ---------------------------------------------
| 1 file changed, 118 deletions(-)
* 2014-02-01(Tal Galili) changed functions names: * trim -> prune * unroot -> unbranch |9ca729c|
| man/prune.Rd | 2 +-
| man/trim.Rd | 48 ------------------------------------------------
| man/trim_leaf.Rd | 32 --------------------------------
| man/unroot.Rd | 50 --------------------------------------------------
| 4 files changed, 1 insertion(+), 131 deletions(-)
* 2014-02-01(Tal Galili) cut_lower_fun acts diffirently on dendextendRcpp vs old dendextend, so I updated the tests to reflect that. |b520e84|
| inst/tests/test-cut_lower_fun.r | 25 ++++++++++++++++++-------
| 1 file changed, 18 insertions(+), 7 deletions(-)
* 2014-02-01(Tal Galili) S3methods no longer seem to be exported (due to something in roxygen2), I chose to update the tests accordingly. * cutree.hclust -> dendextend:::cutree.hclust * cutree.dendrogram -> dendextend:::cutree.dendrogram |e8ac80b|
| R/nleaves.r | 4 ++++
| inst/tests/test-cutree.dendrogram.r | 12 ++++++------
| 2 files changed, 10 insertions(+), 6 deletions(-)
* 2014-01-31(Tal Galili) Added to .Rbuildignore "vignettes/" (we'll deal with this later...) |4ea429e|
| .Rbuildignore | 3 ++-
| 1 file changed, 2 insertions(+), 1 deletion(-)
* 2014-01-31(Tal Galili) leaf_Colors - fix example (added "dend"). |0594889|
| R/color_branches.r | 1 +
| man/leaf_Colors.Rd | 1 +
| 2 files changed, 2 insertions(+)
* 2014-01-31(Tal Galili) exported prune_leaf |c572359|
| NAMESPACE | 1 +
| R/trim.r | 3 ++-
| man/prune_leaf.Rd | 2 +-
| man/trim_leaf.Rd | 2 +-
| 4 files changed, 5 insertions(+), 3 deletions(-)
* 2014-01-31(Tal Galili) README.md - invitation to get credit for using dendextend. |dcc55c3|
| README.md | 17 +++++++++++++++++
| 1 file changed, 17 insertions(+)
* 2014-01-31(Tal Galili) Added to .Rbuildignore: (large files which are not essential) * inst/doc/2013-09-05_Boston-useR * vignettes/figure |a2a4684|
| .Rbuildignore | 4 +++-
| 1 file changed, 3 insertions(+), 1 deletion(-)
* 2014-01-31(Tal Galili) Added "ape::" to as.phylo |e7cbf41|
| R/nleaves.r | 6 ++++--
| R/unbranch.r | 3 ++-
| 2 files changed, 6 insertions(+), 3 deletions(-)
* 2014-01-31(Tal Galili) Fix S3method in NAMESPACE |738d0ed|
| NAMESPACE | 29 +++++++++++------------------
| 1 file changed, 11 insertions(+), 18 deletions(-)
* 2014-01-31(Tal Galili) Fixing .Rd indentation. |8c68f20|
| man/Bk.Rd | 42 +++++-----
| man/Bk_permutations.Rd | 57 +++++++-------
| man/Bk_plot.Rd | 79 +++++++++----------
| man/FM_index.Rd | 56 +++++++-------
| man/FM_index_R.Rd | 54 +++++++------
| man/FM_index_permutation.Rd | 26 +++----
| man/FM_index_profdpm.Rd | 70 +++++++++--------
| man/all_couple_rotations_at_k.Rd | 23 +++---
| man/as_hclust_fixed.Rd | 14 ++--
| man/assign_values_to_branches_edgePar.Rd | 13 ++--
| man/assign_values_to_leaves_nodePar.Rd | 13 ++--
| man/bakers_gamma_for_2_k_matrix.Rd | 9 +--
| man/color_branches.Rd | 85 ++++++++++-----------
| man/color_labels.Rd | 35 +++++----
| man/cor_bakers_gamma.Rd | 82 ++++++++++----------
| man/cor_cophenetic.Rd | 63 ++++++++-------
| man/count_terminal_nodes.Rd | 29 ++++---
| man/cut_lower_fun.Rd | 28 +++----
| man/cutree-methods.Rd | 100 ++++++++++++------------
| man/cutree_1h.dendrogram.Rd | 17 ++---
| man/cutree_1k.dendrogram.Rd | 33 ++++----
| man/dendextend-package.Rd | 6 +-
| man/duplicate_leaf.Rd | 16 ++--
| man/entanglement.Rd | 53 +++++++------
| man/fac2num.Rd | 16 ++--
| man/fix_members_attr.dendrogram.Rd | 10 +--
| man/flatten.dendrogram.Rd | 12 +--
| man/flip_leaves.Rd | 18 ++---
| man/get_branches_attr.Rd | 10 +--
| man/get_branches_heights.Rd | 9 +--
| man/get_childrens_heights.Rd | 10 +--
| man/get_leaves_attr.Rd | 17 ++---
| man/get_nodes_attr.Rd | 24 +++---
| man/hang.dendrogram.Rd | 22 +++---
| man/heights_per_k.dendrogram.Rd | 9 +--
| man/intersect_trees.Rd | 10 +--
| man/is.dendrogram.Rd | 6 +-
| man/is.hclust.Rd | 6 +-
| man/is.natural.number.Rd | 20 ++---
| man/is.phylo.Rd | 6 +-
| man/labels-assign.Rd | 36 +++++----
| man/labels_colors.Rd | 22 +++---
| man/leaf_Colors.Rd | 15 ++--
| man/lowest_common_branch.Rd | 18 ++---
| man/match_order_by_labels.Rd | 22 +++---
| man/match_order_dendrogram_by_old_order.Rd | 37 +++++----
| man/nleaves.Rd | 33 ++++----
| man/nnodes.Rd | 26 +++----
| man/order.dendrogram-assign.Rd | 12 +--
| man/plot_horiz.dendrogram.Rd | 39 +++++-----
| man/prune.Rd | 22 +++---
| man/prune_leaf.Rd | 8 +-
| man/raise.dendrogram.Rd | 6 +-
| man/rank_branches.Rd | 31 ++++----
| man/rank_order.dendrogram.Rd | 14 ++--
| man/remove_branches_edgePar.Rd | 13 ++--
| man/remove_leaves_nodePar.Rd | 12 +--
| man/rllply.Rd | 20 ++---
| man/rotate.Rd | 110 +++++++++++++--------------
| man/sample.dendrogram.Rd | 27 +++----
| man/shuffle.Rd | 37 +++++----
| man/sort_2_clusters_vectors.Rd | 12 +--
| man/sort_dist_mat.Rd | 9 +--
| man/sort_levels_values.Rd | 32 ++++----
| man/tanglegram.Rd | 77 ++++++++++---------
| man/unbranch.Rd | 16 ++--
| man/unclass_dend.Rd | 8 +-
| man/untangle_random_search.Rd | 26 +++----
| man/untangle_step_rotate_1side.Rd | 38 ++++-----
| man/untangle_step_rotate_2side.Rd | 31 ++++----
| 70 files changed, 987 insertions(+), 1030 deletions(-)
* 2014-01-31(Tal Galili) Added a placeholder for "as.dendrogram.randomForest" |2172548|
| R/as.dendrogram.randomForest.r | 54 ++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 54 insertions(+)
* 2013-12-10(Tal Galili) heirarchical -> Hierarchical |ee796c1|
| vignettes/dendextend-tutorial.rnw | 14 +++++++-------
| 1 file changed, 7 insertions(+), 7 deletions(-)
* 2013-09-05(Tal Galili) Added a fix to declare the UTF-8 encoding (for non-Windows users trying to install from github) |9bd9615|
| vignettes/dendextend-tutorial.rnw | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2013-09-01(Tal Galili) NEWS.md file added. |73e0f18|
| .Rbuildignore | 2 +-
| NEWS.md | 383 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| R/zzz.r | 1 +
| README.md | 6 +
| 4 files changed, 391 insertions(+), 1 deletion(-)
* 2013-08-31(Tal Galili) Added R code for the presentations. |e4a1fc2|
| .../2013-09-05_Boston-useR_01_intro.R | 8 +-
| .../2013-09-05_Boston-useR_01_intro.Rpres | 2 +-
| .../2013-09-05_Boston-useR_02_dendextend.R | 4 +-
| .../2013-09-05_Boston-useR_03_untangle_iris.R | 179 ++++++++++++++++++++
| .../2013-09-05_Boston-useR_04_tree_inference.R | 125 ++++++++++++++
| 5 files changed, 314 insertions(+), 4 deletions(-)
* 2013-08-31(Tal Galili) Updated presentations links |3197196|
| README.md | 6 +++++-
| 1 file changed, 5 insertions(+), 1 deletion(-)
* 2013-08-31(Tal Galili) Finished tanglegram and untangle. Finished statistical measures of similarity between trees. |0f265bf|
| DESCRIPTION | 2 +-
| NEWS | 8 +-
| inst/doc/2013-09-05_Boston-useR/.gitignore | 3 +-
| ...chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.RData | Bin 3018 -> 0 bytes
| ...d-chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.rdb | Bin 3642 -> 0 bytes
| ...d-chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.rdx | Bin 175 -> 0 bytes
| .../dend1_plot_1.png | Bin 0 -> 3877 bytes
| .../precip_dend5_plot_2.png | Bin 0 -> 3334 bytes
| .../tanglegram_dend12_1.png | Bin 0 -> 4528 bytes
| .../unnamed-chunk-10.png | Bin 0 -> 7186 bytes
| .../unnamed-chunk-11.png | Bin 0 -> 2578 bytes
| .../unnamed-chunk-12.png | Bin 0 -> 2625 bytes
| .../unnamed-chunk-5.png | Bin 0 -> 4055 bytes
| .../unnamed-chunk-6.png | Bin 0 -> 6754 bytes
| .../unnamed-chunk-7.png | Bin 0 -> 6419 bytes
| .../unnamed-chunk-9.png | Bin 0 -> 2000 bytes
| ...2013-09-05_Boston-useR_04_tree_inference.Rpres | 182 ++-
| .../2013-09-05_Boston-useR_04_tree_inference.html | 1100 +++++++++++++++++++
| .../2013-09-05_Boston-useR_04_tree_inference.md | 229 +++-
| 19 files changed, 1466 insertions(+), 58 deletions(-)
* 2013-08-31(Tal Galili) Vignettes tweaks |c992a7b|
| .gitignore | 1 +
| vignettes/.gitignore | 1 +
| ...hunk-28_a920283370fb5e377c9ab52b0e8e6f00.RData | Bin 3490 -> 0 bytes
| ...-chunk-28_a920283370fb5e377c9ab52b0e8e6f00.rdb | Bin 1057 -> 0 bytes
| ...-chunk-28_a920283370fb5e377c9ab52b0e8e6f00.rdx | Bin 156 -> 0 bytes
| ...hunk-29_12f892b1ead1d73ff2f1d0c38721055f.RData | Bin 3333 -> 0 bytes
| ...-chunk-29_12f892b1ead1d73ff2f1d0c38721055f.rdb | Bin 2564 -> 0 bytes
| ...-chunk-29_12f892b1ead1d73ff2f1d0c38721055f.rdx | Bin 206 -> 0 bytes
| vignettes/dendextend-tutorial-concordance.tex | 2 +-
| vignettes/dendextend-tutorial.log | 22 +-
| vignettes/dendextend-tutorial.pdf | 1569 ++++++++++---------
| vignettes/dendextend-tutorial.synctex.gz | Bin 240665 -> 240890 bytes
| vignettes/dendextend-tutorial.tex | 18 +-
| vignettes/figure/unnamed-chunk-28.pdf | Bin 4694 -> 4694 bytes
| vignettes/figure/unnamed-chunk-29.pdf | Bin 5655 -> 5655 bytes
| 15 files changed, 814 insertions(+), 799 deletions(-)
* 2013-08-30(Tal Galili) "trim" is now called "prune"! |e783d26|
| DESCRIPTION | 7 +-
| NAMESPACE | 10 +-
| NEWS | 9 +-
| R/attr_access.r | 14 +-
| R/cutree.dendrogram.r | 4 +-
| R/sample.dendrogram.r | 6 +-
| R/tanglegram.r | 6 +-
| R/trim.r | 96 +++---
| README.md | 2 +-
| demo/dendextend.r | 2 +-
| .../2013-09-05_Boston-useR_02_dendextend.R | 8 +-
| .../2013-09-05_Boston-useR_02_dendextend.Rpres | 6 +-
| .../2013-09-05_Boston-useR_02_dendextend.html | 8 +-
| .../2013-09-05_Boston-useR_02_dendextend.md | 8 +-
| inst/tests/test-trim.r | 34 +-
| man/fix_members_attr.dendrogram.Rd | 10 +-
| man/intersect_trees.Rd | 14 +-
| man/prune.Rd | 48 +++
| man/prune_leaf.Rd | 32 ++
| man/rank_order.dendrogram.Rd | 4 +-
| man/sample.dendrogram.Rd | 2 +-
| man/tanglegram.Rd | 4 +-
| man/trim.Rd | 30 +-
| man/trim_leaf.Rd | 14 +-
| vignettes/dendextend-tutorial.bib | 2 +-
| vignettes/dendextend-tutorial.log | 4 +-
| vignettes/dendextend-tutorial.pdf | 328 ++++++++++----------
| vignettes/dendextend-tutorial.rnw | 18 +-
| vignettes/dendextend-tutorial.tex | 22 +-
| 29 files changed, 416 insertions(+), 336 deletions(-)
* 2013-08-30(Tal Galili) Finished tanglegram and untangle. We are left with |3689f21|
| NEWS | 3 +
| inst/doc/2013-09-05_Boston-useR/.gitignore | 3 +-
| .../2013-09-05_Boston-useR_01_intro.Rpres | 8 +-
| .../dend_hang_tree_1.png | Bin 0 -> 4731 bytes
| .../dend_rotating_example_1.png | Bin 0 -> 4759 bytes
| .../dend_trimming_example_1.png | Bin 0 -> 4139 bytes
| .../dend_unbranching_example_1.png | Bin 0 -> 4748 bytes
| .../first_tanglegram_with_code.png | Bin 0 -> 40772 bytes
| .../simple_tanglegram_1.png | Bin 2846 -> 3256 bytes
| .../simple_tanglegram_1_worst_case.png | Bin 4124 -> 4577 bytes
| .../simple_tanglegram_one_shuffle_1.png | Bin 2932 -> 3621 bytes
| .../simple_tanglegram_random_search_1.png | Bin 2296 -> 2846 bytes
| ...ple_tanglegram_step_rotate_1side_example_1.png | Bin 0 -> 2822 bytes
| .../tanglegram_iris_untangle_random.png | Bin 0 -> 42100 bytes
| .../unnamed-chunk-15.png | Bin 4731 -> 4755 bytes
| .../unnamed-chunk-16.png | Bin 4755 -> 4759 bytes
| .../unnamed-chunk-17.png | Bin 4731 -> 4748 bytes
| .../unnamed-chunk-18.png | Bin 4759 -> 22344 bytes
| .../unnamed-chunk-19.png | Bin 4748 -> 4759 bytes
| .../unnamed-chunk-20.png | Bin 0 -> 4748 bytes
| .../unnamed-chunk-21.png | Bin 4759 -> 4139 bytes
| .../unnamed-chunk-24.png | Bin 0 -> 22344 bytes
| .../2013-09-05_Boston-useR_02_dendextend.R | 122 +-
| .../2013-09-05_Boston-useR_02_dendextend.Rpres | 103 +-
| .../2013-09-05_Boston-useR_02_dendextend.html | 1666 +++++++++++++++++++
| .../2013-09-05_Boston-useR_02_dendextend.md | 95 +-
| .../first_tanglegram_with_2side_untangle.png | Bin 0 -> 18166 bytes
| .../first_tanglegram_with_2side_untangle_hang.png | Bin 0 -> 26292 bytes
| .../first_tanglegram_with_code.png | Bin 0 -> 29397 bytes
| .../first_tanglegram_with_random_untangle.png | Bin 0 -> 23574 bytes
| .../unnamed-chunk-4.png | Bin 0 -> 23574 bytes
| .../unnamed-chunk-7.png | Bin 0 -> 18112 bytes
| .../unnamed-chunk-9.png | Bin 0 -> 18112 bytes
| .../2013-09-05_Boston-useR_03_untangle_iris.Rpres | 184 ++
| .../2013-09-05_Boston-useR_03_untangle_iris.html | 1058 ++++++++++++
| .../2013-09-05_Boston-useR_03_untangle_iris.md | 200 +++
| .../__packages | 8 +
| ...ordered_ca9a216309a7a760068a06f608ab2ccd.RData | Bin 0 -> 2844 bytes
| ...m_ordered_ca9a216309a7a760068a06f608ab2ccd.rdb | Bin 0 -> 1975 bytes
| ...m_ordered_ca9a216309a7a760068a06f608ab2ccd.rdx | Bin 0 -> 154 bytes
| ...chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.RData | Bin 0 -> 3018 bytes
| ...d-chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.rdb | Bin 0 -> 3642 bytes
| ...d-chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.rdx | Bin 0 -> 175 bytes
| .../iris_tanglegram_ordered.png | Bin 0 -> 18166 bytes
| ...2013-09-05_Boston-useR_04_tree_inference.Rpres | 80 +
| .../2013-09-05_Boston-useR_04_tree_inference.md | 62 +
| 46 files changed, 3471 insertions(+), 121 deletions(-)
* 2013-08-30(Tal Galili) untangle_step_rotate_2side added k_seq parameter. |b3aab6a|
| R/untangle.r | 13 ++++++++-----
| man/untangle_step_rotate_2side.Rd | 7 ++++++-
| 2 files changed, 14 insertions(+), 6 deletions(-)
* 2013-08-30(Tal Galili) tanglegram now has "sub" and "cex_sub" parameters. |eecbd30|
| NEWS | 7 +++++++
| R/tanglegram.r | 7 ++++++-
| man/tanglegram.Rd | 6 +++++-
| 3 files changed, 18 insertions(+), 2 deletions(-)
* 2013-08-30(Tal Galili) Seperated 2013-09-05_Boston-useR.Rpres into two files (since RStudio is not able to handle them) |73d9714|
| NAMESPACE | 90 +-
| NEWS | 2 +
| R/tanglegram.r | 2 +-
| inst/doc/2013-09-05_Boston-useR/.gitignore | 3 +-
| .../first_tanglegram.png | Bin 39575 -> 0 bytes
| .../iris_colored_branches.png | Bin 16950 -> 0 bytes
| .../precip_dend_plot_1.png | Bin 3665 -> 0 bytes
| .../precip_dend_plot_2.png | Bin 3715 -> 0 bytes
| .../precip_subset__hclust_single_plot.png | Bin 3900 -> 0 bytes
| .../precip_subset__hclust_single_plot_rect.png | Bin 3833 -> 0 bytes
| .../unnamed-chunk-10.png | Bin 3862 -> 0 bytes
| .../unnamed-chunk-16.png | Bin 5737 -> 0 bytes
| .../unnamed-chunk-17.png | Bin 5737 -> 0 bytes
| .../unnamed-chunk-18.png | Bin 5737 -> 0 bytes
| .../unnamed-chunk-19.png | Bin 7510 -> 0 bytes
| .../unnamed-chunk-20.png | Bin 7510 -> 0 bytes
| .../unnamed-chunk-21.png | Bin 3900 -> 0 bytes
| .../unnamed-chunk-22.png | Bin 3900 -> 0 bytes
| .../unnamed-chunk-23.png | Bin 18165 -> 0 bytes
| .../unnamed-chunk-24.png | Bin 18165 -> 0 bytes
| .../unnamed-chunk-25.png | Bin 6132 -> 0 bytes
| .../unnamed-chunk-26.png | Bin 6132 -> 0 bytes
| .../unnamed-chunk-27.png | Bin 6132 -> 0 bytes
| .../unnamed-chunk-28.png | Bin 6132 -> 0 bytes
| .../unnamed-chunk-29.png | Bin 5869 -> 0 bytes
| .../unnamed-chunk-30.png | Bin 6132 -> 0 bytes
| .../unnamed-chunk-31.png | Bin 4719 -> 0 bytes
| .../unnamed-chunk-32.png | Bin 5869 -> 0 bytes
| .../unnamed-chunk-33.png | Bin 4755 -> 0 bytes
| .../unnamed-chunk-34.png | Bin 4139 -> 0 bytes
| .../unnamed-chunk-35.png | Bin 4755 -> 0 bytes
| .../unnamed-chunk-36.png | Bin 4731 -> 0 bytes
| .../unnamed-chunk-37.png | Bin 4755 -> 0 bytes
| .../unnamed-chunk-38.png | Bin 4731 -> 0 bytes
| .../unnamed-chunk-39.png | Bin 4759 -> 0 bytes
| .../unnamed-chunk-4.png | Bin 11298 -> 0 bytes
| .../unnamed-chunk-40.png | Bin 4748 -> 0 bytes
| .../unnamed-chunk-41.png | Bin 6132 -> 0 bytes
| .../unnamed-chunk-42.png | Bin 4759 -> 0 bytes
| .../unnamed-chunk-43.png | Bin 4748 -> 0 bytes
| .../unnamed-chunk-44.png | Bin 4139 -> 0 bytes
| .../unnamed-chunk-45.png | Bin 6153 -> 0 bytes
| .../unnamed-chunk-46.png | Bin 4139 -> 0 bytes
| .../unnamed-chunk-47.png | Bin 22344 -> 0 bytes
| .../unnamed-chunk-49.png | Bin 22344 -> 0 bytes
| .../unnamed-chunk-5.png | Bin 11621 -> 0 bytes
| .../unnamed-chunk-8.png | Bin 3862 -> 0 bytes
| .../unnamed-chunk-9.png | Bin 3862 -> 0 bytes
| .../2013-09-05_Boston-useR.R | 459 -----
| .../2013-09-05_Boston-useR.Rpres | 864 ---------
| .../2013-09-05_Boston-useR.html | 1803 -------------------
| .../2013-09-05_Boston-useR.md | 1161 ------------
| .../precip_dend_plot_1.png | Bin 0 -> 3665 bytes
| .../precip_dend_plot_2.png | Bin 0 -> 3715 bytes
| .../precip_subset__hclust_single_plot.png | Bin 0 -> 3900 bytes
| .../precip_subset__hclust_single_plot_rect.png | Bin 0 -> 3833 bytes
| .../unnamed-chunk-17.png | Bin 0 -> 5737 bytes
| .../unnamed-chunk-19.png | Bin 0 -> 7510 bytes
| .../unnamed-chunk-21.png | Bin 0 -> 3900 bytes
| .../unnamed-chunk-5.png | Bin 0 -> 11621 bytes
| .../2013-09-05_Boston-useR_01_intro.R | 192 ++
| .../2013-09-05_Boston-useR_01_intro.Rpres | 448 +++++
| .../2013-09-05_Boston-useR_01_intro.html | 1471 +++++++++++++++
| .../2013-09-05_Boston-useR_01_intro.md | 659 +++++++
| .../first_tanglegram.png | Bin 0 -> 39575 bytes
| .../iris_colored_branches.png | Bin 0 -> 16950 bytes
| .../simple_tanglegram_1.png | Bin 0 -> 2846 bytes
| .../simple_tanglegram_1_worst_case.png | Bin 0 -> 4124 bytes
| .../simple_tanglegram_one_shuffle_1.png | Bin 0 -> 2932 bytes
| .../simple_tanglegram_random_search_1.png | Bin 0 -> 2296 bytes
| .../unnamed-chunk-11.png | Bin 0 -> 5869 bytes
| .../unnamed-chunk-12.png | Bin 0 -> 4755 bytes
| .../unnamed-chunk-14.png | Bin 0 -> 4755 bytes
| .../unnamed-chunk-15.png | Bin 0 -> 4731 bytes
| .../unnamed-chunk-16.png | Bin 0 -> 4755 bytes
| .../unnamed-chunk-17.png | Bin 0 -> 4731 bytes
| .../unnamed-chunk-18.png | Bin 0 -> 4759 bytes
| .../unnamed-chunk-19.png | Bin 0 -> 4748 bytes
| .../unnamed-chunk-2.png | Bin 0 -> 18023 bytes
| .../unnamed-chunk-21.png | Bin 0 -> 4759 bytes
| .../unnamed-chunk-22.png | Bin 0 -> 4748 bytes
| .../unnamed-chunk-23.png | Bin 0 -> 4139 bytes
| .../unnamed-chunk-25.png | Bin 0 -> 4139 bytes
| .../unnamed-chunk-26.png | Bin 0 -> 22344 bytes
| .../unnamed-chunk-33.png | Bin 0 -> 3740 bytes
| .../unnamed-chunk-4.png | Bin 0 -> 6132 bytes
| .../unnamed-chunk-6.png | Bin 0 -> 6132 bytes
| .../unnamed-chunk-8.png | Bin 0 -> 5869 bytes
| .../unnamed-chunk-9.png | Bin 0 -> 6132 bytes
| .../2013-09-05_Boston-useR_02_dendextend.R | 378 ++++
| .../2013-09-05_Boston-useR_02_dendextend.Rpres | 671 +++++++
| .../2013-09-05_Boston-useR_02_dendextend.md | 853 +++++++++
| man/leaf_Colors.Rd | 2 +-
| vignettes/dendextend-tutorial.log | 2 +-
| vignettes/dendextend-tutorial.pdf | 13 +-
| vignettes/dendextend-tutorial.tex | 4 +-
| 96 files changed, 4733 insertions(+), 4344 deletions(-)
* 2013-08-29(Tal Galili) untangle_random_search - made sure the function will return the original trees if no better tree was found. |1d6d9fb|
| NEWS | 2 ++
| R/untangle.r | 2 ++
| 2 files changed, 4 insertions(+)
* 2013-08-29(Tal Galili) tanglegram now returns an invisible list with the two dendrograms (after they have been modified within the function). |d3b0f07|
| NEWS | 1 +
| R/tanglegram.r | 5 +++--
| man/tanglegram.Rd | 3 ++-
| 3 files changed, 6 insertions(+), 3 deletions(-)
* 2013-08-29(Tal Galili) Added "warn" parameter to: assign_values_to_leaves_nodePar, And set it to FALSE when used inside "tanglegram". |5e1abf1|
| NEWS | 1 +
| R/attr_access.r | 9 +++++++--
| R/tanglegram.r | 12 ++++++------
| man/assign_values_to_leaves_nodePar.Rd | 7 ++++++-
| 4 files changed, 20 insertions(+), 9 deletions(-)
* 2013-08-29(Tal Galili) color_labels - added a "warn" parameter. And also set the default (in case no k/h is supplied) - to just color all of the labels. |2fc659e|
| NEWS | 7 +++++++
| R/color_branches.r | 16 ++++++++++++----
| man/color_labels.Rd | 7 ++++++-
| man/tanglegram.Rd | 8 ++++++++
| 4 files changed, 33 insertions(+), 5 deletions(-)
* 2013-08-29(Tal Galili) Version bump to 0.11.0 |10d8cc3|
| DESCRIPTION | 14 ++++++++------
| NEWS | 12 ++++++++++++
| 2 files changed, 20 insertions(+), 6 deletions(-)
* 2013-08-29(Tal Galili) tangelgram - added cex_main parameter. |79ab582|
| R/tanglegram.r | 11 ++++++++++-
| 1 file changed, 10 insertions(+), 1 deletion(-)
* 2013-08-26(Tal Galili) Adding links to the documents, and a better "install" code sequence. |2c9b5b4|
| README.md | 10 ++++++++--
| 1 file changed, 8 insertions(+), 2 deletions(-)
* 2013-08-26(Tal Galili) Added auto purl for extracting the R code. |d86616c|
| .../2013-09-05_Boston-useR.R | 459 ++++++++++++++++++++
| .../2013-09-05_Boston-useR.Rpres | 5 +-
| 2 files changed, 462 insertions(+), 2 deletions(-)
* 2013-08-26(Tal Galili) Boston-useR presentation |d1f14cf|
| inst/doc/2013-09-05_Boston-useR/.gitignore | 1 +
| .../first_tanglegram.png | Bin 0 -> 39575 bytes
| .../iris_colored_branches.png | Bin 0 -> 16950 bytes
| .../precip_dend_plot_1.png | Bin 0 -> 3665 bytes
| .../precip_dend_plot_2.png | Bin 0 -> 3715 bytes
| .../precip_subset__hclust_single_plot.png | Bin 0 -> 3900 bytes
| .../precip_subset__hclust_single_plot_rect.png | Bin 0 -> 3833 bytes
| .../unnamed-chunk-10.png | Bin 0 -> 3862 bytes
| .../unnamed-chunk-16.png | Bin 0 -> 5737 bytes
| .../unnamed-chunk-17.png | Bin 0 -> 5737 bytes
| .../unnamed-chunk-18.png | Bin 0 -> 5737 bytes
| .../unnamed-chunk-19.png | Bin 0 -> 7510 bytes
| .../unnamed-chunk-20.png | Bin 0 -> 7510 bytes
| .../unnamed-chunk-21.png | Bin 0 -> 3900 bytes
| .../unnamed-chunk-22.png | Bin 0 -> 3900 bytes
| .../unnamed-chunk-23.png | Bin 0 -> 18165 bytes
| .../unnamed-chunk-24.png | Bin 0 -> 18165 bytes
| .../unnamed-chunk-25.png | Bin 0 -> 6132 bytes
| .../unnamed-chunk-26.png | Bin 0 -> 6132 bytes
| .../unnamed-chunk-27.png | Bin 0 -> 6132 bytes
| .../unnamed-chunk-28.png | Bin 0 -> 6132 bytes
| .../unnamed-chunk-29.png | Bin 0 -> 5869 bytes
| .../unnamed-chunk-30.png | Bin 0 -> 6132 bytes
| .../unnamed-chunk-31.png | Bin 0 -> 4719 bytes
| .../unnamed-chunk-32.png | Bin 0 -> 5869 bytes
| .../unnamed-chunk-33.png | Bin 0 -> 4755 bytes
| .../unnamed-chunk-34.png | Bin 0 -> 4139 bytes
| .../unnamed-chunk-35.png | Bin 0 -> 4755 bytes
| .../unnamed-chunk-36.png | Bin 0 -> 4731 bytes
| .../unnamed-chunk-37.png | Bin 0 -> 4755 bytes
| .../unnamed-chunk-38.png | Bin 0 -> 4731 bytes
| .../unnamed-chunk-39.png | Bin 0 -> 4759 bytes
| .../unnamed-chunk-4.png | Bin 0 -> 11298 bytes
| .../unnamed-chunk-40.png | Bin 0 -> 4748 bytes
| .../unnamed-chunk-41.png | Bin 0 -> 6132 bytes
| .../unnamed-chunk-42.png | Bin 0 -> 4759 bytes
| .../unnamed-chunk-43.png | Bin 0 -> 4748 bytes
| .../unnamed-chunk-44.png | Bin 0 -> 4139 bytes
| .../unnamed-chunk-45.png | Bin 0 -> 6153 bytes
| .../unnamed-chunk-46.png | Bin 0 -> 4139 bytes
| .../unnamed-chunk-47.png | Bin 0 -> 22344 bytes
| .../unnamed-chunk-49.png | Bin 0 -> 22344 bytes
| .../unnamed-chunk-5.png | Bin 0 -> 11621 bytes
| .../unnamed-chunk-8.png | Bin 0 -> 3862 bytes
| .../unnamed-chunk-9.png | Bin 0 -> 3862 bytes
| .../2013-09-05_Boston-useR.Rpres | 863 +++++++++
| .../2013-09-05_Boston-useR.html | 1803 +++++++++++++++++++
| .../2013-09-05_Boston-useR.md | 1161 ++++++++++++
| 48 files changed, 3828 insertions(+)
* 2013-08-24(Tal Galili) vignette - minor fixes |a286c6e|
| vignettes/dendextend-tutorial.bib | 11 -
| vignettes/dendextend-tutorial.blg | 6 +-
| vignettes/dendextend-tutorial.log | 116 +-
| vignettes/dendextend-tutorial.pdf | 2559 ++++++++++++++--------------
| vignettes/dendextend-tutorial.rnw | 2 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 240127 -> 240665 bytes
| vignettes/dendextend-tutorial.tex | 6 +-
| 7 files changed, 1316 insertions(+), 1384 deletions(-)
* 2013-08-22(Tal Galili) Updated the list of contributors to the package. |325c8df|
| DESCRIPTION | 7 ++++++-
| 1 file changed, 6 insertions(+), 1 deletion(-)
* 2013-08-21(Tal Galili) VIGNETTES: Added FM-index and Bk plot sections. |fba17c3|
| NEWS | 2 +-
| ...xamples_4afbfd2a825a9cb1746e8a947dcd1ada.RData | Bin 0 -> 3520 bytes
| ..._examples_4afbfd2a825a9cb1746e8a947dcd1ada.rdb | Bin 0 -> 9497 bytes
| ..._examples_4afbfd2a825a9cb1746e8a947dcd1ada.rdx | Bin 0 -> 179 bytes
| ...correct_ba0710e2563b1d13774723d2f4cc3bdc.RData | Bin 0 -> 2963 bytes
| ...s_correct_ba0710e2563b1d13774723d2f4cc3bdc.rdb | 0
| ...s_correct_ba0710e2563b1d13774723d2f4cc3bdc.rdx | Bin 0 -> 113 bytes
| ...t_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.RData | Bin 0 -> 3004 bytes
| ...ust_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.rdb | 0
| ...ust_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.rdx | Bin 0 -> 113 bytes
| ...mples_1_029622319f287d8b49913a8360888f62.RData | Bin 0 -> 3268 bytes
| ...xamples_1_029622319f287d8b49913a8360888f62.rdb | Bin 0 -> 4167 bytes
| ...xamples_1_029622319f287d8b49913a8360888f62.rdx | Bin 0 -> 153 bytes
| ...ample_1_5611fd32e4958b7af1d3a861c0b0ac03.RData | Bin 0 -> 3832 bytes
| ...example_1_5611fd32e4958b7af1d3a861c0b0ac03.rdb | Bin 0 -> 20576 bytes
| ...example_1_5611fd32e4958b7af1d3a861c0b0ac03.rdx | Bin 0 -> 266 bytes
| ...ample_2_7b84c47fe53f8a70663ff1fa00920e54.RData | Bin 0 -> 2924 bytes
| ...example_2_7b84c47fe53f8a70663ff1fa00920e54.rdb | Bin 0 -> 27124 bytes
| ...example_2_7b84c47fe53f8a70663ff1fa00920e54.rdx | Bin 0 -> 264 bytes
| ...ample_3_7a56e3e58e6a7be600fce19c6856dc94.RData | Bin 0 -> 2923 bytes
| ...example_3_7a56e3e58e6a7be600fce19c6856dc94.rdb | Bin 0 -> 16398 bytes
| ...example_3_7a56e3e58e6a7be600fce19c6856dc94.rdx | Bin 0 -> 265 bytes
| ...hunk-40_72720aff4e60fb7daa0fc155de695631.RData | Bin 0 -> 4201 bytes
| ...-chunk-40_72720aff4e60fb7daa0fc155de695631.rdb | Bin 0 -> 9497 bytes
| ...-chunk-40_72720aff4e60fb7daa0fc155de695631.rdx | Bin 0 -> 179 bytes
| ...hunk-40_d1ed410d3974e8360057fdf7e68751fb.RData | Bin 3125 -> 0 bytes
| ...-chunk-40_d1ed410d3974e8360057fdf7e68751fb.rdb | Bin 1509 -> 0 bytes
| ...-chunk-40_d1ed410d3974e8360057fdf7e68751fb.rdx | Bin 160 -> 0 bytes
| vignettes/dendextend-tutorial-concordance.tex | 6 +-
| vignettes/dendextend-tutorial.log | 270 +-
| vignettes/dendextend-tutorial.pdf | 4212 ++++++++++++-------
| vignettes/dendextend-tutorial.rnw | 232 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 223345 -> 240127 bytes
| vignettes/dendextend-tutorial.tex | 322 +-
| vignettes/figure/Bk_examples.pdf | Bin 0 -> 20539 bytes
| vignettes/figure/Bk_plot_for_dends_correct.pdf | Bin 0 -> 20591 bytes
| vignettes/figure/Bk_plot_for_hclust_WRONG.pdf | Bin 0 -> 29264 bytes
| vignettes/figure/FM_permutation_example_1.pdf | Bin 0 -> 10674 bytes
| vignettes/figure/FM_permutation_example_2.pdf | Bin 0 -> 10392 bytes
| vignettes/figure/FM_permutation_example_3.pdf | Bin 0 -> 9977 bytes
| vignettes/figure/unnamed-chunk-40.pdf | Bin 0 -> 20539 bytes
| 41 files changed, 3391 insertions(+), 1653 deletions(-)
* 2013-08-21(Tal Galili) New tests for Bk methods and some minor doc changes. |35df06c|
| NEWS | 4 ++++
| R/bk_method.r | 5 +++-
| inst/tests/test-bk_method.r | 56 +++++++++++++++++++++++++++++++++++++++++++
| man/FM_index_permutation.Rd | 1 +
| 4 files changed, 65 insertions(+), 1 deletion(-)
* 2013-08-20(Tal Galili) Version bump - 0.10.0 |0079a2c|
| DESCRIPTION | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2013-08-20(Tal Galili) Vignette - cut_lower_fun PDF and extra files are updated. |c08cec1|
| ...wer_fun_11e6d15e4d39a2eca09990d42c1235c0.RData | Bin 0 -> 3255 bytes
| ...lower_fun_11e6d15e4d39a2eca09990d42c1235c0.rdb | Bin 0 -> 2727 bytes
| ...lower_fun_11e6d15e4d39a2eca09990d42c1235c0.rdx | Bin 0 -> 136 bytes
| vignettes/dendextend-tutorial-concordance.tex | 4 +-
| vignettes/dendextend-tutorial.log | 62 +-
| vignettes/dendextend-tutorial.pdf | 1653 +++++++++----------
| vignettes/dendextend-tutorial.synctex.gz | Bin 223843 -> 223345 bytes
| vignettes/dendextend-tutorial.tex | 70 +-
| 8 files changed, 880 insertions(+), 909 deletions(-)
* 2013-08-20(Tal Galili) cut_lower_fun function added - it wraps the "cut" function, and is built to be masked by the function in dendextendRcpp in order to gain 4-14 speed gain. |987af61|
| DESCRIPTION | 1 +
| NAMESPACE | 1 +
| NEWS | 13 ++++++
| R/cut_lower_fun.r | 86 +++++++++++++++++++++++++++++++++++++
| R/cutree.dendrogram.r | 3 +-
| R/zzz.r | 15 +++++--
| inst/tests/test-cut_lower_fun.r | 78 +++++++++++++++++++++++++++++++++
| man/cut_lower_fun.Rd | 59 +++++++++++++++++++++++++
| vignettes/dendextend-tutorial.rnw | 12 ++++++
| 9 files changed, 263 insertions(+), 5 deletions(-)
* 2013-08-20(Tal Galili) cor_bakers_gamma.hclust function added. |9bd41bf|
| NAMESPACE | 1 +
| NEWS | 10 ++++++++++
| R/cor_bakers_gamma.r | 16 +++++++++++++++-
| R/cutree.dendrogram.r | 2 ++
| man/cutree-methods.Rd | 4 ++--
| 5 files changed, 30 insertions(+), 3 deletions(-)
* 2013-08-20(Tal Galili) Vignettes - some Bk thoery, and Rcpp section. |c534cc0|
| NEWS | 3 +
| ...heights_849ab68f2f2a2097dd7a0ed7aff83b86.RData | Bin 0 -> 3252 bytes
| ...s_heights_849ab68f2f2a2097dd7a0ed7aff83b86.rdb | Bin 0 -> 2727 bytes
| ...s_heights_849ab68f2f2a2097dd7a0ed7aff83b86.rdx | Bin 0 -> 130 bytes
| ...s_per_k_f9a2db4f130fcab9432e1d1577484543.RData | Bin 0 -> 3248 bytes
| ...hts_per_k_f9a2db4f130fcab9432e1d1577484543.rdb | Bin 0 -> 2727 bytes
| ...hts_per_k_f9a2db4f130fcab9432e1d1577484543.rdx | Bin 0 -> 130 bytes
| ...drogram_4e659e16709537f25caa621e291d2794.RData | Bin 0 -> 3222 bytes
| ...endrogram_4e659e16709537f25caa621e291d2794.rdb | Bin 0 -> 2727 bytes
| ...endrogram_4e659e16709537f25caa621e291d2794.rdx | Bin 0 -> 130 bytes
| vignettes/cache/__packages | 4 +
| ...hunk-40_b48b442cc366777991b02835121a00b7.RData | Bin 3657 -> 0 bytes
| ...-chunk-40_b48b442cc366777991b02835121a00b7.rdb | Bin 6426 -> 0 bytes
| ...-chunk-40_b48b442cc366777991b02835121a00b7.rdx | Bin 205 -> 0 bytes
| ...hunk-40_d1ed410d3974e8360057fdf7e68751fb.RData | Bin 0 -> 3125 bytes
| ...-chunk-40_d1ed410d3974e8360057fdf7e68751fb.rdb | Bin 0 -> 1509 bytes
| ...-chunk-40_d1ed410d3974e8360057fdf7e68751fb.rdx | Bin 0 -> 160 bytes
| vignettes/dendextend-tutorial-concordance.tex | 6 +-
| vignettes/dendextend-tutorial.bib | 110 +-
| vignettes/dendextend-tutorial.blg | 2 +-
| vignettes/dendextend-tutorial.log | 129 +-
| vignettes/dendextend-tutorial.pdf | 3607 ++++++++++---------
| vignettes/dendextend-tutorial.rnw | 69 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 203406 -> 223843 bytes
| vignettes/dendextend-tutorial.tex | 153 +-
| 25 files changed, 2376 insertions(+), 1707 deletions(-)
* 2013-08-19(Tal Galili) Create hidden backups of the R functions which are replaced by the Rcpp function so that we will be able to benchmark them. |a8b17c0|
| DESCRIPTION | 4 ++--
| R/zzz.r | 8 ++++++++
| 2 files changed, 10 insertions(+), 2 deletions(-)
* 2013-08-19(Tal Galili) UPDATED FUNCTIONS: * Bk_plot - now adds dots for the asymptotic lines in case of NA's * Bk - now calculates cutree once for all relevant k's - and only then goes forth with FM_index. |0d4d3dd|
| NEWS | 20 +++++++++++--
| R/bk_method.r | 85 +++++++++++++++++++++++++++++++++++++++++++++--------
| man/Bk.Rd | 15 ++++++++--
| man/Bk_plot.Rd | 1 +
| man/FM_index_R.Rd | 5 ++++
| 5 files changed, 108 insertions(+), 18 deletions(-)
* 2013-08-19(Tal Galili) Rename the package RcppDend-> dendextendRcpp |8903084|
| DESCRIPTION | 2 +-
| NEWS | 3 ++-
| R/color_branches.r | 2 +-
| R/zzz.r | 22 +++++++++++-----------
| inst/tests/test-cutree.dendrogram.r | 2 +-
| tests/test-all.r | 2 +-
| 6 files changed, 17 insertions(+), 16 deletions(-)
* 2013-08-19(Tal Galili) note on labels.dendrogram. |740aaf7|
| R/zzz.r | 12 ++++++++++++
| 1 file changed, 12 insertions(+)
* 2013-08-19(Tal Galili) color_labels - added "labels" parameter for selective coloring of labels by name. |730cf25|
| NEWS | 1 +
| R/color_branches.r | 20 +++++++++++++++++---
| man/color_labels.Rd | 9 ++++++++-
| 3 files changed, 26 insertions(+), 4 deletions(-)
* 2013-08-19(Tal Galili) Make RcppDend loads and override core functions in dendextend in order to make it MUCH faster :) |ffb7187|
| R/zzz.r | 70 ++++++++++++++++++++++++++++++++++++++++++++----------
| tests/test-all.r | 1 +
| 2 files changed, 59 insertions(+), 12 deletions(-)
* 2013-08-19(Tal Galili) add more explenation in the tests for how labels.dendrogram acts when there are missing labels. (in stats vs RcppDend package) |979beed|
| inst/tests/test-cutree.dendrogram.r | 9 ++++++++-
| 1 file changed, 8 insertions(+), 1 deletion(-)
* 2013-08-19(Tal Galili) T -> TRUE |fc3ea18|
| R/trim.r | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2013-08-19(Tal Galili) being explisit about "sort" in get_branches_heights |f532205|
| R/cutree.dendrogram.r | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2013-08-18(Tal Galili) Bk_plot function added! |814a668|
| NAMESPACE | 1 +
| NEWS | 3 +-
| R/bk_method.r | 382 ++++++++++++++++++++----------------------------
| R/cutree.dendrogram.r | 2 +-
| R/sample.dendrogram.r | 2 +-
| man/Bk.Rd | 83 -----------
| man/Bk_plot.Rd | 180 +++++++++++++++++++++++
| man/cutree-methods.Rd | 4 +-
| 8 files changed, 343 insertions(+), 314 deletions(-)
* 2013-08-18(Tal Galili) Bk_permutations function added. |d5a24cd|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/bk_method.r | 232 +++++++++++++++++++++++++++++++++++++++++++++++
| man/Bk.Rd | 83 +++++++++++++++++
| man/Bk_permutations.Rd | 93 +++++++++++++++++++
| 5 files changed, 410 insertions(+)
* 2013-08-18(Tal Galili) Bk Function added! |bf73478|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/bk_method.r | 207 +++++++++++++++++++++++++++++---------------------------
| man/Bk.Rd | 93 +++++++++++++++++++++++++
| 4 files changed, 202 insertions(+), 100 deletions(-)
* 2013-08-18(Tal Galili) Exaplin what happens to FM distribution for different values of k. |feb6432|
| R/bk_method.r | 7 ++++++-
| man/FM_index_permutation.Rd | 7 ++++++-
| 2 files changed, 12 insertions(+), 2 deletions(-)
* 2013-08-18(Tal Galili) FM_index_permutation function added |4cc208d|
| DESCRIPTION | 6 ++-
| NAMESPACE | 1 +
| NEWS | 25 ++++++++++-
| R/bk_method.r | 102 ++++++++++++++++++++++++++++++++++++++++++
| inst/tests/test-bk_method.r | 34 ++++++++++++++
| man/FM_index_permutation.Rd | 85 +++++++++++++++++++++++++++++++++++
| 6 files changed, 250 insertions(+), 3 deletions(-)
* 2013-08-18(Tal Galili) tests for FM_index_R and FM_index |ee50173|
| inst/tests/test-bk_method.r | 112 ++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 112 insertions(+)
* 2013-08-18(Tal Galili) FM_index_R and FM_index functions added. |e7a250b|
| NAMESPACE | 2 +
| R/bk_method.r | 244 +++++++++++++++++++++++++++++++++++++++-------
| man/FM_index.Rd | 113 +++++++++++++++++++++
| man/FM_index_R.Rd | 94 ++++++++++++++++++
| man/FM_index_profdpm.Rd | 13 ++-
| 5 files changed, 427 insertions(+), 39 deletions(-)
* 2013-08-18(Tal Galili) sort_2_clusters_vectors function added. |e4913b5|
| NAMESPACE | 1 +
| R/bk_method.r | 99 +++++++++++++++++++++++++++++++---------
| inst/tests/test-bk_method.r | 52 +++++++++++++++------
| man/sort_2_clusters_vectors.Rd | 59 ++++++++++++++++++++++++
| 4 files changed, 177 insertions(+), 34 deletions(-)
* 2013-08-18(Tal Galili) export lowest_common_branch. |f2dc78b|
| NAMESPACE | 1 +
| R/cor_bakers_gamma.r | 1 +
| 2 files changed, 2 insertions(+)
* 2013-08-18(Tal Galili) FM_index_profdpm function added. |35cf12d|
| NAMESPACE | 1 +
| R/bk_method.r | 338 +++++++++++++++++++++++++++++++++++-------
| inst/tests/test-bk_method.r | 58 ++++++++
| man/FM_index_profdpm.Rd | 96 ++++++++++++
| man/color_labels.Rd | 3 +-
| 5 files changed, 437 insertions(+), 59 deletions(-)
* 2013-08-18(Tal Galili) Change variable names from "." to "_" |858167f|
| R/bk_method.r | 98 ++++++++++++++++++++++++++++++++++-----------------------
| 1 file changed, 59 insertions(+), 39 deletions(-)
* 2013-08-17(Tal Galili) Added a commented-out section which could (in the future) be the basis of an Rcpp cutree (actually cutree_1h.dendrogram) function! |cde09ff|
| R/cutree.dendrogram.r | 46 ++++++++++++++++++++++++++++++++++++++++++++--
| 1 file changed, 44 insertions(+), 2 deletions(-)
* 2013-08-16(Tal Galili) color_labels_by_labels - code added (now need to document, and add to color_labels). |88c8685|
| R/color_branches.r | 64 ++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 64 insertions(+)
* 2013-08-16(Tal Galili) color_labels - removed unused 'groupLabels' parameter. |4680820|
| R/color_branches.r | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2013-08-16(Tal Galili) copyright notice. |02c1f28|
| R/bk_method.r | 19 +++++++++++++++++++
| 1 file changed, 19 insertions(+)
* 2013-08-16(Tal Galili) Bk-method.r file added |5db46e6|
| R/bk_method.r | 260 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 260 insertions(+)
* 2013-08-15(Tal Galili) Added some ref for tanglegram problem |f5fbc66|
| vignettes/dendextend-tutorial.bib | 12 +++++-------
| 1 file changed, 5 insertions(+), 7 deletions(-)
* 2013-08-14(Tal Galili) Vignettes - Cophenetic correlation |8d83bee|
| NEWS | 1 +
| ...ample_1_49438132f802c72c76330a0c6277e5c9.RData | Bin 0 -> 3844 bytes
| ...example_1_49438132f802c72c76330a0c6277e5c9.rdb | Bin 0 -> 1636 bytes
| ...example_1_49438132f802c72c76330a0c6277e5c9.rdx | Bin 0 -> 174 bytes
| ...ation_2_f52d3297030e8ccb9446f2dc58662c66.RData | Bin 0 -> 3525 bytes
| ...ulation_2_f52d3297030e8ccb9446f2dc58662c66.rdb | Bin 0 -> 9947 bytes
| ...ulation_2_f52d3297030e8ccb9446f2dc58662c66.rdx | Bin 0 -> 264 bytes
| ...on_CI_3_3243f384d2df989a75438b63f85f44f5.RData | Bin 0 -> 3884 bytes
| ...tion_CI_3_3243f384d2df989a75438b63f85f44f5.rdb | Bin 0 -> 9380 bytes
| ...tion_CI_3_3243f384d2df989a75438b63f85f44f5.rdx | Bin 0 -> 308 bytes
| ...on_CI_4_dd6497988cbed58310cbeaaabb6163b2.RData | Bin 0 -> 3904 bytes
| ...tion_CI_4_dd6497988cbed58310cbeaaabb6163b2.rdb | Bin 0 -> 8389 bytes
| ...tion_CI_4_dd6497988cbed58310cbeaaabb6163b2.rdx | Bin 0 -> 308 bytes
| vignettes/dendextend-tutorial-concordance.tex | 3 +-
| vignettes/dendextend-tutorial.bib | 16 +
| vignettes/dendextend-tutorial.blg | 6 +-
| vignettes/dendextend-tutorial.log | 152 +-
| vignettes/dendextend-tutorial.pdf | 2769 +++++++++++--------
| vignettes/dendextend-tutorial.rnw | 213 ++
| vignettes/dendextend-tutorial.synctex.gz | Bin 182727 -> 203406 bytes
| vignettes/dendextend-tutorial.tex | 299 ++
| vignettes/figure/cor_cophenetic_simulation_2.pdf | Bin 0 -> 7663 bytes
| .../figure/cor_cophenetic_simulation_CI_3.pdf | Bin 0 -> 7152 bytes
| .../figure/cor_cophenetic_simulation_CI_4.pdf | Bin 0 -> 7524 bytes
| 24 files changed, 2315 insertions(+), 1144 deletions(-)
* 2013-08-14(Tal Galili) cor_cophenetic function added (also sort_dist_mat) |cecaa2a|
| DESCRIPTION | 1 +
| NAMESPACE | 3 +
| NEWS | 6 +-
| R/cor_bakers_gamma.r | 4 +-
| R/cor_cophenetic.r | 187 ++++++++++++++++++++++++++++++++++++++++++++++
| man/cor_bakers_gamma.Rd | 7 +-
| man/cor_cophenetic.Rd | 112 +++++++++++++++++++++++++++
| man/sort_dist_mat.Rd | 28 +++++++
| 8 files changed, 341 insertions(+), 7 deletions(-)
* 2013-08-14(Tal Galili) Adding copyright notice |87bce54|
| R/sample.dendrogram.r | 20 ++++++++++++++++++++
| 1 file changed, 20 insertions(+)
* 2013-08-14(Tal Galili) VIGNETTES: Added a bootstrap and permutation examples for inference on Baker's Gamma. |08fb0c3|
| NEWS | 1 +
| R/sample.dendrogram.r | 2 +-
| ...ation_1_80285bbfbf4a8a4612444b6a03b5bfa2.RData | Bin 3496 -> 0 bytes
| ...ulation_1_80285bbfbf4a8a4612444b6a03b5bfa2.rdb | Bin 7993 -> 0 bytes
| ...ulation_1_80285bbfbf4a8a4612444b6a03b5bfa2.rdx | Bin 257 -> 0 bytes
| ...ation_1_dd930ca5c4802d808d8e1ff37bc0edef.RData | Bin 0 -> 3502 bytes
| ...ulation_1_dd930ca5c4802d808d8e1ff37bc0edef.rdb | Bin 0 -> 7988 bytes
| ...ulation_1_dd930ca5c4802d808d8e1ff37bc0edef.rdx | Bin 0 -> 257 bytes
| ...ation_2_a386542ebf46e61430ae6d546755ef8a.RData | Bin 0 -> 3513 bytes
| ...ulation_2_a386542ebf46e61430ae6d546755ef8a.rdb | Bin 0 -> 8768 bytes
| ...ulation_2_a386542ebf46e61430ae6d546755ef8a.rdx | Bin 0 -> 259 bytes
| ...ation_2_faf7c50fae3d6d1cf2dedf6718056d8a.RData | Bin 3503 -> 0 bytes
| ...ulation_2_faf7c50fae3d6d1cf2dedf6718056d8a.rdb | Bin 8761 -> 0 bytes
| ...ulation_2_faf7c50fae3d6d1cf2dedf6718056d8a.rdx | Bin 259 -> 0 bytes
| ...ation_3_1728f5856aa0b70528c40164da84c605.RData | Bin 3522 -> 0 bytes
| ...ulation_3_1728f5856aa0b70528c40164da84c605.rdb | Bin 9119 -> 0 bytes
| ...ulation_3_1728f5856aa0b70528c40164da84c605.rdx | Bin 268 -> 0 bytes
| ...ation_3_a2067a06e2dadc01a424503feeb67ad9.RData | Bin 0 -> 3527 bytes
| ...ulation_3_a2067a06e2dadc01a424503feeb67ad9.rdb | Bin 0 -> 9118 bytes
| ...ulation_3_a2067a06e2dadc01a424503feeb67ad9.rdx | Bin 0 -> 269 bytes
| ...on_CI_4_a4452373b91f83c32fa8ad187e0fa475.RData | Bin 0 -> 3914 bytes
| ...tion_CI_4_a4452373b91f83c32fa8ad187e0fa475.rdb | Bin 0 -> 8375 bytes
| ...tion_CI_4_a4452373b91f83c32fa8ad187e0fa475.rdx | Bin 0 -> 310 bytes
| vignettes/dendextend-tutorial-concordance.tex | 4 +-
| vignettes/dendextend-tutorial.log | 110 +-
| vignettes/dendextend-tutorial.pdf | 1667 ++++++++++++-------
| vignettes/dendextend-tutorial.rnw | 71 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 175961 -> 182727 bytes
| vignettes/dendextend-tutorial.tex | 107 +-
| .../figure/cor_bakers_gamma_simulation_1.pdf | Bin 7148 -> 7148 bytes
| .../figure/cor_bakers_gamma_simulation_2.pdf | Bin 7609 -> 7609 bytes
| .../figure/cor_bakers_gamma_simulation_3.pdf | Bin 7596 -> 7596 bytes
| .../figure/cor_bakers_gamma_simulation_CI_41.pdf | Bin 0 -> 5047 bytes
| .../figure/cor_bakers_gamma_simulation_CI_42.pdf | Bin 0 -> 4848 bytes
| .../figure/cor_bakers_gamma_simulation_CI_43.pdf | Bin 0 -> 7496 bytes
| 35 files changed, 1307 insertions(+), 655 deletions(-)
* 2013-08-14(Tal Galili) Added a "warn" parameter to cor_bakers_gamma |f6f62b2|
| R/cor_bakers_gamma.r | 8 +++++---
| man/cor_bakers_gamma.Rd | 4 ++++
| 2 files changed, 9 insertions(+), 3 deletions(-)
* 2013-08-14(Tal Galili) sample.dendrogram function added - it allows for permutation and bootstrap tests for comparing two trees. |e02436f|
| NAMESPACE | 1 +
| NEWS | 7 +-
| R/sample.dendrogram.r | 229 +++++++++++++++++++++++++++++++++++++++++++--
| man/duplicate_leaf.Rd | 53 +++++++++++
| man/sample.dendrogram.Rd | 77 +++++++++++++++
| 5 files changed, 355 insertions(+), 12 deletions(-)
* 2013-08-14(Tal Galili) Fix cor_bakers_gamma to work in case if trees with only leaves. |e264773|
| R/cor_bakers_gamma.r | 6 +++++-
| 1 file changed, 5 insertions(+), 1 deletion(-)
* 2013-08-14(Tal Galili) nleaves - fix doc. |8735d55|
| R/nleaves.r | 2 +-
| man/nleaves.Rd | 4 ++--
| 2 files changed, 3 insertions(+), 3 deletions(-)
* 2013-08-14(Tal Galili) More protection for cutree by forcing nleaves to use method order. |aa129cd|
| R/cutree.dendrogram.r | 7 ++++---
| 1 file changed, 4 insertions(+), 3 deletions(-)
* 2013-08-14(Tal Galili) fix_members_attr.dendrogram - fixed a bug introduced by the new "members" method in nleaves. (test added) |6ba6295|
| DESCRIPTION | 2 +-
| NEWS | 2 ++
| R/attr_access.r | 2 +-
| inst/tests/test-attr_access.r | 15 +++++++++++++++
| 4 files changed, 19 insertions(+), 2 deletions(-)
* 2013-08-14(Tal Galili) sample.dendrogram function added. Only works for replace = FALSE |c213ffc|
| DESCRIPTION | 5 +++--
| NAMESPACE | 1 +
| NEWS | 5 +++++
| R/sample.dendrogram.r | 38 ++++++++++++++++++++++++++++++++++++++
| 4 files changed, 47 insertions(+), 2 deletions(-)
* 2013-08-14(Tal Galili) rank_order.dendrogram function added. |39a5237|
| NAMESPACE | 2 +
| R/attr_access.r | 95 ++++++++++++++++++++++++++++++++++++++++++
| R/trim.r | 49 ----------------------
| man/rank_order.dendrogram.Rd | 33 +++++++++++++++
| 4 files changed, 130 insertions(+), 49 deletions(-)
* 2013-08-14(Tal Galili) added ref to Baker 1974 |33390db|
| man/cor_bakers_gamma.Rd | 6 ++++++
| 1 file changed, 6 insertions(+)
* 2013-08-14(Tal Galili) Vignettes: adding a third simulation |bfef209|
| ...ation_3_1728f5856aa0b70528c40164da84c605.RData | Bin 0 -> 3522 bytes
| ...ulation_3_1728f5856aa0b70528c40164da84c605.rdb | Bin 0 -> 9119 bytes
| ...ulation_3_1728f5856aa0b70528c40164da84c605.rdx | Bin 0 -> 268 bytes
| vignettes/dendextend-tutorial-concordance.tex | 4 +-
| vignettes/dendextend-tutorial.log | 67 +-
| vignettes/dendextend-tutorial.pdf | 1024 +++++++++++--------
| vignettes/dendextend-tutorial.rnw | 34 +
| vignettes/dendextend-tutorial.synctex.gz | Bin 172701 -> 175961 bytes
| vignettes/dendextend-tutorial.tex | 58 +-
| .../figure/cor_bakers_gamma_simulation_3.pdf | Bin 0 -> 7596 bytes
| 10 files changed, 730 insertions(+), 457 deletions(-)
* 2013-08-14(Tal Galili) VIGNETTES - Added the Baker's Gamma Index section. |9dd5cdd|
| NEWS | 3 +
| ...ample_1_a6f852561e8ce9d553b9d2b27b424b22.RData | Bin 0 -> 3823 bytes
| ...example_1_a6f852561e8ce9d553b9d2b27b424b22.rdb | Bin 0 -> 2409 bytes
| ...example_1_a6f852561e8ce9d553b9d2b27b424b22.rdx | Bin 0 -> 204 bytes
| ...ation_1_80285bbfbf4a8a4612444b6a03b5bfa2.RData | Bin 0 -> 3496 bytes
| ...ulation_1_80285bbfbf4a8a4612444b6a03b5bfa2.rdb | Bin 0 -> 7993 bytes
| ...ulation_1_80285bbfbf4a8a4612444b6a03b5bfa2.rdx | Bin 0 -> 257 bytes
| ...ation_2_faf7c50fae3d6d1cf2dedf6718056d8a.RData | Bin 0 -> 3503 bytes
| ...ulation_2_faf7c50fae3d6d1cf2dedf6718056d8a.rdb | Bin 0 -> 8761 bytes
| ...ulation_2_faf7c50fae3d6d1cf2dedf6718056d8a.rdx | Bin 0 -> 259 bytes
| vignettes/dendextend-tutorial-concordance.tex | 3 +-
| vignettes/dendextend-tutorial.log | 175 +-
| vignettes/dendextend-tutorial.pdf | 3073 ++++++++++++-------
| vignettes/dendextend-tutorial.rnw | 153 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 154731 -> 172701 bytes
| vignettes/dendextend-tutorial.tex | 283 +-
| vignettes/figure/cor_bakers_gamma_example_11.pdf | Bin 0 -> 5053 bytes
| vignettes/figure/cor_bakers_gamma_example_12.pdf | Bin 0 -> 5082 bytes
| vignettes/figure/cor_bakers_gamma_example_13.pdf | Bin 0 -> 5053 bytes
| vignettes/figure/cor_bakers_gamma_example_14.pdf | Bin 0 -> 5056 bytes
| .../figure/cor_bakers_gamma_simulation_1.pdf | Bin 0 -> 7148 bytes
| .../figure/cor_bakers_gamma_simulation_2.pdf | Bin 0 -> 7609 bytes
| 22 files changed, 2500 insertions(+), 1190 deletions(-)
* 2013-08-14(Tal Galili) Adding reference to Baker's paper from 1974. |5a0209d|
| R/cor_bakers_gamma.r | 7 +++++++
| vignettes/dendextend-tutorial.bib | 36 ++++++++++++++++++++++++++++++++++++
| 2 files changed, 43 insertions(+)
* 2013-08-14(Tal Galili) cor_bakers_gamma function added. |8857952|
| DESCRIPTION | 2 +-
| NAMESPACE | 3 +
| NEWS | 9 ++
| R/cor_bakers_gamma.r | 210 +++++++++++++++++++++++++++++++++++
| inst/tests/test-cor_bakers_gamma.r | 48 ++++++++
| man/bakers_gamma_for_2_k_matrix.Rd | 31 ++++++
| man/cor_bakers_gamma.Rd | 99 +++++++++++++++++
| man/lowest_common_branch.Rd | 35 ++++++
| 8 files changed, 436 insertions(+), 1 deletion(-)
* 2013-08-14(Tal Galili) Added {} |da980a9|
| R/trim.r | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2013-08-14(Tal Galili) tanglegram - added the match_order_by_labels parameter. |646329a|
| R/tanglegram.r | 9 ++++++++-
| man/tanglegram.Rd | 7 +++++++
| 2 files changed, 15 insertions(+), 1 deletion(-)
* 2013-08-14(Tal Galili) Added test for cutree's use_labels_not_values parameter. |733f127|
| inst/tests/test-cutree.dendrogram.r | 11 +++++++++++
| 1 file changed, 11 insertions(+)
* 2013-08-14(Tal Galili) tanglegram - added the hang parameter. |82b3bd2|
| NEWS | 1 +
| R/tanglegram.r | 11 +-
| man/tanglegram.Rd | 6 +-
| ...example_802a64d3a4c0dd3e9bb0e2a4dee353da.RData | Bin 0 -> 3699 bytes
| ...e_example_802a64d3a4c0dd3e9bb0e2a4dee353da.rdb | Bin 0 -> 6426 bytes
| ...e_example_802a64d3a4c0dd3e9bb0e2a4dee353da.rdx | Bin 0 -> 205 bytes
| ...example_bb4ceb1d930b3bb07d6747839ba48794.RData | Bin 3657 -> 0 bytes
| ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdb | Bin 6426 -> 0 bytes
| ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdx | Bin 205 -> 0 bytes
| vignettes/dendextend-tutorial-concordance.tex | 2 +-
| vignettes/dendextend-tutorial.log | 59 +-
| vignettes/dendextend-tutorial.pdf | 1103 +++++++++++--------
| vignettes/dendextend-tutorial.rnw | 11 +
| vignettes/dendextend-tutorial.synctex.gz | Bin 153993 -> 154731 bytes
| vignettes/dendextend-tutorial.tex | 14 +
| .../untangle_step_rotate_2side_example1.pdf | Bin 6158 -> 6158 bytes
| .../untangle_step_rotate_2side_example2.pdf | Bin 6137 -> 6137 bytes
| .../untangle_step_rotate_2side_example3.pdf | Bin 6154 -> 6154 bytes
| .../untangle_step_rotate_2side_example4.pdf | Bin 6141 -> 6141 bytes
| .../untangle_step_rotate_2side_example5.pdf | Bin 5714 -> 5714 bytes
| .../untangle_step_rotate_2side_example6.pdf | Bin 0 -> 6163 bytes
| 21 files changed, 694 insertions(+), 513 deletions(-)
* 2013-08-14(Tal Galili) Version bump 0.7.3 |2bb5655|
| DESCRIPTION | 4 +-
| NEWS | 41 +-
| ...hunk-40_9f83c05b11ed630ecb319c8a28110b35.RData | Bin 3466 -> 0 bytes
| ...-chunk-40_9f83c05b11ed630ecb319c8a28110b35.rdb | Bin 6426 -> 0 bytes
| ...-chunk-40_9f83c05b11ed630ecb319c8a28110b35.rdx | Bin 205 -> 0 bytes
| ...hunk-40_b48b442cc366777991b02835121a00b7.RData | Bin 0 -> 3657 bytes
| ...-chunk-40_b48b442cc366777991b02835121a00b7.rdb | Bin 0 -> 6426 bytes
| ...-chunk-40_b48b442cc366777991b02835121a00b7.rdx | Bin 0 -> 205 bytes
| ...example_bb4ceb1d930b3bb07d6747839ba48794.RData | Bin 0 -> 3657 bytes
| ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdb | Bin 0 -> 6426 bytes
| ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdx | Bin 0 -> 205 bytes
| vignettes/dendextend-tutorial-concordance.tex | 2 +-
| vignettes/dendextend-tutorial.log | 259 +--
| vignettes/dendextend-tutorial.pdf | 2039 +++++++------------
| vignettes/dendextend-tutorial.rnw | 11 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 153579 -> 153993 bytes
| vignettes/dendextend-tutorial.tex | 36 +-
| vignettes/figure/unnamed-chunk-34.pdf | Bin 6773 -> 0 bytes
| vignettes/figure/unnamed-chunk-35.pdf | Bin 6766 -> 0 bytes
| vignettes/figure/unnamed-chunk-36.pdf | Bin 6737 -> 0 bytes
| vignettes/figure/unnamed-chunk-37.pdf | Bin 6739 -> 0 bytes
| vignettes/figure/unnamed-chunk-38.pdf | Bin 6722 -> 0 bytes
| vignettes/figure/unnamed-chunk-39.pdf | Bin 6857 -> 0 bytes
| vignettes/figure/unnamed-chunk-401.pdf | Bin 6078 -> 0 bytes
| vignettes/figure/unnamed-chunk-402.pdf | Bin 6027 -> 0 bytes
| vignettes/figure/unnamed-chunk-403.pdf | Bin 6036 -> 0 bytes
| vignettes/figure/unnamed-chunk-404.pdf | Bin 6016 -> 0 bytes
| .../untangle_step_rotate_2side_example1.pdf | Bin 0 -> 6158 bytes
| .../untangle_step_rotate_2side_example2.pdf | Bin 0 -> 6137 bytes
| .../untangle_step_rotate_2side_example3.pdf | Bin 0 -> 6154 bytes
| .../untangle_step_rotate_2side_example4.pdf | Bin 0 -> 6141 bytes
| .../untangle_step_rotate_2side_example5.pdf | Bin 0 -> 5714 bytes
| 32 files changed, 946 insertions(+), 1446 deletions(-)
* 2013-08-14(Tal Galili) tanglegram - fixed the right tree's labels position relative to the leaves tips. (they were too far away because of a combination of text_adj with dLeaf) |5c0f75e|
| R/tanglegram.r | 15 +++++++++++----
| man/plot_horiz.dendrogram.Rd | 6 ++----
| man/tanglegram.Rd | 4 ++++
| 3 files changed, 17 insertions(+), 8 deletions(-)
* 2013-08-14(Tal Galili) rank_branches function added. |f56a9d8|
| NAMESPACE | 2 +
| R/attr_access.r | 104 ++++++++++++++++++++++++++++++++++++++--
| R/tanglegram.r | 12 +++--
| inst/tests/test-attr_access.r | 11 +++++
| man/get_childrens_heights.Rd | 27 +++++++++++
| man/rank_branches.Rd | 48 +++++++++++++++++++
| man/tanglegram.Rd | 8 +++-
| 7 files changed, 204 insertions(+), 8 deletions(-)
* 2013-08-14(Tal Galili) sort_levels_values now deals with vectors haing NA values (just returning the vector as is) |62631fa|
| R/cutree.dendrogram.r | 17 ++++++++++++-----
| man/get_heights.dendrogram.Rd | 26 --------------------------
| man/sort_levels_values.Rd | 13 ++++++++-----
| 3 files changed, 20 insertions(+), 36 deletions(-)
* 2013-08-13(Tal Galili) Version bump to 0.7.2 |7d8ae64|
| DESCRIPTION | 5 +++--
| NEWS | 17 ++++++++++++++++-
| 2 files changed, 19 insertions(+), 3 deletions(-)
* 2013-08-13(Tal Galili) tanglegram - labels are now alligned to the leaves tips in the right dendrogram. |e153fd2|
| R/tanglegram.r | 384 +++++++++++++++++++++++++++++++++++------
| man/cutree-methods.Rd | 10 +-
| man/plot_horiz.dendrogram.Rd | 53 ++++--
| man/tanglegram.Rd | 27 ++-
| 4 files changed, 406 insertions(+), 68 deletions(-)
* 2013-08-13(Tal Galili) Set sort_cluster_numbers = TRUE for cutree, in order to make it compatible with stats:::cutree |e7a0dcb|
| NEWS | 3 +-
| R/cutree.dendrogram.r | 60 +++++++++++++++++++++++++++++++----
| inst/tests/test-cutree.dendrogram.r | 13 ++++++--
| 3 files changed, 66 insertions(+), 10 deletions(-)
* 2013-08-13(Tal Galili) Fix untangle_step_rotate_1side to work with non-missing dend_heights_per_k |3ed6210|
| NEWS | 8 ++++++++
| R/untangle.r | 8 +++-----
| 2 files changed, 11 insertions(+), 5 deletions(-)
* 2013-08-13(Tal Galili) Fix some names in untangle_step_rotate_2side test |889c0e8|
| inst/tests/test-untangle.r | 9 ++++++---
| 1 file changed, 6 insertions(+), 3 deletions(-)
* 2013-08-13(Tal Galili) Make a quicker test for untangle_step_rotate_2side |0d4b138|
| inst/tests/test-untangle.r | 69 ++++++++++++++++++++++++++++----------------
| 1 file changed, 44 insertions(+), 25 deletions(-)
* 2013-08-12(Tal Galili) Set print_times=FALSE for tests. |b36c95d|
| inst/tests/test-untangle.r | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2013-08-12(Tal Galili) Version bump to 0.7.1 |3109111|
| DESCRIPTION | 4 ++--
| NEWS | 2 ++
| 2 files changed, 4 insertions(+), 2 deletions(-)
* 2013-08-12(Tal Galili) Vignettes - untangle_step_rotate_2side |1026419|
| vignettes/cache/__packages | 1 +
| ...hunk-34_4cad004366f0784e24de81f2f1e1a5b1.RData | Bin 0 -> 3372 bytes
| ...-chunk-34_4cad004366f0784e24de81f2f1e1a5b1.rdb | Bin 0 -> 3305 bytes
| ...-chunk-34_4cad004366f0784e24de81f2f1e1a5b1.rdx | Bin 0 -> 211 bytes
| ...hunk-34_8ffad53bb8af151a2dcefeff754912dc.RData | Bin 3083 -> 0 bytes
| ...-chunk-34_8ffad53bb8af151a2dcefeff754912dc.rdb | 0
| ...-chunk-34_8ffad53bb8af151a2dcefeff754912dc.rdx | Bin 113 -> 0 bytes
| ...hunk-35_c84407e79fe989eb7f3fdc6fddcdb3b9.RData | Bin 0 -> 3107 bytes
| ...-chunk-35_c84407e79fe989eb7f3fdc6fddcdb3b9.rdb | Bin 0 -> 1824 bytes
| ...-chunk-35_c84407e79fe989eb7f3fdc6fddcdb3b9.rdx | Bin 0 -> 136 bytes
| ...hunk-36_69145b2450999a80e4893d8ba64db6dd.RData | Bin 0 -> 3282 bytes
| ...-chunk-36_69145b2450999a80e4893d8ba64db6dd.rdb | Bin 0 -> 1339 bytes
| ...-chunk-36_69145b2450999a80e4893d8ba64db6dd.rdx | Bin 0 -> 164 bytes
| ...hunk-37_b1ba3f3d9a8a8cc37716b304f0834850.RData | Bin 0 -> 3130 bytes
| ...-chunk-37_b1ba3f3d9a8a8cc37716b304f0834850.rdb | Bin 0 -> 1017 bytes
| ...-chunk-37_b1ba3f3d9a8a8cc37716b304f0834850.rdx | Bin 0 -> 137 bytes
| ...hunk-38_536de094e0e3e4ccc261c1918659f094.RData | Bin 0 -> 3116 bytes
| ...-chunk-38_536de094e0e3e4ccc261c1918659f094.rdb | Bin 0 -> 1035 bytes
| ...-chunk-38_536de094e0e3e4ccc261c1918659f094.rdx | Bin 0 -> 136 bytes
| ...hunk-39_6081bd526faf34d32cd6a13be83e6937.RData | Bin 0 -> 3071 bytes
| ...-chunk-39_6081bd526faf34d32cd6a13be83e6937.rdb | 0
| ...-chunk-39_6081bd526faf34d32cd6a13be83e6937.rdx | Bin 0 -> 113 bytes
| ...hunk-40_9f83c05b11ed630ecb319c8a28110b35.RData | Bin 0 -> 3466 bytes
| ...-chunk-40_9f83c05b11ed630ecb319c8a28110b35.rdb | Bin 0 -> 6426 bytes
| ...-chunk-40_9f83c05b11ed630ecb319c8a28110b35.rdx | Bin 0 -> 205 bytes
| vignettes/dendextend-tutorial-concordance.tex | 7 +-
| vignettes/dendextend-tutorial.log | 673 ++-
| vignettes/dendextend-tutorial.pdf | 5274 ++++++++++++-------
| vignettes/dendextend-tutorial.rnw | 65 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 133707 -> 153579 bytes
| vignettes/dendextend-tutorial.tex | 357 +-
| vignettes/figure/unnamed-chunk-34.pdf | Bin 0 -> 6773 bytes
| vignettes/figure/unnamed-chunk-35.pdf | Bin 0 -> 6766 bytes
| vignettes/figure/unnamed-chunk-36.pdf | Bin 0 -> 6737 bytes
| vignettes/figure/unnamed-chunk-37.pdf | Bin 0 -> 6739 bytes
| vignettes/figure/unnamed-chunk-38.pdf | Bin 0 -> 6722 bytes
| vignettes/figure/unnamed-chunk-39.pdf | Bin 0 -> 6857 bytes
| vignettes/figure/unnamed-chunk-401.pdf | Bin 0 -> 6078 bytes
| vignettes/figure/unnamed-chunk-402.pdf | Bin 0 -> 6027 bytes
| vignettes/figure/unnamed-chunk-403.pdf | Bin 0 -> 6036 bytes
| vignettes/figure/unnamed-chunk-404.pdf | Bin 0 -> 6016 bytes
| 41 files changed, 4214 insertions(+), 2163 deletions(-)
* 2013-08-12(Tal Galili) untangle_step_rotate_2side - added tests |af6c7bf|
| inst/tests/test-untangle.r | 35 ++++++++++++++++++++++++++++++++++-
| 1 file changed, 34 insertions(+), 1 deletion(-)
* 2013-08-12(Tal Galili) Moving old code done (maybe I will document it in the future, and maybe not...) |08ba75f|
| R/untangle.r | 169 +++++++++++++++++++++++++++++++--------------------------
| 1 file changed, 92 insertions(+), 77 deletions(-)
* 2013-08-12(Tal Galili) untangle_step_rotate_2side function added. |07e1fb0|
| NAMESPACE | 1 +
| NEWS | 9 +++
| R/untangle.r | 123 ++++++++++++++++++++++++++++++------
| man/untangle_step_rotate_1side.Rd | 7 +-
| man/untangle_step_rotate_2side.Rd | 85 +++++++++++++++++++++++++
| 5 files changed, 203 insertions(+), 22 deletions(-)
* 2013-08-12(Tal Galili) Version bump to 0.7 |ddd2552|
| DESCRIPTION | 4 ++--
| NEWS | 3 +++
| 2 files changed, 5 insertions(+), 2 deletions(-)
* 2013-08-12(Tal Galili) Vignettes doc for untangaling trees. |e208ba3|
| vignettes/dendextend-tutorial.rnw | 103 ++++++++++++++++++++++++++++++++++++
| 1 file changed, 103 insertions(+)
* 2013-08-12(Tal Galili) Added k_seq and dend_heights_per_k to untangle_step_rotate_1side. |581245c|
| R/untangle.r | 26 ++++++++++++++++++--------
| man/untangle_step_rotate_1side.Rd | 13 +++++++++++--
| 2 files changed, 29 insertions(+), 10 deletions(-)
* 2013-08-12(Tal Galili) Rename: untangle_forward_rotate_1side -> untangle_step_rotate_1side |43178f5|
| NAMESPACE | 2 +-
| R/untangle.r | 68 ++++++++++++++++------------------
| inst/tests/test-untangle.r | 7 +++-
| man/untangle_forward_rotate_1side.Rd | 59 -----------------------------
| man/untangle_step_rotate_1side.Rd | 65 ++++++++++++++++++++++++++++++++
| 5 files changed, 103 insertions(+), 98 deletions(-)
* 2013-08-11(Tal Galili) untangle_forward_rotate_1side function added! |f721906|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/untangle.r | 84 +++++++++++++++++++++++++---------
| inst/tests/test-untangle.r | 18 ++++++++
| man/all_couple_rotations_at_k.Rd | 2 +-
| man/untangle_forward_rotate_1side.Rd | 59 ++++++++++++++++++++++++
| 6 files changed, 142 insertions(+), 23 deletions(-)
* 2013-08-11(Tal Galili) There is some problem with match_order_dendrogram_by_old_order - might need to revisit this in the future... |88175b6|
| R/entanglement.r | 2 ++
| inst/tests/test-entanglement.r | 31 ++++++++++++++++++++++++++++---
| 2 files changed, 30 insertions(+), 3 deletions(-)
* 2013-08-11(Tal Galili) Added shuffle to the namespace. |a85ad68|
| NAMESPACE | 3 ++
| R/untangle.r | 66 ++++++++++++++++----------------------
| man/all_couple_rotations_at_k.Rd | 8 +++++
| man/shuffle.Rd | 6 ++++
| 4 files changed, 45 insertions(+), 38 deletions(-)
* 2013-08-11(Tal Galili) all_couple_rotations_at_k function added. |6acc7e7|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/untangle.r | 105 +++++++++++++++++++++----------------
| inst/tests/test-attr_access.r | 2 +-
| inst/tests/test-untangle.r | 13 ++++-
| man/all_couple_rotations_at_k.Rd | 47 +++++++++++++++++
| 6 files changed, 123 insertions(+), 46 deletions(-)
* 2013-08-11(Tal Galili) scaler -> scalar |01b489e|
| R/attr_access.r | 4 ++--
| man/get_leaves_attr.Rd | 2 +-
| man/get_nodes_attr.Rd | 2 +-
| 3 files changed, 4 insertions(+), 4 deletions(-)
* 2013-08-11(Tal Galili) donotrun -> dontrun |2b65ab3|
| R/cutree.dendrogram.r | 2 +-
| man/heights_per_k.dendrogram.Rd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2013-08-11(Tal Galili) flip_leaves function added |3d9fda5|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/untangle.r | 111 ++++++++++++++++++++++++-------------------
| inst/tests/test-untangle.r | 19 ++++++--
| man/flip_leaves.Rd | 42 ++++++++++++++++
| 5 files changed, 121 insertions(+), 53 deletions(-)
* 2013-08-11(Tal Galili) move some code down the file. |7e840b5|
| R/untangle.r | 126 ++++++++++++++++++++++++++++++---------------------------
| 1 file changed, 66 insertions(+), 60 deletions(-)
* 2013-08-11(Tal Galili) untangle_random_search function added - random search for two trees with low entanglement. |4fe24f9|
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/untangle.r | 92 +++++++++++++++++++++++----
| man/shuffle.Rd | 137 +++++++---------------------------------
| man/untangle_random_search.Rd | 84 ++++++++++++++++++++++++
| 5 files changed, 190 insertions(+), 126 deletions(-)
* 2013-08-11(Tal Galili) shuffle function added. |79ec35e|
| NAMESPACE | 1 +
| NEWS | 4 ++
| R/untangle.r | 71 +++++++++++++++-----
| inst/tests/test-entanglement.r | 2 +-
| inst/tests/test-untangle.r | 23 +++++++
| man/shuffle.Rd | 137 +++++++++++++++++++++++++++++++++++++++
| 6 files changed, 222 insertions(+), 16 deletions(-)
* 2013-08-11(Tal Galili) rotate - minor code and doc improvements. |270ae47|
| NAMESPACE | 1 -
| NEWS | 8 ++++++++
| R/rotate.r | 18 ++++++++++--------
| man/rotate.Rd | 6 ++++--
| 4 files changed, 22 insertions(+), 11 deletions(-)
* 2013-08-11(Tal Galili) Bump version to 0.6 |b483d57|
| DESCRIPTION | 2 +-
| NEWS | 7 ++++++-
| 2 files changed, 7 insertions(+), 2 deletions(-)
* 2013-08-11(Tal Galili) Vignettes - added tanglegram and entanglement. |4e258d0|
| ...glegram_4820b99e23c40b3df4be2cd55320490f.RData | Bin 0 -> 3205 bytes
| ...anglegram_4820b99e23c40b3df4be2cd55320490f.rdb | Bin 0 -> 8590 bytes
| ...anglegram_4820b99e23c40b3df4be2cd55320490f.rdx | Bin 0 -> 170 bytes
| ...ranches_aff39ef9c0e2ae1c023d06d324642a04.RData | Bin 3692 -> 0 bytes
| ..._branches_aff39ef9c0e2ae1c023d06d324642a04.rdb | Bin 51879 -> 0 bytes
| ..._branches_aff39ef9c0e2ae1c023d06d324642a04.rdx | Bin 189 -> 0 bytes
| ...ranches_df7b6dfc097a9c6cde2152189b405e32.RData | Bin 0 -> 3828 bytes
| ..._branches_df7b6dfc097a9c6cde2152189b405e32.rdb | Bin 0 -> 51879 bytes
| ..._branches_df7b6dfc097a9c6cde2152189b405e32.rdx | Bin 0 -> 189 bytes
| ...rs_plot_8dfe5036560ecb02840d07882d498136.RData | Bin 3124 -> 0 bytes
| ...airs_plot_8dfe5036560ecb02840d07882d498136.rdb | Bin 127 -> 0 bytes
| ...airs_plot_8dfe5036560ecb02840d07882d498136.rdx | Bin 148 -> 0 bytes
| ...rs_plot_daac58f156bd023132ab44332d441f28.RData | Bin 0 -> 3161 bytes
| ...airs_plot_daac58f156bd023132ab44332d441f28.rdb | Bin 0 -> 127 bytes
| ...airs_plot_daac58f156bd023132ab44332d441f28.rdx | Bin 0 -> 148 bytes
| ...hunk-10_0854e43359590ce23429966d09b02815.RData | Bin 0 -> 307 bytes
| ...-chunk-10_0854e43359590ce23429966d09b02815.rdb | 0
| ...-chunk-10_0854e43359590ce23429966d09b02815.rdx | Bin 0 -> 113 bytes
| ...hunk-10_9e4d22ca7258b454f2701d1413ab82d0.RData | Bin 297 -> 0 bytes
| ...-chunk-10_9e4d22ca7258b454f2701d1413ab82d0.rdb | 0
| ...-chunk-10_9e4d22ca7258b454f2701d1413ab82d0.rdx | Bin 113 -> 0 bytes
| ...hunk-11_a45b2e60d746184500f34c0344888b6d.RData | Bin 315 -> 0 bytes
| ...-chunk-11_a45b2e60d746184500f34c0344888b6d.rdb | Bin 36 -> 0 bytes
| ...-chunk-11_a45b2e60d746184500f34c0344888b6d.rdx | Bin 130 -> 0 bytes
| ...hunk-11_d0998d8fbc02d1b6575b886950562355.RData | Bin 0 -> 327 bytes
| ...-chunk-11_d0998d8fbc02d1b6575b886950562355.rdb | Bin 0 -> 36 bytes
| ...-chunk-11_d0998d8fbc02d1b6575b886950562355.rdx | Bin 0 -> 130 bytes
| ...hunk-12_ad4eab6c111317bd487ccce36f736a90.RData | Bin 0 -> 368 bytes
| ...-chunk-12_ad4eab6c111317bd487ccce36f736a90.rdb | Bin 0 -> 67 bytes
| ...-chunk-12_ad4eab6c111317bd487ccce36f736a90.rdx | Bin 0 -> 130 bytes
| ...hunk-12_bfd3fdad8685afee49dc53382ab9b940.RData | Bin 348 -> 0 bytes
| ...-chunk-12_bfd3fdad8685afee49dc53382ab9b940.rdb | Bin 67 -> 0 bytes
| ...-chunk-12_bfd3fdad8685afee49dc53382ab9b940.rdx | Bin 130 -> 0 bytes
| ...hunk-13_8532ab73d0f73d385c6b97323ab25374.RData | Bin 288 -> 0 bytes
| ...-chunk-13_8532ab73d0f73d385c6b97323ab25374.rdb | Bin 67 -> 0 bytes
| ...-chunk-13_8532ab73d0f73d385c6b97323ab25374.rdx | Bin 130 -> 0 bytes
| ...hunk-13_a9b7eef6382ba74e22dd9268dc381f13.RData | Bin 0 -> 311 bytes
| ...-chunk-13_a9b7eef6382ba74e22dd9268dc381f13.rdb | Bin 0 -> 67 bytes
| ...-chunk-13_a9b7eef6382ba74e22dd9268dc381f13.rdx | Bin 0 -> 130 bytes
| ...hunk-14_864583e5f4bccdbe4e9384020d05f60b.RData | Bin 2996 -> 0 bytes
| ...-chunk-14_864583e5f4bccdbe4e9384020d05f60b.rdb | Bin 265 -> 0 bytes
| ...-chunk-14_864583e5f4bccdbe4e9384020d05f60b.rdx | Bin 128 -> 0 bytes
| ...hunk-14_8bdeda75791482f7fe0c15ca4add7f4d.RData | Bin 0 -> 3006 bytes
| ...-chunk-14_8bdeda75791482f7fe0c15ca4add7f4d.rdb | Bin 0 -> 265 bytes
| ...-chunk-14_8bdeda75791482f7fe0c15ca4add7f4d.rdx | Bin 0 -> 128 bytes
| ...hunk-15_bc3ceeeb91232d23574416482184aa73.RData | Bin 0 -> 3092 bytes
| ...-chunk-15_bc3ceeeb91232d23574416482184aa73.rdb | Bin 0 -> 296 bytes
| ...-chunk-15_bc3ceeeb91232d23574416482184aa73.rdx | Bin 0 -> 131 bytes
| ...hunk-15_dd0f20489ecc43d1b15fa7e75d86d497.RData | Bin 3074 -> 0 bytes
| ...-chunk-15_dd0f20489ecc43d1b15fa7e75d86d497.rdb | Bin 296 -> 0 bytes
| ...-chunk-15_dd0f20489ecc43d1b15fa7e75d86d497.rdx | Bin 131 -> 0 bytes
| ...hunk-16_4566da6efa80cf3df53d8a91be5f5cc3.RData | Bin 0 -> 3194 bytes
| ...-chunk-16_4566da6efa80cf3df53d8a91be5f5cc3.rdb | Bin 0 -> 666 bytes
| ...-chunk-16_4566da6efa80cf3df53d8a91be5f5cc3.rdx | Bin 0 -> 163 bytes
| ...hunk-16_771a6ce242d89b845f40ea3896192cee.RData | Bin 3169 -> 0 bytes
| ...-chunk-16_771a6ce242d89b845f40ea3896192cee.rdb | Bin 666 -> 0 bytes
| ...-chunk-16_771a6ce242d89b845f40ea3896192cee.rdx | Bin 163 -> 0 bytes
| ...hunk-17_180ef22b097680ce8849623318fc5899.RData | Bin 0 -> 2860 bytes
| ...-chunk-17_180ef22b097680ce8849623318fc5899.rdb | 0
| ...-chunk-17_180ef22b097680ce8849623318fc5899.rdx | Bin 0 -> 113 bytes
| ...hunk-17_72778f36fe1ace467acaa29a9b2284d6.RData | Bin 2862 -> 0 bytes
| ...-chunk-17_72778f36fe1ace467acaa29a9b2284d6.rdb | 0
| ...-chunk-17_72778f36fe1ace467acaa29a9b2284d6.rdx | Bin 113 -> 0 bytes
| ...hunk-18_23e2cce2d0b15bd185767d94b20a1183.RData | Bin 3127 -> 0 bytes
| ...-chunk-18_23e2cce2d0b15bd185767d94b20a1183.rdb | 0
| ...-chunk-18_23e2cce2d0b15bd185767d94b20a1183.rdx | Bin 113 -> 0 bytes
| ...hunk-18_718657d68309d4e0c45b4501ea8a9e83.RData | Bin 0 -> 3131 bytes
| ...-chunk-18_718657d68309d4e0c45b4501ea8a9e83.rdb | 0
| ...-chunk-18_718657d68309d4e0c45b4501ea8a9e83.rdx | Bin 0 -> 113 bytes
| ...hunk-19_0fdbdabbe9e648a253d59bdafafcdc8a.RData | Bin 3431 -> 0 bytes
| ...-chunk-19_0fdbdabbe9e648a253d59bdafafcdc8a.rdb | Bin 512 -> 0 bytes
| ...-chunk-19_0fdbdabbe9e648a253d59bdafafcdc8a.rdx | Bin 143 -> 0 bytes
| ...hunk-19_d1af6f9960f0c005eccb931d7793bf6b.RData | Bin 0 -> 3474 bytes
| ...-chunk-19_d1af6f9960f0c005eccb931d7793bf6b.rdb | Bin 0 -> 512 bytes
| ...-chunk-19_d1af6f9960f0c005eccb931d7793bf6b.rdx | Bin 0 -> 143 bytes
| ...hunk-20_455b1a3886dfbac3f95e22d03843c020.RData | Bin 2943 -> 0 bytes
| ...-chunk-20_455b1a3886dfbac3f95e22d03843c020.rdb | Bin 519 -> 0 bytes
| ...-chunk-20_455b1a3886dfbac3f95e22d03843c020.rdx | Bin 143 -> 0 bytes
| ...hunk-20_9f866b5b953b10f3b8d5b092eed33057.RData | Bin 0 -> 2964 bytes
| ...-chunk-20_9f866b5b953b10f3b8d5b092eed33057.rdb | Bin 0 -> 519 bytes
| ...-chunk-20_9f866b5b953b10f3b8d5b092eed33057.rdx | Bin 0 -> 143 bytes
| ...hunk-21_8a160c3dee2afef22ce093e3668819de.RData | Bin 0 -> 3472 bytes
| ...-chunk-21_8a160c3dee2afef22ce093e3668819de.rdb | Bin 0 -> 761 bytes
| ...-chunk-21_8a160c3dee2afef22ce093e3668819de.rdx | Bin 0 -> 155 bytes
| ...hunk-21_eaa8e7d7a586b81daf2136174b1ac324.RData | Bin 3447 -> 0 bytes
| ...-chunk-21_eaa8e7d7a586b81daf2136174b1ac324.rdb | Bin 761 -> 0 bytes
| ...-chunk-21_eaa8e7d7a586b81daf2136174b1ac324.rdx | Bin 155 -> 0 bytes
| ...hunk-22_705cf338f5523ee13659e8bec07a7cd3.RData | Bin 3149 -> 0 bytes
| ...-chunk-22_705cf338f5523ee13659e8bec07a7cd3.rdb | 0
| ...-chunk-22_705cf338f5523ee13659e8bec07a7cd3.rdx | Bin 113 -> 0 bytes
| ...hunk-22_a00ca74792504d853d3e8938a2d4dc0f.RData | Bin 0 -> 3164 bytes
| ...-chunk-22_a00ca74792504d853d3e8938a2d4dc0f.rdb | 0
| ...-chunk-22_a00ca74792504d853d3e8938a2d4dc0f.rdx | Bin 0 -> 113 bytes
| ...hunk-23_32ab7758407c06a18f8c0738d91da189.RData | Bin 0 -> 3266 bytes
| ...-chunk-23_32ab7758407c06a18f8c0738d91da189.rdb | Bin 0 -> 985 bytes
| ...-chunk-23_32ab7758407c06a18f8c0738d91da189.rdx | Bin 0 -> 169 bytes
| ...hunk-23_60c53081752d1b02584bb6e1587ddc3b.RData | Bin 3205 -> 0 bytes
| ...-chunk-23_60c53081752d1b02584bb6e1587ddc3b.rdb | Bin 985 -> 0 bytes
| ...-chunk-23_60c53081752d1b02584bb6e1587ddc3b.rdx | Bin 169 -> 0 bytes
| ...hunk-24_2d5911b3224001929238ff0fe466dc63.RData | Bin 3052 -> 0 bytes
| ...-chunk-24_2d5911b3224001929238ff0fe466dc63.rdb | Bin 1028 -> 0 bytes
| ...-chunk-24_2d5911b3224001929238ff0fe466dc63.rdx | Bin 176 -> 0 bytes
| ...hunk-24_e2fb976bd1c4ddd539d48664c820d3e8.RData | Bin 0 -> 3092 bytes
| ...-chunk-24_e2fb976bd1c4ddd539d48664c820d3e8.rdb | Bin 0 -> 1028 bytes
| ...-chunk-24_e2fb976bd1c4ddd539d48664c820d3e8.rdx | Bin 0 -> 176 bytes
| ...hunk-25_2cc05c3512d29f056fb93aff83fa874a.RData | Bin 3144 -> 0 bytes
| ...-chunk-25_2cc05c3512d29f056fb93aff83fa874a.rdb | Bin 1071 -> 0 bytes
| ...-chunk-25_2cc05c3512d29f056fb93aff83fa874a.rdx | Bin 172 -> 0 bytes
| ...hunk-25_cebb76da215882e646d5949e7741bb6f.RData | Bin 0 -> 3201 bytes
| ...-chunk-25_cebb76da215882e646d5949e7741bb6f.rdb | Bin 0 -> 1071 bytes
| ...-chunk-25_cebb76da215882e646d5949e7741bb6f.rdx | Bin 0 -> 172 bytes
| ...hunk-26_0e0107d0f8512329816b878a6f5a1aa5.RData | Bin 3477 -> 0 bytes
| ...-chunk-26_0e0107d0f8512329816b878a6f5a1aa5.rdb | Bin 570 -> 0 bytes
| ...-chunk-26_0e0107d0f8512329816b878a6f5a1aa5.rdx | Bin 141 -> 0 bytes
| ...hunk-26_565dc1be57a60e1f915586415a455837.RData | Bin 0 -> 3458 bytes
| ...-chunk-26_565dc1be57a60e1f915586415a455837.rdb | Bin 0 -> 562 bytes
| ...-chunk-26_565dc1be57a60e1f915586415a455837.rdx | Bin 0 -> 141 bytes
| ...hunk-27_2b1e0e0b0ed387ea5b59f6dde28cb372.RData | Bin 0 -> 3288 bytes
| ...-chunk-27_2b1e0e0b0ed387ea5b59f6dde28cb372.rdb | Bin 0 -> 1952 bytes
| ...-chunk-27_2b1e0e0b0ed387ea5b59f6dde28cb372.rdx | Bin 0 -> 172 bytes
| ...hunk-27_ad7c7972c155de2058ccf7cf0120ac61.RData | Bin 3241 -> 0 bytes
| ...-chunk-27_ad7c7972c155de2058ccf7cf0120ac61.rdb | Bin 1962 -> 0 bytes
| ...-chunk-27_ad7c7972c155de2058ccf7cf0120ac61.rdx | Bin 174 -> 0 bytes
| ...hunk-28_957f0b22af25177623f2dad88f375c7e.RData | Bin 3444 -> 0 bytes
| ...-chunk-28_957f0b22af25177623f2dad88f375c7e.rdb | Bin 1067 -> 0 bytes
| ...-chunk-28_957f0b22af25177623f2dad88f375c7e.rdx | Bin 156 -> 0 bytes
| ...hunk-28_a920283370fb5e377c9ab52b0e8e6f00.RData | Bin 0 -> 3490 bytes
| ...-chunk-28_a920283370fb5e377c9ab52b0e8e6f00.rdb | Bin 0 -> 1057 bytes
| ...-chunk-28_a920283370fb5e377c9ab52b0e8e6f00.rdx | Bin 0 -> 156 bytes
| ...hunk-29_12f892b1ead1d73ff2f1d0c38721055f.RData | Bin 0 -> 3333 bytes
| ...-chunk-29_12f892b1ead1d73ff2f1d0c38721055f.rdb | Bin 0 -> 2564 bytes
| ...-chunk-29_12f892b1ead1d73ff2f1d0c38721055f.rdx | Bin 0 -> 206 bytes
| ...hunk-29_2cd9396a66e20aa45d42fde8ce02f59b.RData | Bin 3272 -> 0 bytes
| ...-chunk-29_2cd9396a66e20aa45d42fde8ce02f59b.rdb | Bin 2586 -> 0 bytes
| ...-chunk-29_2cd9396a66e20aa45d42fde8ce02f59b.rdx | Bin 208 -> 0 bytes
| ...chunk-2_b1697d1b75fe3245bc27d5ec4a380a72.RData | Bin 459 -> 0 bytes
| ...d-chunk-2_b1697d1b75fe3245bc27d5ec4a380a72.rdb | 0
| ...d-chunk-2_b1697d1b75fe3245bc27d5ec4a380a72.rdx | Bin 113 -> 0 bytes
| ...chunk-2_b4628ab5709db378bcab1727e34e1a30.RData | Bin 0 -> 488 bytes
| ...d-chunk-2_b4628ab5709db378bcab1727e34e1a30.rdb | 0
| ...d-chunk-2_b4628ab5709db378bcab1727e34e1a30.rdx | Bin 0 -> 113 bytes
| ...hunk-30_637cf7993ed915d704a1112cb31c306e.RData | Bin 3313 -> 0 bytes
| ...-chunk-30_637cf7993ed915d704a1112cb31c306e.rdb | Bin 766 -> 0 bytes
| ...-chunk-30_637cf7993ed915d704a1112cb31c306e.rdx | Bin 141 -> 0 bytes
| ...hunk-30_81ab30eb315472d1e8c00b2edf11b5d8.RData | Bin 0 -> 3347 bytes
| ...-chunk-30_81ab30eb315472d1e8c00b2edf11b5d8.rdb | Bin 0 -> 760 bytes
| ...-chunk-30_81ab30eb315472d1e8c00b2edf11b5d8.rdx | Bin 0 -> 141 bytes
| ...hunk-31_c0f390969f965340b112bb54614c5ea0.RData | Bin 0 -> 4255 bytes
| ...-chunk-31_c0f390969f965340b112bb54614c5ea0.rdb | Bin 0 -> 954 bytes
| ...-chunk-31_c0f390969f965340b112bb54614c5ea0.rdx | Bin 0 -> 158 bytes
| ...hunk-31_f2b7319faf2b67ca3ccdf80cf827c120.RData | Bin 4205 -> 0 bytes
| ...-chunk-31_f2b7319faf2b67ca3ccdf80cf827c120.rdb | Bin 954 -> 0 bytes
| ...-chunk-31_f2b7319faf2b67ca3ccdf80cf827c120.rdx | Bin 158 -> 0 bytes
| ...hunk-32_035887295a5884b323b1e65c8c65dd5a.RData | Bin 0 -> 3314 bytes
| ...-chunk-32_035887295a5884b323b1e65c8c65dd5a.rdb | Bin 0 -> 9082 bytes
| ...-chunk-32_035887295a5884b323b1e65c8c65dd5a.rdx | Bin 0 -> 202 bytes
| ...hunk-33_c9bfcda22efd46a0858e444c19ad4d39.RData | Bin 0 -> 3165 bytes
| ...-chunk-33_c9bfcda22efd46a0858e444c19ad4d39.rdb | Bin 0 -> 8534 bytes
| ...-chunk-33_c9bfcda22efd46a0858e444c19ad4d39.rdx | Bin 0 -> 182 bytes
| ...hunk-34_8ffad53bb8af151a2dcefeff754912dc.RData | Bin 0 -> 3083 bytes
| ...-chunk-34_8ffad53bb8af151a2dcefeff754912dc.rdb | 0
| ...-chunk-34_8ffad53bb8af151a2dcefeff754912dc.rdx | Bin 0 -> 113 bytes
| ...chunk-3_2b65de8658503fe47d1d10c4cb83073c.RData | Bin 0 -> 514 bytes
| ...d-chunk-3_2b65de8658503fe47d1d10c4cb83073c.rdb | Bin 0 -> 1847 bytes
| ...d-chunk-3_2b65de8658503fe47d1d10c4cb83073c.rdx | Bin 0 -> 175 bytes
| ...chunk-3_4ef8fe5aacf608de0ba1979299093591.RData | Bin 495 -> 0 bytes
| ...d-chunk-3_4ef8fe5aacf608de0ba1979299093591.rdb | Bin 1847 -> 0 bytes
| ...d-chunk-3_4ef8fe5aacf608de0ba1979299093591.rdx | Bin 175 -> 0 bytes
| ...chunk-4_8d9acbb5d1f738b78a4e4d01a7c12331.RData | Bin 0 -> 518 bytes
| ...d-chunk-4_8d9acbb5d1f738b78a4e4d01a7c12331.rdb | 0
| ...d-chunk-4_8d9acbb5d1f738b78a4e4d01a7c12331.rdx | Bin 0 -> 113 bytes
| ...chunk-4_bba12a841818c3c67f69ec6e4524dcbd.RData | Bin 513 -> 0 bytes
| ...d-chunk-4_bba12a841818c3c67f69ec6e4524dcbd.rdb | 0
| ...d-chunk-4_bba12a841818c3c67f69ec6e4524dcbd.rdx | Bin 113 -> 0 bytes
| ...chunk-5_47af34f72262629ec1361d6f77945080.RData | Bin 0 -> 463 bytes
| ...d-chunk-5_47af34f72262629ec1361d6f77945080.rdb | Bin 0 -> 38 bytes
| ...d-chunk-5_47af34f72262629ec1361d6f77945080.rdx | Bin 0 -> 135 bytes
| ...chunk-5_af11743ad81164feb1b10cd39101f245.RData | Bin 464 -> 0 bytes
| ...d-chunk-5_af11743ad81164feb1b10cd39101f245.rdb | Bin 38 -> 0 bytes
| ...d-chunk-5_af11743ad81164feb1b10cd39101f245.rdx | Bin 135 -> 0 bytes
| ...chunk-6_5ea308b9fdde39d7ccaac454435731f3.RData | Bin 473 -> 0 bytes
| ...d-chunk-6_5ea308b9fdde39d7ccaac454435731f3.rdb | 0
| ...d-chunk-6_5ea308b9fdde39d7ccaac454435731f3.rdx | Bin 113 -> 0 bytes
| ...chunk-6_9fd4890494b261cc7b5cb2c7169b4458.RData | Bin 0 -> 473 bytes
| ...d-chunk-6_9fd4890494b261cc7b5cb2c7169b4458.rdb | 0
| ...d-chunk-6_9fd4890494b261cc7b5cb2c7169b4458.rdx | Bin 0 -> 113 bytes
| ...chunk-7_1027ff91092bfb1b34b33071e7672401.RData | Bin 0 -> 287 bytes
| ...d-chunk-7_1027ff91092bfb1b34b33071e7672401.rdb | 0
| ...d-chunk-7_1027ff91092bfb1b34b33071e7672401.rdx | Bin 0 -> 113 bytes
| ...chunk-7_7f6291cd0484ecb01f8cff789ae06888.RData | Bin 276 -> 0 bytes
| ...d-chunk-7_7f6291cd0484ecb01f8cff789ae06888.rdb | 0
| ...d-chunk-7_7f6291cd0484ecb01f8cff789ae06888.rdx | Bin 113 -> 0 bytes
| ...chunk-8_215ee19122915a3934fdfa0be0fc6b44.RData | Bin 434 -> 0 bytes
| ...d-chunk-8_215ee19122915a3934fdfa0be0fc6b44.rdb | Bin 1862 -> 0 bytes
| ...d-chunk-8_215ee19122915a3934fdfa0be0fc6b44.rdx | Bin 176 -> 0 bytes
| ...chunk-8_8fb95628a4ed34b21ac6737e13bd30fd.RData | Bin 0 -> 456 bytes
| ...d-chunk-8_8fb95628a4ed34b21ac6737e13bd30fd.rdb | Bin 0 -> 1866 bytes
| ...d-chunk-8_8fb95628a4ed34b21ac6737e13bd30fd.rdx | Bin 0 -> 176 bytes
| ...chunk-9_936345d3e011ace1a79be34607704491.RData | Bin 269 -> 0 bytes
| ...d-chunk-9_936345d3e011ace1a79be34607704491.rdb | 0
| ...d-chunk-9_936345d3e011ace1a79be34607704491.rdx | Bin 113 -> 0 bytes
| ...chunk-9_fa9394504afd6a07fa83f4d539ad4911.RData | Bin 0 -> 270 bytes
| ...d-chunk-9_fa9394504afd6a07fa83f4d539ad4911.rdb | 0
| ...d-chunk-9_fa9394504afd6a07fa83f4d539ad4911.rdx | Bin 0 -> 113 bytes
| vignettes/dendextend-tutorial-concordance.tex | 11 +-
| vignettes/dendextend-tutorial.log | 639 +--
| vignettes/dendextend-tutorial.pdf | 4052 +++++++++++--------
| vignettes/dendextend-tutorial.rnw | 53 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 122873 -> 133707 bytes
| vignettes/dendextend-tutorial.tex | 819 ++--
| vignettes/dendextend-tutorial.toc | 0
| vignettes/figure/first_tanglegram.pdf | Bin 0 -> 15798 bytes
| vignettes/figure/first_tanglegram1.pdf | Bin 0 -> 3450 bytes
| vignettes/figure/first_tanglegram2.pdf | Bin 0 -> 15825 bytes
| vignettes/figure/iris_colored_branches.pdf | Bin 17744 -> 17747 bytes
| vignettes/figure/iris_colored_pairs_plot.pdf | Bin 74472 -> 74472 bytes
| vignettes/figure/unnamed-chunk-19.pdf | Bin 4578 -> 4578 bytes
| vignettes/figure/unnamed-chunk-23.pdf | Bin 4921 -> 4921 bytes
| vignettes/figure/unnamed-chunk-24.pdf | Bin 4576 -> 4576 bytes
| vignettes/figure/unnamed-chunk-25.pdf | Bin 4925 -> 4925 bytes
| vignettes/figure/unnamed-chunk-26.pdf | Bin 4564 -> 4564 bytes
| vignettes/figure/unnamed-chunk-27.pdf | Bin 5273 -> 5273 bytes
| vignettes/figure/unnamed-chunk-28.pdf | Bin 4694 -> 4694 bytes
| vignettes/figure/unnamed-chunk-29.pdf | Bin 5655 -> 5655 bytes
| vignettes/figure/unnamed-chunk-30.pdf | Bin 5369 -> 5374 bytes
| vignettes/figure/unnamed-chunk-32.pdf | Bin 0 -> 15665 bytes
| vignettes/figure/unnamed-chunk-321.pdf | Bin 0 -> 3448 bytes
| vignettes/figure/unnamed-chunk-322.pdf | Bin 0 -> 15508 bytes
| vignettes/figure/unnamed-chunk-33.pdf | Bin 0 -> 15732 bytes
| vignettes/figure/unnamed-chunk-331.pdf | Bin 0 -> 3448 bytes
| vignettes/figure/unnamed-chunk-332.pdf | Bin 0 -> 15665 bytes
| vignettes/figure/unnamed-chunk-333.pdf | Bin 0 -> 15739 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| 233 files changed, 3207 insertions(+), 2367 deletions(-)
* 2013-08-11(Tal Galili) entanglement - added .Rd example |1cf03a8|
| R/entanglement.r | 3 ++-
| man/entanglement.Rd | 43 +++++++++++++++++++++++++++++++++++++++----
| 2 files changed, 41 insertions(+), 5 deletions(-)
* 2013-08-11(Tal Galili) tanglegram - added a "main" parameter. |af21484|
| R/tanglegram.r | 4 +++-
| man/tanglegram.Rd | 2 ++
| 2 files changed, 5 insertions(+), 1 deletion(-)
* 2013-08-10(Tal Galili) entanglement function added! |df51acb|
| DESCRIPTION | 1 -
| NAMESPACE | 4 +
| NEWS | 1 +
| R/entanglement.r | 238 +++++++++++++++++++++++++++++----------
| R/nleaves.r | 6 +-
| inst/tests/test-entanglement.r | 44 ++++++++
| man/entanglement.Rd | 83 ++++++++++++++
| man/nleaves.Rd | 2 +-
| 8 files changed, 313 insertions(+), 66 deletions(-)
* 2013-08-10(Tal Galili) moved code from entanglement.r. -> to -> untangle.r |a10f2bd|
| DESCRIPTION | 1 +
| R/entanglement.r | 760 ----------------------------------------------------
| R/untangle.r | 772 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| 3 files changed, 773 insertions(+), 760 deletions(-)
* 2013-08-10(Tal Galili) Rename: 'untangle.r' -> 'entanglement.r' |83e7293|
| DESCRIPTION | 3 +-
| R/entanglement.r | 1080 +++++++++++++++++++++++++++++++++++++
| R/untangle.r | 1082 --------------------------------------
| inst/tests/test-entanglement.r | 64 +++
| inst/tests/test-untangle.r | 64 ---
| 5 files changed, 1146 insertions(+), 1147 deletions(-)
* 2013-08-10(Tal Galili) match_order_dendrogram_by_old_order function added. |3a1c4e2|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/tanglegram.r | 4 +
| R/untangle.r | 158 +++++++++++++++++----------
| inst/tests/test-untangle.r | 34 ++++++
| man/match_order_by_labels.Rd | 6 +-
| man/match_order_dendrogram_by_old_order.Rd | 76 +++++++++++++
| 7 files changed, 219 insertions(+), 61 deletions(-)
* 2013-08-10(Tal Galili) nleaves - now allow the use of the "members" attr of a dendrogram for telling us the size of the tree. |52e15fe|
| NEWS | 1 +
| R/nleaves.r | 42 ++++++++++++++++++++++++++++++++----------
| inst/tests/test-nleaves.r | 6 ++++++
| man/nleaves.Rd | 10 +++++++++-
| 4 files changed, 48 insertions(+), 11 deletions(-)
* 2013-08-10(Tal Galili) length(order.dendrogram(object)) -> nleaves(object) |9c65dd8|
| R/untangle.r | 6 +++---
| 1 file changed, 3 insertions(+), 3 deletions(-)
* 2013-08-10(Tal Galili) abels_order_labels -> labels |d8932be|
| R/untangle.r | 15 +++++++--------
| inst/tests/test-untangle.r | 3 +++
| 2 files changed, 10 insertions(+), 8 deletions(-)
* 2013-08-10(Tal Galili) match_order_by_labels function added. |c11b0ee|
| NAMESPACE | 1 +
| NEWS | 2 +
| R/untangle.r | 243 +++++++++++++++++++++++------------------
| inst/tests/test-untangle.r | 34 ++++--
| man/match_order_by_labels.Rd | 51 +++++++++
| 5 files changed, 215 insertions(+), 116 deletions(-)
* 2013-08-10(Tal Galili) dendo -> dend |4080be6|
| R/untangle.r | 625 +++++++++++++++++++++++++++++----------------------------
| 1 file changed, 322 insertions(+), 303 deletions(-)
* 2013-08-10(Tal Galili) leaves.values -> order.dendrogram |38073ca|
| R/untangle.r | 80 ++++++++++++++++++++++++++++++----------------------------
| 1 file changed, 42 insertions(+), 38 deletions(-)
* 2013-08-10(Tal Galili) Old code added (it now requires modifications) |022419b|
| R/untangle.r | 955 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 955 insertions(+)
* 2013-08-10(Tal Galili) untangle.r file added |1f6319a|
| DESCRIPTION | 1 +
| NEWS | 3 +++
| R/untangle.r | 28 ++++++++++++++++++++++++++++
| inst/tests/test-rotate.r | 2 +-
| inst/tests/test-untangle.r | 17 +++++++++++++++++
| 5 files changed, 50 insertions(+), 1 deletion(-)
* 2013-08-10(Tal Galili) vignettes - added an example of the tanglegram. |13b84b9|
| vignettes/dendextend-tutorial.rnw | 27 +++++++++++++++++++++++++++
| 1 file changed, 27 insertions(+)
* 2013-08-10(Tal Galili) tanglegram function officially added! |48ea0d0|
| NAMESPACE | 9 +-
| NEWS | 1 +
| R/tanglegram.r | 312 +++++++++++++++++++++++++++-------------------------
| man/tanglegram.Rd | 152 +++++++++++++++++++++++++
| 4 files changed, 324 insertions(+), 150 deletions(-)
* 2013-08-10(Tal Galili) nleaves - changed some export rules. |90c8b95|
| R/nleaves.r | 3 +--
| 1 file changed, 1 insertion(+), 2 deletions(-)
* 2013-08-10(Tal Galili) fix tests for the automatic addition of pch=NA. |da98bde|
| inst/tests/test-attr_access.r | 7 ++++---
| 1 file changed, 4 insertions(+), 3 deletions(-)
* 2013-08-10(Tal Galili) Makes sure pch==NA if we are modifying a nodePar value which is other than pch (and pch did not exist before) - in assign_values_to_leaves_nodePar |307f0b0|
| NEWS | 3 +++
| R/attr_access.r | 18 +++++++++++++++++-
| man/assign_values_to_leaves_nodePar.Rd | 4 ++++
| 3 files changed, 24 insertions(+), 1 deletion(-)
* 2013-08-10(Tal Galili) assign_values_to_branches_edgePar function added |d11873b|
| NEWS | 2 +
| R/attr_access.r | 80 ++++++++++++++++++++++++++++++
| man/assign_values_to_branches_edgePar.Rd | 43 ++++++++++++++++
| man/remove_branches_edgePar.Rd | 35 +++++++++++++
| 4 files changed, 160 insertions(+)
* 2013-08-10(Tal Galili) remove_leaves_nodePar function added. |d15f8d6|
| NEWS | 2 +-
| R/attr_access.r | 48 +++++++++++++++++++++++++++++++++++++++++
| inst/tests/test-attr_access.r | 15 +++++++++++++
| man/get_leaves_attr.Rd | 2 ++
| man/remove_leaves_nodePar.Rd | 40 ++++++++++++++++++++++++++++++++++
| 5 files changed, 106 insertions(+), 1 deletion(-)
* 2013-08-10(Tal Galili) plot_horiz.dendrogram function added |0badd90|
| DESCRIPTION | 4 +-
| NAMESPACE | 1 +
| NEWS | 6 +
| R/tanglegram.r | 321 +++++++++++++++++++++++++++++++++++++----
| man/plot_horiz.dendrogram.Rd | 84 +++++++++++
| 5 files changed, 389 insertions(+), 27 deletions(-)
* 2013-08-10(Tal Galili) fix donotrun ->dontrun |8ad570c|
| R/attr_access.r | 4 ++--
| man/assign_values_to_leaves_nodePar.Rd | 2 +-
| man/get_nodes_attr.Rd | 2 +-
| 3 files changed, 4 insertions(+), 4 deletions(-)
* 2013-08-05(Tal Galili) intersect_trees - added the "warn" parameter. |fed9f78|
| NEWS | 1 +
| R/trim.r | 16 +++++++++++-----
| man/intersect_trees.Rd | 5 ++++-
| 3 files changed, 16 insertions(+), 6 deletions(-)
* 2013-08-05(Tal Galili) Changed "dend1" -> "tree1", and added methods for hclust/phylo (by simply turning them into dendrograms) |055fad9|
| R/tanglegram.r | 42 ++++++++++++++++++++++++------------------
| 1 file changed, 24 insertions(+), 18 deletions(-)
* 2013-08-05(Tal Galili) fac2num - updated doc |980e0c5|
| R/rotate.r | 24 ++++++++++++++++++++++++
| man/fac2num.Rd | 9 ++++++---
| man/rotate.Rd | 8 ++++++++
| 3 files changed, 38 insertions(+), 3 deletions(-)
* 2013-08-05(Tal Galili) tanglegram- remove un-needed comments |11ffb1f|
| R/tanglegram.r | 69 +++++++++++---------------------------------------------
| 1 file changed, 13 insertions(+), 56 deletions(-)
* 2013-08-05(Tal Galili) tanglegram - more parameters. Made it so that the labels will be handled by plot.dendrogram (instead of by me) |4edbc4d|
| R/tanglegram.r | 107 +++++++++++++++++++++++++++++++++++--------------------
| 1 file changed, 69 insertions(+), 38 deletions(-)
* 2013-08-05(Tal Galili) tanglegram file/function added! |61b7f11|
| DESCRIPTION | 1 +
| NEWS | 2 +
| R/tanglegram.r | 162 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 3 files changed, 165 insertions(+)
* 2013-08-05(Tal Galili) order.dendrogram - added tests and made the function a bit more optimized. |3468f62|
| R/labels.r | 22 +++++++++++++++-------
| inst/tests/test-labels-assign.r | 25 +++++++++++++++++++++++++
| 2 files changed, 40 insertions(+), 7 deletions(-)
* 2013-08-05(Tal Galili) fac2num - added tests and a keep_names parameter |cdde4d4|
| NEWS | 4 ++++
| R/cutree.dendrogram.r | 8 +++++---
| inst/tests/test-cutree.dendrogram.r | 13 ++++++++++++-
| 3 files changed, 21 insertions(+), 4 deletions(-)
* 2013-08-05(Tal Galili) rotate - fixes calling the same functions more than once (minor improvements) |28e6de1|
| NEWS | 9 +++++++++
| R/labels.r | 4 ++--
| R/rotate.r | 19 +++++++++++++------
| inst/tests/test-rotate.r | 3 +++
| 4 files changed, 27 insertions(+), 8 deletions(-)
* 2013-08-04(Tal Galili) Change title |b9a64d9|
| vignettes/dendextend-tutorial.rnw | 6 +++---
| 1 file changed, 3 insertions(+), 3 deletions(-)
* 2013-08-02(Tal Galili) bump date, and added a link to where I'll publish posts about the package. |f7e66bc|
| DESCRIPTION | 5 +++--
| 1 file changed, 3 insertions(+), 2 deletions(-)
* 2013-08-02(Tal Galili) Vignettes - added Coloring branches example! |89e6431|
| NEWS | 5 +-
| man/leaf_Colors.Rd | 35 +
| vignettes/cache/__packages | 1 +
| ...ranches_aff39ef9c0e2ae1c023d06d324642a04.RData | Bin 0 -> 3692 bytes
| ..._branches_aff39ef9c0e2ae1c023d06d324642a04.rdb | Bin 0 -> 51879 bytes
| ..._branches_aff39ef9c0e2ae1c023d06d324642a04.rdx | Bin 0 -> 189 bytes
| ...rs_plot_8dfe5036560ecb02840d07882d498136.RData | Bin 0 -> 3124 bytes
| ...airs_plot_8dfe5036560ecb02840d07882d498136.rdb | Bin 0 -> 127 bytes
| ...airs_plot_8dfe5036560ecb02840d07882d498136.rdx | Bin 0 -> 148 bytes
| ...hunk-10_9e4d22ca7258b454f2701d1413ab82d0.RData | Bin 0 -> 297 bytes
| ...-chunk-10_9e4d22ca7258b454f2701d1413ab82d0.rdb | 0
| ...-chunk-10_9e4d22ca7258b454f2701d1413ab82d0.rdx | Bin 0 -> 113 bytes
| ...hunk-11_a45b2e60d746184500f34c0344888b6d.RData | Bin 0 -> 315 bytes
| ...-chunk-11_a45b2e60d746184500f34c0344888b6d.rdb | Bin 0 -> 36 bytes
| ...-chunk-11_a45b2e60d746184500f34c0344888b6d.rdx | Bin 0 -> 130 bytes
| ...hunk-12_bfd3fdad8685afee49dc53382ab9b940.RData | Bin 0 -> 348 bytes
| ...-chunk-12_bfd3fdad8685afee49dc53382ab9b940.rdb | Bin 0 -> 67 bytes
| ...-chunk-12_bfd3fdad8685afee49dc53382ab9b940.rdx | Bin 0 -> 130 bytes
| ...hunk-13_8532ab73d0f73d385c6b97323ab25374.RData | Bin 0 -> 288 bytes
| ...-chunk-13_8532ab73d0f73d385c6b97323ab25374.rdb | Bin 0 -> 67 bytes
| ...-chunk-13_8532ab73d0f73d385c6b97323ab25374.rdx | Bin 0 -> 130 bytes
| ...hunk-14_864583e5f4bccdbe4e9384020d05f60b.RData | Bin 0 -> 2996 bytes
| ...-chunk-14_864583e5f4bccdbe4e9384020d05f60b.rdb | Bin 0 -> 265 bytes
| ...-chunk-14_864583e5f4bccdbe4e9384020d05f60b.rdx | Bin 0 -> 128 bytes
| ...hunk-15_dd0f20489ecc43d1b15fa7e75d86d497.RData | Bin 0 -> 3074 bytes
| ...-chunk-15_dd0f20489ecc43d1b15fa7e75d86d497.rdb | Bin 0 -> 296 bytes
| ...-chunk-15_dd0f20489ecc43d1b15fa7e75d86d497.rdx | Bin 0 -> 131 bytes
| ...hunk-16_771a6ce242d89b845f40ea3896192cee.RData | Bin 0 -> 3169 bytes
| ...-chunk-16_771a6ce242d89b845f40ea3896192cee.rdb | Bin 0 -> 666 bytes
| ...-chunk-16_771a6ce242d89b845f40ea3896192cee.rdx | Bin 0 -> 163 bytes
| ...hunk-17_72778f36fe1ace467acaa29a9b2284d6.RData | Bin 0 -> 2862 bytes
| ...-chunk-17_72778f36fe1ace467acaa29a9b2284d6.rdb | 0
| ...-chunk-17_72778f36fe1ace467acaa29a9b2284d6.rdx | Bin 0 -> 113 bytes
| ...hunk-18_23e2cce2d0b15bd185767d94b20a1183.RData | Bin 0 -> 3127 bytes
| ...-chunk-18_23e2cce2d0b15bd185767d94b20a1183.rdb | 0
| ...-chunk-18_23e2cce2d0b15bd185767d94b20a1183.rdx | Bin 0 -> 113 bytes
| ...hunk-18_d9d3a2e4138d97442a69288b169de349.RData | Bin 3121 -> 0 bytes
| ...-chunk-18_d9d3a2e4138d97442a69288b169de349.rdb | 0
| ...-chunk-18_d9d3a2e4138d97442a69288b169de349.rdx | Bin 113 -> 0 bytes
| ...hunk-19_0fdbdabbe9e648a253d59bdafafcdc8a.RData | Bin 0 -> 3431 bytes
| ...-chunk-19_0fdbdabbe9e648a253d59bdafafcdc8a.rdb | Bin 0 -> 512 bytes
| ...-chunk-19_0fdbdabbe9e648a253d59bdafafcdc8a.rdx | Bin 0 -> 143 bytes
| ...hunk-20_455b1a3886dfbac3f95e22d03843c020.RData | Bin 0 -> 2943 bytes
| ...-chunk-20_455b1a3886dfbac3f95e22d03843c020.rdb | Bin 0 -> 519 bytes
| ...-chunk-20_455b1a3886dfbac3f95e22d03843c020.rdx | Bin 0 -> 143 bytes
| ...hunk-21_eaa8e7d7a586b81daf2136174b1ac324.RData | Bin 0 -> 3447 bytes
| ...-chunk-21_eaa8e7d7a586b81daf2136174b1ac324.rdb | Bin 0 -> 761 bytes
| ...-chunk-21_eaa8e7d7a586b81daf2136174b1ac324.rdx | Bin 0 -> 155 bytes
| ...hunk-22_705cf338f5523ee13659e8bec07a7cd3.RData | Bin 0 -> 3149 bytes
| ...-chunk-22_705cf338f5523ee13659e8bec07a7cd3.rdb | 0
| ...-chunk-22_705cf338f5523ee13659e8bec07a7cd3.rdx | Bin 0 -> 113 bytes
| ...hunk-23_60c53081752d1b02584bb6e1587ddc3b.RData | Bin 0 -> 3205 bytes
| ...-chunk-23_60c53081752d1b02584bb6e1587ddc3b.rdb | Bin 0 -> 985 bytes
| ...-chunk-23_60c53081752d1b02584bb6e1587ddc3b.rdx | Bin 0 -> 169 bytes
| ...hunk-24_2d5911b3224001929238ff0fe466dc63.RData | Bin 0 -> 3052 bytes
| ...-chunk-24_2d5911b3224001929238ff0fe466dc63.rdb | Bin 0 -> 1028 bytes
| ...-chunk-24_2d5911b3224001929238ff0fe466dc63.rdx | Bin 0 -> 176 bytes
| ...hunk-25_2cc05c3512d29f056fb93aff83fa874a.RData | Bin 0 -> 3144 bytes
| ...-chunk-25_2cc05c3512d29f056fb93aff83fa874a.rdb | Bin 0 -> 1071 bytes
| ...-chunk-25_2cc05c3512d29f056fb93aff83fa874a.rdx | Bin 0 -> 172 bytes
| ...hunk-26_0e0107d0f8512329816b878a6f5a1aa5.RData | Bin 0 -> 3477 bytes
| ...-chunk-26_0e0107d0f8512329816b878a6f5a1aa5.rdb | Bin 0 -> 570 bytes
| ...-chunk-26_0e0107d0f8512329816b878a6f5a1aa5.rdx | Bin 0 -> 141 bytes
| ...hunk-27_ad7c7972c155de2058ccf7cf0120ac61.RData | Bin 0 -> 3241 bytes
| ...-chunk-27_ad7c7972c155de2058ccf7cf0120ac61.rdb | Bin 0 -> 1962 bytes
| ...-chunk-27_ad7c7972c155de2058ccf7cf0120ac61.rdx | Bin 0 -> 174 bytes
| ...hunk-28_957f0b22af25177623f2dad88f375c7e.RData | Bin 0 -> 3444 bytes
| ...-chunk-28_957f0b22af25177623f2dad88f375c7e.rdb | Bin 0 -> 1067 bytes
| ...-chunk-28_957f0b22af25177623f2dad88f375c7e.rdx | Bin 0 -> 156 bytes
| ...hunk-29_2cd9396a66e20aa45d42fde8ce02f59b.RData | Bin 0 -> 3272 bytes
| ...-chunk-29_2cd9396a66e20aa45d42fde8ce02f59b.rdb | Bin 0 -> 2586 bytes
| ...-chunk-29_2cd9396a66e20aa45d42fde8ce02f59b.rdx | Bin 0 -> 208 bytes
| ...chunk-2_b1697d1b75fe3245bc27d5ec4a380a72.RData | Bin 0 -> 459 bytes
| ...d-chunk-2_b1697d1b75fe3245bc27d5ec4a380a72.rdb | 0
| ...d-chunk-2_b1697d1b75fe3245bc27d5ec4a380a72.rdx | Bin 0 -> 113 bytes
| ...hunk-30_637cf7993ed915d704a1112cb31c306e.RData | Bin 0 -> 3313 bytes
| ...-chunk-30_637cf7993ed915d704a1112cb31c306e.rdb | Bin 0 -> 766 bytes
| ...-chunk-30_637cf7993ed915d704a1112cb31c306e.rdx | Bin 0 -> 141 bytes
| ...hunk-30_cc171774502992645f046bd982a86244.RData | Bin 4206 -> 0 bytes
| ...-chunk-30_cc171774502992645f046bd982a86244.rdb | Bin 954 -> 0 bytes
| ...-chunk-30_cc171774502992645f046bd982a86244.rdx | Bin 156 -> 0 bytes
| ...hunk-31_79bbada7960ab7612f76987dabda2a1b.RData | Bin 4203 -> 0 bytes
| ...-chunk-31_79bbada7960ab7612f76987dabda2a1b.rdb | Bin 954 -> 0 bytes
| ...-chunk-31_79bbada7960ab7612f76987dabda2a1b.rdx | Bin 156 -> 0 bytes
| ...hunk-31_f2b7319faf2b67ca3ccdf80cf827c120.RData | Bin 0 -> 4205 bytes
| ...-chunk-31_f2b7319faf2b67ca3ccdf80cf827c120.rdb | Bin 0 -> 954 bytes
| ...-chunk-31_f2b7319faf2b67ca3ccdf80cf827c120.rdx | Bin 0 -> 158 bytes
| ...chunk-3_4ef8fe5aacf608de0ba1979299093591.RData | Bin 0 -> 495 bytes
| ...d-chunk-3_4ef8fe5aacf608de0ba1979299093591.rdb | Bin 0 -> 1847 bytes
| ...d-chunk-3_4ef8fe5aacf608de0ba1979299093591.rdx | Bin 0 -> 175 bytes
| ...chunk-4_bba12a841818c3c67f69ec6e4524dcbd.RData | Bin 0 -> 513 bytes
| ...d-chunk-4_bba12a841818c3c67f69ec6e4524dcbd.rdb | 0
| ...d-chunk-4_bba12a841818c3c67f69ec6e4524dcbd.rdx | Bin 0 -> 113 bytes
| ...chunk-5_af11743ad81164feb1b10cd39101f245.RData | Bin 0 -> 464 bytes
| ...d-chunk-5_af11743ad81164feb1b10cd39101f245.rdb | Bin 0 -> 38 bytes
| ...d-chunk-5_af11743ad81164feb1b10cd39101f245.rdx | Bin 0 -> 135 bytes
| ...chunk-6_5ea308b9fdde39d7ccaac454435731f3.RData | Bin 0 -> 473 bytes
| ...d-chunk-6_5ea308b9fdde39d7ccaac454435731f3.rdb | 0
| ...d-chunk-6_5ea308b9fdde39d7ccaac454435731f3.rdx | Bin 0 -> 113 bytes
| ...chunk-7_7f6291cd0484ecb01f8cff789ae06888.RData | Bin 0 -> 276 bytes
| ...d-chunk-7_7f6291cd0484ecb01f8cff789ae06888.rdb | 0
| ...d-chunk-7_7f6291cd0484ecb01f8cff789ae06888.rdx | Bin 0 -> 113 bytes
| ...chunk-8_215ee19122915a3934fdfa0be0fc6b44.RData | Bin 0 -> 434 bytes
| ...d-chunk-8_215ee19122915a3934fdfa0be0fc6b44.rdb | Bin 0 -> 1862 bytes
| ...d-chunk-8_215ee19122915a3934fdfa0be0fc6b44.rdx | Bin 0 -> 176 bytes
| ...chunk-9_936345d3e011ace1a79be34607704491.RData | Bin 0 -> 269 bytes
| ...d-chunk-9_936345d3e011ace1a79be34607704491.rdb | 0
| ...d-chunk-9_936345d3e011ace1a79be34607704491.rdx | Bin 0 -> 113 bytes
| vignettes/dendextend-tutorial-concordance.tex | 12 +-
| vignettes/dendextend-tutorial.log | 463 +--
| vignettes/dendextend-tutorial.pdf | 3359 +++++++++++--------
| vignettes/dendextend-tutorial.rnw | 105 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 110745 -> 122873 bytes
| vignettes/dendextend-tutorial.tex | 278 +-
| vignettes/figure/iris_colored_branches.pdf | Bin 0 -> 17744 bytes
| vignettes/figure/iris_colored_pairs_plot.pdf | Bin 0 -> 74472 bytes
| vignettes/figure/unnamed-chunk-19.pdf | Bin 4578 -> 4578 bytes
| vignettes/figure/unnamed-chunk-20.pdf | Bin 4921 -> 0 bytes
| vignettes/figure/unnamed-chunk-21.pdf | Bin 4576 -> 0 bytes
| vignettes/figure/unnamed-chunk-22.pdf | Bin 4921 -> 0 bytes
| vignettes/figure/unnamed-chunk-23.pdf | Bin 4921 -> 4921 bytes
| vignettes/figure/unnamed-chunk-24.pdf | Bin 4576 -> 4576 bytes
| vignettes/figure/unnamed-chunk-25.pdf | Bin 4925 -> 4925 bytes
| vignettes/figure/unnamed-chunk-26.pdf | Bin 4897 -> 4564 bytes
| vignettes/figure/unnamed-chunk-27.pdf | Bin 5801 -> 5273 bytes
| vignettes/figure/unnamed-chunk-28.pdf | Bin 5132 -> 4694 bytes
| vignettes/figure/unnamed-chunk-29.pdf | Bin 6930 -> 5655 bytes
| vignettes/figure/unnamed-chunk-30.pdf | Bin 6361 -> 5369 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| 129 files changed, 2543 insertions(+), 1715 deletions(-)
* 2013-08-02(Tal Galili) Added an example to color_branches |b34b15b|
| R/color_branches.r | 39 ++++++++++++++++++++++++++++++++++++---
| inst/tests/test-attr_access.r | 25 +++++++++++++++++++++++++
| man/color_branches.Rd | 38 +++++++++++++++++++++++++++++++++++---
| 3 files changed, 96 insertions(+), 6 deletions(-)
* 2013-08-02(Tal Galili) "labels_colors<-" - fix the classes of the tree's branches. |7e97f68|
| R/labels_colors.r | 11 +++++++++--
| 1 file changed, 9 insertions(+), 2 deletions(-)
* 2013-08-02(Tal Galili) Function added: assign_values_to_leaves_nodePar - allows for complex manipulation of dendrogram's leaves parameters. |b9c5d91|
| NAMESPACE | 1 +
| NEWS | 4 +-
| R/attr_access.r | 88 ++++++++++++++++++++++++++++++--
| man/assign_values_to_leaves_nodePar.Rd | 55 ++++++++++++++++++++
| man/get_leaves_attr.Rd | 14 +++--
| 5 files changed, 154 insertions(+), 8 deletions(-)
* 2013-08-02(Tal Galili) test to show that labels with integer values are VERY possible. |94f1aa7|
| inst/tests/test-labels-assign.r | 10 ++++++++++
| 1 file changed, 10 insertions(+)
* 2013-08-02(Tal Galili) test-unroot.r -> test-unbranch.r |cefa337|
| inst/tests/test-unbranch.r | 45 ++++++++++++++++++++++++++++++++++++++++++++
| inst/tests/test-unroot.r | 45 --------------------------------------------
| 2 files changed, 45 insertions(+), 45 deletions(-)
* 2013-08-02(Tal Galili) as.phylo.dendrogram function added |ff0b4bc|
| NAMESPACE | 1 +
| NEWS | 3 ++-
| R/nleaves.r | 4 +++-
| 3 files changed, 6 insertions(+), 2 deletions(-)
* 2013-08-02(Tal Galili) Renaming the file: unroot.r -> unbranch.r |d467113|
| DESCRIPTION | 2 +-
| R/unbranch.r | 245 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| R/unroot.r | 237 -------------------------------------------------------
| 3 files changed, 246 insertions(+), 238 deletions(-)
* 2013-08-02(Tal Galili) unroot -> unbranch: modify .Rd files |a05d617|
| NAMESPACE | 10 ++++----
| NEWS | 2 +-
| man/color_branches.Rd | 2 +-
| man/cutree-methods.Rd | 22 ++++++++---------
| man/heights_per_k.dendrogram.Rd | 6 ++---
| man/unbranch.Rd | 50 +++++++++++++++++++++++++++++++++++++++
| 6 files changed, 71 insertions(+), 21 deletions(-)
* 2013-08-02(Tal Galili) Renaming the unroot function -> to -> unbranch |938a300|
| R/color_branches.r | 2 +-
| R/cutree.dendrogram.r | 28 ++++++++++----------
| R/unroot.r | 50 +++++++++++++++++------------------
| R/zzz.r | 2 +-
| inst/tests/test-attr_access.r | 16 +++++------
| inst/tests/test-cutree.dendrogram.r | 46 ++++++++++++++++----------------
| inst/tests/test-trim.r | 22 +++++++--------
| inst/tests/test-unroot.r | 20 +++++++-------
| 8 files changed, 93 insertions(+), 93 deletions(-)
* 2013-08-02(Tal Galili) cutree.dendogram - Prevent R from crashing when using cutree on a subset tree (e.g: dend[[1]]) |1cd0014|
| NEWS | 5 ++
| R/cutree.dendrogram.r | 36 ++++++++++++-
| inst/tests/test-cutree.dendrogram.r | 96 ++++++++++++++++++++++++-----------
| man/cutree-methods.Rd | 2 +-
| 4 files changed, 106 insertions(+), 33 deletions(-)
* 2013-08-02(Tal Galili) "order.dendrogram<-" - now returns an integer (instead of numeric) |cc0d038|
| R/labels.r | 33 +++++++++++++++++++++++++++++++--
| inst/tests/test-labels-assign.r | 22 ++++++++++++++++++++++
| man/order.dendrogram-assign.Rd | 13 +++++++++++++
| 3 files changed, 66 insertions(+), 2 deletions(-)
* 2013-08-02(Tal Galili) making sure labels.hclust is exported! |af9751e|
| NAMESPACE | 5 +++++
| R/labels.r | 12 ++++++------
| 2 files changed, 11 insertions(+), 6 deletions(-)
* 2013-08-02(Tal Galili) Fixed a bug in color_branches when the tree's labels are integers! |32e2a42|
| NEWS | 4 +--
| R/color_branches.r | 51 ++++++++++++++++++++++++++++++++---
| inst/tests/test-cutree.dendrogram.r | 41 ++++++++++++++++++++++++++++
| man/color_branches.Rd | 46 ++++++++++++++++++++++++++++++-
| 4 files changed, 136 insertions(+), 6 deletions(-)
* 2013-08-02(Tal Galili) Extend color_branches to allow REPEATED cluster color assignments to branches on to the same tree. Something which the original function was not able to handle. |479ca6f|
| NEWS | 4 ++--
| R/color_branches.r | 53 ++++++++++++++++++++++++++++++++++++++++---------
| man/color_branches.Rd | 24 +++++++++++++++++++++-
| man/color_labels.Rd | 3 +++
| 4 files changed, 72 insertions(+), 12 deletions(-)
* 2013-08-01(Tal Galili) "labels_colors<-" - fixed it so that by default it would not add phc=1 to the leaves. |7d8d9d0|
| NEWS | 2 +-
| R/labels_colors.r | 20 +++++++++++++++++++-
| 2 files changed, 20 insertions(+), 2 deletions(-)
* 2013-08-01(Tal Galili) color_labels function added. |c17a1d1|
| NAMESPACE | 1 +
| NEWS | 2 +
| R/color_branches.r | 111 +++++++++++++++++++++++++++++++++++++++++++++---
| man/color_branches.Rd | 5 ++-
| man/color_labels.Rd | 70 ++++++++++++++++++++++++++++++
| 5 files changed, 182 insertions(+), 7 deletions(-)
* 2013-08-01(Tal Galili) Fix cutree.dendrogram for the case of using hclust - so it will respect sort_cluster_numbers! |f4bd3ce|
| R/cutree.dendrogram.r | 4 +++-
| 1 file changed, 3 insertions(+), 1 deletion(-)
* 2013-08-01(Tal Galili) fix missed \code{ and added "..." |21b2009|
| man/color_branches.Rd | 8 +++++---
| 1 file changed, 5 insertions(+), 3 deletions(-)
* 2013-08-01(Tal Galili) Another test for intersect_trees |c5b15e4|
| inst/tests/test-trim.r | 13 +++++++++++++
| 1 file changed, 13 insertions(+)
* 2013-08-01(Tal Galili) color_branches function added. |243a91b|
| NAMESPACE | 4 ++
| NEWS | 1 +
| R/color_branches.r | 125 ++++++++++++++++++++++++++++++++----------------
| man/color_branches.Rd | 77 +++++++++++++++++++++++++++++
| 4 files changed, 167 insertions(+), 40 deletions(-)
* 2013-08-01(Tal Galili) Fixed typo |af1128d|
| R/labels_colors.r | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2013-08-01(Tal Galili) Updated the is.X functions docs |606044e|
| NEWS | 10 +++++++++-
| man/is.dendrogram.Rd | 6 ++++++
| man/is.hclust.Rd | 6 ++++++
| man/is.phylo.Rd | 6 ++++++
| 4 files changed, 27 insertions(+), 1 deletion(-)
* 2013-08-01(Tal Galili) sort_levels_values function added. |d591a2d|
| R/cutree.dendrogram.r | 126 ++++++++++++++++++++++++++++++++++
| inst/tests/test-cutree.dendrogram.r | 96 ++++++++++++++++++++++++++
| man/cutree-methods.Rd | 20 +++++-
| man/fac2num.Rd | 31 +++++++++
| man/sort_levels_values.Rd | 67 ++++++++++++++++++
| 5 files changed, 337 insertions(+), 3 deletions(-)
* 2013-08-01(Tal Galili) color_branches.r file added - it includes the original "colour_clusters" and "leaf_colours" from the {dendroextras} package. |a0d3281|
| DESCRIPTION | 1 +
| R/color_branches.r | 133 +++++++++++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 134 insertions(+)
* 2013-08-01(Tal Galili) Fix license reference (now pointing to http://www.r-project.org/Licenses/) |5330e51|
| DESCRIPTION | 2 +-
| R/attr_access.r | 20 +++++++++++++++++---
| R/cutree.dendrogram.r | 19 +++++++++++++++++++
| R/dendextend-package.r | 5 +++--
| R/dendextend.r | 5 +++--
| R/labels.r | 5 +++--
| R/labels_colors.r | 5 +++--
| R/nleaves.r | 5 +++--
| R/rotate.r | 5 +++--
| R/trim.r | 5 +++--
| R/unroot.r | 5 +++--
| R/zzz.r | 5 +++--
| 12 files changed, 64 insertions(+), 22 deletions(-)
* 2013-07-31(Tal Galili) vignettes - adding examples for cutree.dendrogram and hang.dendrogram. |1d9844d|
| vignettes/cache/__packages | 8 +-
| ...hunk-30_cc171774502992645f046bd982a86244.RData | Bin 0 -> 4206 bytes
| ...-chunk-30_cc171774502992645f046bd982a86244.rdb | Bin 0 -> 954 bytes
| ...-chunk-30_cc171774502992645f046bd982a86244.rdx | Bin 0 -> 156 bytes
| ...hunk-31_79bbada7960ab7612f76987dabda2a1b.RData | Bin 0 -> 4203 bytes
| ...-chunk-31_79bbada7960ab7612f76987dabda2a1b.rdb | Bin 0 -> 954 bytes
| ...-chunk-31_79bbada7960ab7612f76987dabda2a1b.rdx | Bin 0 -> 156 bytes
| vignettes/dendextend-tutorial-concordance.tex | 4 +-
| vignettes/dendextend-tutorial.log | 265 ++-
| vignettes/dendextend-tutorial.pdf | 2322 ++++++++++---------
| vignettes/dendextend-tutorial.rnw | 85 +
| vignettes/dendextend-tutorial.synctex.gz | Bin 92717 -> 110745 bytes
| vignettes/dendextend-tutorial.tex | 234 +-
| vignettes/figure/unnamed-chunk-19.pdf | Bin 4578 -> 4578 bytes
| vignettes/figure/unnamed-chunk-23.pdf | Bin 4921 -> 4921 bytes
| vignettes/figure/unnamed-chunk-24.pdf | Bin 4576 -> 4576 bytes
| vignettes/figure/unnamed-chunk-25.pdf | Bin 4925 -> 4925 bytes
| vignettes/figure/unnamed-chunk-26.pdf | Bin 4897 -> 4897 bytes
| vignettes/figure/unnamed-chunk-27.pdf | Bin 5132 -> 5801 bytes
| vignettes/figure/unnamed-chunk-28.pdf | Bin 6930 -> 5132 bytes
| vignettes/figure/unnamed-chunk-29.pdf | Bin 6361 -> 6930 bytes
| vignettes/figure/unnamed-chunk-30.pdf | Bin 0 -> 6361 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| 23 files changed, 1769 insertions(+), 1149 deletions(-)
* 2013-07-31(Tal Galili) cutree.dendrogram function added. With many docs and tests! |715711a|
| NAMESPACE | 6 +
| NEWS | 8 +
| R/cutree.dendrogram.r | 305 +++++++++++++++++++++++++++++-----
| inst/tests/test-attr_access.r | 2 +-
| inst/tests/test-cutree.dendrogram.r | 114 ++++++++++++-
| man/cutree-methods.Rd | 167 +++++++++++++++++++
| man/cutree.dendrogram.Rd | 118 +++++++++++++
| man/cutree_1h.dendrogram.Rd | 5 +-
| man/cutree_1k.dendrogram.Rd | 6 +-
| man/is.dendrogram.Rd | 10 ++
| man/is.hclust.Rd | 10 ++
| man/is.phylo.Rd | 10 ++
| 12 files changed, 714 insertions(+), 47 deletions(-)
* 2013-07-31(Tal Galili) cutree_1k.dendrogram - added tests |e58929f|
| R/cutree.dendrogram.r | 33 +++++++++++++++++++-----
| inst/tests/test-cutree.dendrogram.r | 48 +++++++++++++++++++++++++++++++++++
| 2 files changed, 75 insertions(+), 6 deletions(-)
* 2013-07-31(Tal Galili) dendrogram_heights_per_k -> dend_heights_per_k |2e971e2|
| R/cutree.dendrogram.r | 36 +++++++++++++++++++----------------
| inst/tests/test-cutree.dendrogram.r | 9 ++-------
| man/cutree_1k.dendrogram.Rd | 28 +++++++++++++++------------
| 3 files changed, 38 insertions(+), 35 deletions(-)
* 2013-07-31(Tal Galili) cutree_1k.dendrogram function added. |7c5fff9|
| NAMESPACE | 1 +
| NEWS | 4 +-
| R/cutree.dendrogram.r | 126 ++++++++++++++++++++++++++++++------------
| man/cutree_1h.dendrogram.Rd | 21 ++++---
| man/cutree_1k.dendrogram.Rd | 88 +++++++++++++++++++++++++++++
| man/is.natural.number.Rd | 2 +-
| 6 files changed, 197 insertions(+), 45 deletions(-)
* 2013-07-31(Tal Galili) Moving hang.dendrogram from cutree.dendrogram.r to attr_access.r |4dc03d9|
| R/attr_access.r | 97 +++++++++++++++++++++++++++++++++++
| R/cutree.dendrogram.r | 89 --------------------------------
| inst/tests/test-attr_access.r | 31 +++++++++++
| inst/tests/test-cutree.dendrogram.r | 32 ------------
| 4 files changed, 128 insertions(+), 121 deletions(-)
* 2013-07-31(Tal Galili) Make cutree_1h.dendrogram identical to cutree when height is above ALL clusters |0395b13|
| R/cutree.dendrogram.r | 10 ++++++++--
| inst/tests/test-cutree.dendrogram.r | 12 ++++++------
| 2 files changed, 14 insertions(+), 8 deletions(-)
* 2013-07-31(Tal Galili) Fix a major bug in cutree_1h.dendrogram due to some line getting erased at some point (not clear when that bug was introduced). |981a6a3|
| NEWS | 2 ++
| R/cutree.dendrogram.r | 16 ++++++++++++----
| inst/tests/test-cutree.dendrogram.r | 30 ++++++++++++++++++++++++++++++
| man/heights_per_k.dendrogram.Rd | 7 +++++++
| 4 files changed, 51 insertions(+), 4 deletions(-)
* 2013-07-31(Tal Galili) vignettes - added some attr extraction examples. |6779acf|
| vignettes/dendextend-tutorial-concordance.tex | 8 +-
| vignettes/dendextend-tutorial.log | 509 +++--
| vignettes/dendextend-tutorial.pdf | 2724 ++++++++++++-----------
| vignettes/dendextend-tutorial.rnw | 81 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 82110 -> 92717 bytes
| vignettes/dendextend-tutorial.tex | 243 +-
| vignettes/figure/unnamed-chunk-19.pdf | Bin 4578 -> 4578 bytes
| vignettes/figure/unnamed-chunk-22.pdf | Bin 4925 -> 4921 bytes
| vignettes/figure/unnamed-chunk-23.pdf | Bin 4897 -> 4921 bytes
| vignettes/figure/unnamed-chunk-24.pdf | Bin 5132 -> 4576 bytes
| vignettes/figure/unnamed-chunk-25.pdf | Bin 6930 -> 4925 bytes
| vignettes/figure/unnamed-chunk-26.pdf | Bin 6361 -> 4897 bytes
| vignettes/figure/unnamed-chunk-27.pdf | Bin 0 -> 5132 bytes
| vignettes/figure/unnamed-chunk-28.pdf | Bin 0 -> 6930 bytes
| vignettes/figure/unnamed-chunk-29.pdf | Bin 0 -> 6361 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| 16 files changed, 2013 insertions(+), 1552 deletions(-)
* 2013-07-31(Tal Galili) test when get_nodes_attr doesn't get an attribute |b333ba4|
| inst/tests/test-attr_access.r | 3 +++
| 1 file changed, 3 insertions(+)
* 2013-07-31(Tal Galili) hang.dendrogram - added a test, and source ref for the function |7fa3d0e|
| inst/tests/test-cutree.dendrogram.r | 22 +++++++++++++++++++---
| man/hang.dendrogram.Rd | 5 +++++
| 2 files changed, 24 insertions(+), 3 deletions(-)
* 2013-07-31(Tal Galili) fix_members_attr.dendrogram function added. |b471984|
| NEWS | 1 +
| R/labels.r | 1 +
| R/trim.r | 56 +++++++++++++++++++++++++++++++++++++++++++++++++++++---
| 3 files changed, 55 insertions(+), 3 deletions(-)
* 2013-07-31(Tal Galili) bumping version to 0.4 (we'll stay here for a while...) |8a55104|
| DESCRIPTION | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2013-07-31(Tal Galili) fix .bib (commas were missing) |fb394a7|
| vignettes/dendextend-tutorial.bib | 8 ++++----
| 1 file changed, 4 insertions(+), 4 deletions(-)
* 2013-07-31(Tal Galili) get_nodes_attr function added |01613a2|
| NAMESPACE | 3 +-
| NEWS | 4 +-
| R/attr_access.r | 218 +++++++++++++++++++++++++++++++++++++++-
| R/cutree.dendrogram.r | 92 +++--------------
| inst/tests/test-attr_access.r | 78 ++++++++++++++
| man/get_branches_heights.Rd | 30 ++++++
| man/get_leaves_attr.Rd | 12 ++-
| man/get_nodes_attr.Rd | 84 ++++++++++++++++
| 8 files changed, 436 insertions(+), 85 deletions(-)
* 2013-07-31(Tal Galili) nnodes function added - count the number of nodes in a tree |1187719|
| NAMESPACE | 8 ++++
| NEWS | 6 +++
| R/nleaves.r | 89 ++++++++++++++++++++++++++++++++++++++++++++-
| inst/tests/test-nleaves.r | 16 +++++++-
| man/nleaves.Rd | 7 ++++
| man/nnodes.Rd | 47 ++++++++++++++++++++++++
| 6 files changed, 170 insertions(+), 3 deletions(-)
* 2013-07-30(Tal Galili) vignettes - expended the abstract a bit. |f8491a5|
| vignettes/dendextend-tutorial.bib | 69 +++++++++++++++++++++++++++++++++++++
| vignettes/dendextend-tutorial.rnw | 13 ++++---
| 2 files changed, 77 insertions(+), 5 deletions(-)
* 2013-07-30(Tal Galili) hang.dendrogram function added, including tests and doc. |82846ea|
| NAMESPACE | 8 ++
| NEWS | 5 +-
| R/cutree.dendrogram.r | 262 +++++++++++++++++++++++++++++-----
| inst/tests/test-cutree.dendrogram.r | 17 +++
| man/fix_members_attr.dendrogram.Rd | 38 +++++
| man/get_heights.dendrogram.Rd | 26 ++++
| man/hang.dendrogram.Rd | 53 +++++++
| man/heights_per_k.dendrogram.Rd | 31 ++++
| man/rllply.Rd | 50 +++++++
| 9 files changed, 452 insertions(+), 38 deletions(-)
* 2013-07-28(Tal Galili) cutree_1h.dendrogram function added (with doc and tests) - like cutree, but only for 1 height |4754ba0|
| NAMESPACE | 3 +
| NEWS | 6 +-
| R/cutree.dendrogram.r | 119 +++++++++++++++++++++++-----------
| inst/tests/test-cutree.dendrogram.r | 39 +++++++++--
| man/cutree_1h.dendrogram.Rd | 63 ++++++++++++++++++
| man/get_leaves_attr.Rd | 10 +--
| man/is.natural.number.Rd | 40 ++++++++++++
| 7 files changed, 225 insertions(+), 55 deletions(-)
* 2013-07-28(Tal Galili) Changed functions names to be more S3 like. |2d125d0|
| R/cutree.dendrogram.r | 99 +++++++++++++++++--------------------------------
| 1 file changed, 33 insertions(+), 66 deletions(-)
* 2013-07-28(Tal Galili) is.natural.number function added (with tests and documentation) |58922db|
| NEWS | 3 +++
| R/cutree.dendrogram.r | 43 ++++++++++++++++++++++++-----------
| inst/tests/test-cutree.dendrogram.r | 22 ++++++++++++++----
| 3 files changed, 51 insertions(+), 17 deletions(-)
* 2013-07-28(Tal Galili) cutree.dendrogram.r - added first version of the file (with the old functions which will now be revised to newer naming conventions and documentation) |55598e4|
| DESCRIPTION | 1 +
| NEWS | 12 +-
| R/attr_access.r | 12 +-
| R/cutree.dendrogram.r | 265 ++++++++++++++++++++++++++++++++++
| inst/tests/test-cutree.dendrogram.r | 14 ++
| vignettes/dendextend-tutorial.rnw | 2 +-
| 6 files changed, 295 insertions(+), 11 deletions(-)
* 2013-07-27(Tal Galili) Vignettes - updated noisense files. |6793d20|
| vignettes/dendextend-tutorial-concordance.tex | 5 +-
| vignettes/dendextend-tutorial.blg | 2 +
| vignettes/dendextend-tutorial.log | 356 ++++++++++++------------
| vignettes/dendextend-tutorial.synctex.gz | Bin 65670 -> 82110 bytes
| vignettes/dendextend-tutorial.tex | 102 ++++++-
| vignettes/figure/unnamed-chunk-19.pdf | Bin 4578 -> 4578 bytes
| vignettes/figure/unnamed-chunk-20.pdf | Bin 4921 -> 4921 bytes
| vignettes/figure/unnamed-chunk-21.pdf | Bin 4576 -> 4576 bytes
| vignettes/figure/unnamed-chunk-22.pdf | Bin 4925 -> 4925 bytes
| vignettes/figure/unnamed-chunk-23.pdf | Bin 4897 -> 4897 bytes
| vignettes/figure/unnamed-chunk-24.pdf | Bin 5126 -> 5132 bytes
| vignettes/figure/unnamed-chunk-25.pdf | Bin 6930 -> 6930 bytes
| vignettes/figure/unnamed-chunk-26.pdf | Bin 0 -> 6361 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| 14 files changed, 274 insertions(+), 191 deletions(-)
* 2013-07-27(Tal Galili) Various changes to rotate - adding documentation and testing! |74ece8d|
| NAMESPACE | 3 +-
| NEWS | 7 +-
| R/rotate.r | 52 +-
| inst/tests/test-rotate.r | 74 ++
| man/as_hclust_fixed.Rd | 3 +-
| man/get_leaves_attr.Rd | 42 +
| man/rotate.Rd | 40 +-
| vignettes/dendextend-tutorial.pdf | 1754 +++++++++++++++++++----------------
| vignettes/dendextend-tutorial.rnw | 53 +-
| 9 files changed, 1198 insertions(+), 830 deletions(-)
* 2013-07-27(Tal Galili) Some work on attr_access.r (not sure if this would be used later or not...). |5d6414e|
| DESCRIPTION | 1 +
| R/attr_access.r | 43 +++++++++++++++++++++++++++++++++++++++++++
| 2 files changed, 44 insertions(+)
* 2013-07-27(Tal Galili) as_hclust_fixed - now works just as as.hclust when hc is missing. |a613071|
| R/dendextend.r | 22 ++++++++++++++--------
| 1 file changed, 14 insertions(+), 8 deletions(-)
* 2013-07-27(Tal Galili) Bump release date for DESCRIPTION (although it will keep moving until a specific stage is released...) |a74140f|
| DESCRIPTION | 4 ++--
| NEWS | 4 ++--
| 2 files changed, 4 insertions(+), 4 deletions(-)
* 2013-07-27(Tal Galili) Move from length(order.dendrogram(x)) to nleaves(x) |1e0501a|
| R/labels.r | 8 ++++----
| 1 file changed, 4 insertions(+), 4 deletions(-)
* 2013-07-27(Tal Galili) Vignettes - adding references to other packages. |8b105cd|
| vignettes/dendextend-tutorial-concordance.tex | 6 +-
| vignettes/dendextend-tutorial.bib | 78 +
| vignettes/dendextend-tutorial.pdf | 2740 +++++++++++++----------
| vignettes/dendextend-tutorial.rnw | 20 +-
| vignettes/dendextend.bib | 636 ------
| 5 files changed, 1633 insertions(+), 1847 deletions(-)
* 2013-07-27(Tal Galili) Forcing {ape} to load before {dendextend}, thus allowing for both rotate and unroot to work for BOTH packages. It does add extra noise when loading the package, but it is the best solution I can think of at this point. |ae741d8|
| R/zzz.r | 22 ++++++++++++++++++++--
| 1 file changed, 20 insertions(+), 2 deletions(-)
* 2013-07-27(Tal Galili) labels_colors - added checks for "dendrogram" class |fb6dad9|
| R/labels_colors.r | 4 ++++
| inst/tests/test-labels_colors.r | 9 +++++++++
| vignettes/dendextend-tutorial.rnw | 27 +++++++++++++++++++--------
| 3 files changed, 32 insertions(+), 8 deletions(-)
* 2013-07-27(Tal Galili) Fix a wrong variable name. |1c96d06|
| inst/tests/test-trim.r | 4 ++--
| 1 file changed, 2 insertions(+), 2 deletions(-)
* 2013-07-27(Tal Galili) Testing for partial assignment. |197370e|
| inst/tests/test-labels-assign.r | 11 +++++++++++
| 1 file changed, 11 insertions(+)
* 2013-07-27(Tal Galili) Adding credit. |634a7a7|
| R/labels.r | 6 +++++-
| 1 file changed, 5 insertions(+), 1 deletion(-)
* 2013-07-27(Tal Galili) labels_colors - adding leaves labels as names to the color vector. Giving credit to Gregory Jefferis. |0d61899|
| R/labels_colors.r | 19 ++++++++++----
| inst/tests/test-labels_colors.r | 53 ++++++++++++++++++++++++++++++++++++---
| man/labels-assign.Rd | 2 ++
| man/labels_colors.Rd | 16 +++++++++---
| 4 files changed, 78 insertions(+), 12 deletions(-)
* 2013-07-26(Tal Galili) Vignettes PDF - updated |e74fe57|
| vignettes/dendextend-tutorial-concordance.tex | 6 +-
| vignettes/dendextend-tutorial.log | 607 +++++-
| vignettes/dendextend-tutorial.pdf | 2378 ++++++++++++++++-------
| vignettes/dendextend-tutorial.synctex.gz | Bin 44992 -> 65670 bytes
| vignettes/dendextend-tutorial.tex | 400 +++-
| vignettes/dendextend-tutorial.toc | 0
| vignettes/figure/unnamed-chunk-19.pdf | Bin 4626 -> 4578 bytes
| vignettes/figure/unnamed-chunk-20.pdf | Bin 0 -> 4921 bytes
| vignettes/figure/unnamed-chunk-21.pdf | Bin 0 -> 4576 bytes
| vignettes/figure/unnamed-chunk-22.pdf | Bin 0 -> 4925 bytes
| vignettes/figure/unnamed-chunk-23.pdf | Bin 0 -> 4897 bytes
| vignettes/figure/unnamed-chunk-24.pdf | Bin 0 -> 5126 bytes
| vignettes/figure/unnamed-chunk-25.pdf | Bin 0 -> 6930 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| 14 files changed, 2570 insertions(+), 821 deletions(-)
* 2013-07-26(Tal Galili) Updated NEWS/DESCRIPTION (still not done with V0.3) |e389f99|
| DESCRIPTION | 2 ++
| NEWS | 13 +++++++++----
| vignettes/dendextend-tutorial.rnw | 6 +++---
| 3 files changed, 14 insertions(+), 7 deletions(-)
* 2013-07-26(Tal Galili) Vignettes - added a section on labels_colors |9a558ea|
| vignettes/dendextend-tutorial.rnw | 62 ++++++++++++++++++++++++++++---------
| 1 file changed, 47 insertions(+), 15 deletions(-)
* 2013-07-26(Tal Galili) labels_colors - moved to their own file, Also added new tests. |68eba04|
| R/dendextend.r | 84 ------------------------------
| R/labels_colors.r | 105 ++++++++++++++++++++++++++++++++++++++
| inst/tests/test-labels_colors.r | 25 +++++++++
| man/labels_colors.Rd | 4 ++
| 4 files changed, 134 insertions(+), 84 deletions(-)
* 2013-07-26(Tal Galili) Trimming by labels. |2ea1933|
| R/trim.r | 10 +++--
| inst/tests/test-trim.r | 68 +++++++++++++++++++++++++++++++++
| vignettes/dendextend-tutorial.rnw | 75 ++++++++++++++++++++++++++++++++++++-
| 3 files changed, 148 insertions(+), 5 deletions(-)
* 2013-07-26(Tal Galili) Vignettes - unroot, raise.dendrogram |d7402e7|
| vignettes/dendextend-tutorial.rnw | 89 +++++++++++++++++++++++++++++++++++++
| 1 file changed, 89 insertions(+)
* 2013-07-26(Tal Galili) Fixes and extensions to unroot |9085f8d|
| R/unroot.r | 117 +++++++++++++++++++++++++-----------------
| inst/tests/test-unroot.r | 45 ++++++++++++++++
| man/count_terminal_nodes.Rd | 8 ++-
| man/flatten.dendrogram.Rd | 4 +-
| man/get_branches_attr.Rd | 9 +++-
| man/unclass_dend.Rd | 4 +-
| man/unroot.Rd | 3 +-
| 7 files changed, 134 insertions(+), 56 deletions(-)
* 2013-07-25(Tal Galili) vignettes - spell checked. |7d6cb65|
| vignettes/dendextend-tutorial.rnw | 28 ++++++++++++++--------------
| 1 file changed, 14 insertions(+), 14 deletions(-)
* 2013-07-25(Tal Galili) Added tests for tree size :) |f95c928|
| DESCRIPTION | 7 ++++---
| NEWS | 4 +++-
| inst/tests/test-nleaves.r | 50 +++++++++++++++++++++++++++++++++++++++++++++
| 3 files changed, 57 insertions(+), 4 deletions(-)
* 2013-07-25(Tal Galili) Vignettes - assignment recycling and tree sizes |da05752|
| vignettes/cache/__packages | 10 +
| ...hunk-18_d9d3a2e4138d97442a69288b169de349.RData | Bin 0 -> 3121 bytes
| ...-chunk-18_d9d3a2e4138d97442a69288b169de349.rdb | 0
| ...-chunk-18_d9d3a2e4138d97442a69288b169de349.rdx | Bin 0 -> 113 bytes
| vignettes/dendextend-tutorial-concordance.tex | 7 +-
| vignettes/dendextend-tutorial.log | 297 +++-
| vignettes/dendextend-tutorial.pdf | 1743 +++++++++++--------
| vignettes/dendextend-tutorial.rnw | 102 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 30645 -> 44992 bytes
| vignettes/dendextend-tutorial.tex | 357 +++-
| vignettes/figure/unnamed-chunk-19.pdf | Bin 0 -> 4626 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| 12 files changed, 1582 insertions(+), 934 deletions(-)
* 2013-07-25(Tal Galili) fix labeels-assign.Rd |14a1e5e|
| R/labels.r | 2 +-
| man/labels-assign.Rd | 2 +-
| 2 files changed, 2 insertions(+), 2 deletions(-)
* 2013-07-25(Tal Galili) unclass_dend now uses dendrapply |6e287f4|
| R/nleaves.r | 29 ++++++++++++++++++-----------
| 1 file changed, 18 insertions(+), 11 deletions(-)
* 2013-07-25(Tal Galili) Vignettes: a section on dendrapply |cea57f9|
| vignettes/dendextend-tutorial-concordance.tex | 6 +-
| vignettes/dendextend-tutorial.log | 421 +++---
| vignettes/dendextend-tutorial.pdf | 1379 ++++++++++---------
| vignettes/dendextend-tutorial.rnw | 59 +-
| vignettes/dendextend-tutorial.synctex.gz | Bin 27918 -> 30645 bytes
| vignettes/dendextend-tutorial.tex | 109 +-
| vignettes/dendextend.bib | 636 +++++++++
| vignettes/figure/unnamed-chunk-4.pdf | Bin 4198 -> 4198 bytes
| vignettes/jss.bst | 1631 +++++++++++++++++++++++
| vignettes/jss.cls | 487 +++++++
| vignettes/jsslogo.jpg | Bin 0 -> 22731 bytes
| 11 files changed, 3907 insertions(+), 821 deletions(-)
* 2013-07-25(Tal Galili) Fix assignment recycling And also class of nodes are no longer "dendrogram" after label assignment |fec015c|
| NEWS | 1 +
| R/labels.r | 40 ++++++++++++++++++++---
| inst/tests/test-labels-assign.r | 68 +++++++++++++++++++++++++++++++++------
| 3 files changed, 95 insertions(+), 14 deletions(-)
* 2013-07-25(Tal Galili) Vignettes: switched from markdown to LaTeX (to make it easier to submit to a journal later on) |15d1492|
| .Rbuildignore | 8 +-
| NEWS | 4 +-
| dendextend.Rproj | 2 +-
| vignettes/dendextend-tutorial-concordance.tex | 4 +
| vignettes/dendextend-tutorial.Rmd | 169 ---
| vignettes/dendextend-tutorial.bib | 636 +++++++++
| vignettes/dendextend-tutorial.blg | 3 +
| vignettes/dendextend-tutorial.html | 482 -------
| vignettes/dendextend-tutorial.log | 896 +++++++++++++
| vignettes/dendextend-tutorial.md | 382 ------
| vignettes/dendextend-tutorial.pdf | 1576 +++++++++++++++++++++++
| vignettes/dendextend-tutorial.rnw | 400 ++++++
| vignettes/dendextend-tutorial.synctex.gz | Bin 0 -> 27918 bytes
| vignettes/dendextend-tutorial.tex | 664 ++++++++++
| vignettes/figure/unnamed-chunk-11.png | Bin 9139 -> 0 bytes
| vignettes/figure/unnamed-chunk-3.png | Bin 2766 -> 0 bytes
| vignettes/figure/unnamed-chunk-4.pdf | Bin 0 -> 4198 bytes
| vignettes/figure/unnamed-chunk-8.png | Bin 9139 -> 0 bytes
| vignettes/figure/unnamed-chunk-9.png | Bin 9139 -> 0 bytes
| 19 files changed, 4189 insertions(+), 1037 deletions(-)
* 2013-07-25(Tal Galili) Added a clear GPL-2 copyright notice on each r file. |aebbbc0|
| NEWS | 6 ++++--
| R/dendextend-package.r | 21 +++++++++++++++++++++
| R/dendextend.r | 23 +++++++++++++++++++++++
| R/labels.r | 26 ++++++++++++++++++++++++++
| R/nleaves.r | 24 ++++++++++++++++++++++++
| R/rotate.r | 16 ++++++++++++++++
| R/trim.r | 24 ++++++++++++++++++++++++
| R/unroot.r | 20 ++++++++++++++++++++
| R/zzz.r | 18 ++++++++++++++++++
| 9 files changed, 176 insertions(+), 2 deletions(-)
* 2013-07-24(Tal Galili) Updated NEWS and DESCRIPTION |35db6ed|
| DESCRIPTION | 17 ++++++++++++-----
| NEWS | 31 +++++++++++++++++++++++++++++++
| 2 files changed, 43 insertions(+), 5 deletions(-)
* 2013-07-24(Tal Galili) vingettes - labels assignment for vectors. |5a20227|
| inst/tests/test-labels-assign.r | 2 +-
| vignettes/dendextend-tutorial.Rmd | 49 +++++++++++++++--
| vignettes/dendextend-tutorial.html | 73 ++++++++++++++++++++++++-
| vignettes/dendextend-tutorial.md | 100 +++++++++++++++++++++++++++++++++--
| 4 files changed, 215 insertions(+), 9 deletions(-)
* 2013-07-24(Tal Galili) "labels.hclust" and "labels.hclust<-" - now both use order=TRUE as default. this makes them consistent with labels.dendrogram. Proper tests have been implemented. |34151cb|
| R/labels.r | 4 ++--
| inst/tests/test-labels-assign.r | 28 ++++++++++++++++++++++++----
| 2 files changed, 26 insertions(+), 6 deletions(-)
* 2013-07-24(Tal Galili) tests - changed names, and added quick way for checking the code while developing the package. |7b1d8f9|
| inst/tests/test-labels-assign.r | 2 +-
| tests/test-all.r | 2 ++
| 2 files changed, 3 insertions(+), 1 deletion(-)
* 2013-07-24(Tal Galili) vignettes - first part of the introduction written (it is a very rough draft, but readable). |6304231|
| .Rbuildignore | 4 +-
| vignettes/dendextend-tutorial.Rmd | 123 ++++++++-------
| vignettes/dendextend-tutorial.html | 223 ++++++++++++++++++++-------
| vignettes/dendextend-tutorial.md | 257 +++++++++++++++++++++++++-------
| vignettes/figure/unnamed-chunk-11.png | Bin 0 -> 9139 bytes
| vignettes/figure/unnamed-chunk-3.png | Bin 9139 -> 2766 bytes
| vignettes/figure/unnamed-chunk-8.png | Bin 0 -> 9139 bytes
| vignettes/figure/unnamed-chunk-9.png | Bin 0 -> 9139 bytes
| 8 files changed, 441 insertions(+), 166 deletions(-)
* 2013-07-24(Tal Galili) Added tests for labels assignment |10e9885|
| inst/tests/test-labels-assign.r | 55 +++++++++++++++++++++++++++++++++++++++
| 1 file changed, 55 insertions(+)
* 2013-07-24(Tal Galili) Fixes for CMD CHECK |5ee9655|
| R/labels.r | 7 +--
| demo/00Index | 2 +-
| man/labels-assign.Rd | 108 +++++++++++++++++++++++++++++++++++++++
| man/labels-set.Rd | 108 ---------------------------------------
| man/order.dendrogram-assign.Rd | 39 ++++++++++++++
| man/order.dendrogram-set.Rd | 39 --------------
| tests/test-all.r | 2 +-
| 7 files changed, 153 insertions(+), 152 deletions(-)
* 2013-07-24(Tal Galili) New: demo, vignettes (knitr), tests (testthat) - |857e081|
| .Rbuildignore | 3 +
| demo/00Index | 1 +
| demo/dendextend.r | 23 +++
| dendextend.Rproj | 2 +-
| tests/test-all.r | 4 +
| vignettes/dendextend-tutorial.Rmd | 109 ++++++++++++
| vignettes/dendextend-tutorial.html | 298 +++++++++++++++++++++++++++++++++
| vignettes/dendextend-tutorial.md | 147 ++++++++++++++++
| vignettes/figure/unnamed-chunk-3.png | Bin 0 -> 9139 bytes
| 9 files changed, 586 insertions(+), 1 deletion(-)
* 2013-07-24(Tal Galili) labels.hclust - added the 'order' parameter |3f515a1|
| R/labels.r | 41 ++++++++++++++++++++++++++++++++++++-----
| 1 file changed, 36 insertions(+), 5 deletions(-)
* 2013-07-24(Tal Galili) Updated doc - |b3eed86|
| R/dendextend-package.r | 8 ++++++
| R/rotate.r | 65 +++++++++++++++++++++++++++++++++++---------
| R/unroot.r | 1 +
| R/zzz.r | 66 +++++++++++++++++++++++++++++++++++++++++++++
| man/dendextend-package.Rd | 15 +++++++++++
| man/get_branches_attr.Rd | 1 +
| man/intersect_trees.Rd | 6 ++---
| man/labels-set.Rd | 15 +++++++++--
| man/rotate.Rd | 25 ++++++++++-------
| 9 files changed, 176 insertions(+), 26 deletions(-)
* 2013-04-10(Tal Galili) intersect_trees function added |988374d|
| NAMESPACE | 1 +
| NEWS | 3 ++-
| R/trim.r | 50 +++++++++++++++++++++++++++++++++++++++++++++++-
| README.md | 3 ++-
| man/intersect_trees.Rd | 37 +++++++++++++++++++++++++++++++++++
| 5 files changed, 91 insertions(+), 3 deletions(-)
* 2013-04-06(Tal Galili) order.dendrogram<- function added. |cf1c863|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/labels.r | 55 +++++++++++++++++++++++++++++++++++++++++++
| README.md | 1 +
| man/order.dendrogram-set.Rd | 39 ++++++++++++++++++++++++++++++
| 5 files changed, 97 insertions(+)
* 2013-04-06(Tal Galili) Notes on rotate and {ape} masking it. |ca4edad|
| NEWS | 3 ++-
| R/rotate.r | 1 +
| README.md | 4 ++--
| man/rotate.Rd | 6 ++++++
| 4 files changed, 11 insertions(+), 3 deletions(-)
* 2013-04-06(Tal Galili) updated README |0549266|
| README.md | 23 +++++++----------------
| 1 file changed, 7 insertions(+), 16 deletions(-)
* 2013-04-06(Tal Galili) unroot (S3'd), raise.dendrogram, flatten.dendrogram |a765a29|
| DESCRIPTION | 1 +
| NAMESPACE | 8 ++
| NEWS | 5 +-
| R/nleaves.r | 3 -
| R/rotate.r | 6 +-
| R/trim.r | 4 +-
| R/unroot.r | 194 ++++++++++++++++++++++++++++++++++++++++++++
| man/flatten.dendrogram.Rd | 36 ++++++++
| man/get_branches_attr.Rd | 31 +++++++
| man/raise.dendrogram.Rd | 29 +++++++
| man/rotate.Rd | 6 +-
| man/unroot.Rd | 49 +++++++++++
| 12 files changed, 365 insertions(+), 7 deletions(-)
* 2013-04-06(Tal Galili) as_hclust_fixed function added (and implemented in trim and rotate) |67b220e|
| NAMESPACE | 1 +
| NEWS | 2 ++
| R/dendextend.r | 25 ++++++++++++++++++++++++-
| R/rotate.r | 7 +------
| R/trim.r | 16 +++++++++-------
| man/as_hclust_fixed.Rd | 34 ++++++++++++++++++++++++++++++++++
| man/trim.Rd | 2 +-
| man/trim_leaf.Rd | 2 +-
| 8 files changed, 73 insertions(+), 16 deletions(-)
* 2013-04-06(Tal Galili) trim (leaves by labels) function added :) |0fcde8e|
| DESCRIPTION | 1 +
| NAMESPACE | 5 ++
| NEWS | 1 +
| R/nleaves.r | 9 +++-
| R/trim.r | 148 +++++++++++++++++++++++++++++++++++++++++++++++++++++
| man/rotate.Rd | 9 +++-
| man/trim.Rd | 48 +++++++++++++++++
| man/trim_leaf.Rd | 32 ++++++++++++
| 8 files changed, 250 insertions(+), 3 deletions(-)
* 2013-04-06(Tal Galili) rotate.phylo S3 method (and doc) added. |7228393|
| DESCRIPTION | 2 ++
| NAMESPACE | 1 +
| NEWS | 2 +-
| R/rotate.r | 12 ++++++++++--
| README.md | 2 +-
| man/rotate.Rd | 13 +++++++++++--
| 6 files changed, 26 insertions(+), 6 deletions(-)
* 2013-04-06(Tal Galili) rotate, sort, flip, nleaves functions were added! |84ccfd6|
| DESCRIPTION | 2 +
| NAMESPACE | 11 ++++
| NEWS | 7 +-
| R/dendextend.r | 102 -----------------------------
| R/nleaves.r | 148 ++++++++++++++++++++++++++++++++++++++++++
| R/rotate.r | 113 ++++++++++++++++++++++++++++++++
| README.md | 5 ++
| man/count_terminal_nodes.Rd | 14 ++--
| man/nleaves.Rd | 44 +++++++++++++
| man/rotate.Rd | 86 ++++++++++++++++++++++++
| man/unclass_dend.Rd | 3 +
| 11 files changed, 426 insertions(+), 109 deletions(-)
* 2013-04-06(Tal Galili) head.dendrogram S3 method to head |fe4dbbb|
| DESCRIPTION | 2 ++
| NAMESPACE | 2 ++
| NEWS | 1 +
| R/dendextend.r | 13 +++++++++++++
| 4 files changed, 18 insertions(+)
* 2013-04-06(Tal Galili) unclass_dend function added |b37a26b|
| NAMESPACE | 1 +
| NEWS | 1 +
| R/dendextend.r | 36 ++++++++++++++++++++++++++++++++++++
| README.md | 5 +++--
| man/unclass_dend.Rd | 29 +++++++++++++++++++++++++++++
| 5 files changed, 70 insertions(+), 2 deletions(-)
* 2013-04-06(Tal Galili) labels_colors function added |718899f|
| NAMESPACE | 4 +-
| NEWS | 5 ++-
| R/dendextend.r | 102 +++++++++++++++++++++++++++++++++++++++---
| man/count.terminal.nodes.Rd | 48 --------------------
| man/count_terminal_nodes.Rd | 48 ++++++++++++++++++++
| man/labels_colors.Rd | 49 ++++++++++++++++++++
| 6 files changed, 200 insertions(+), 56 deletions(-)
* 2013-04-06(Tal Galili) "labels<-.dendrogram" updated - to allow duplicate labels, and shorter labels than the size of the tree. |f82ed9b|
| NEWS | 2 ++
| R/dendextend.r | 2 +-
| R/labels.r | 47 +++++++++++++++++++----------------------------
| man/labels-set.Rd | 4 ++++
| 4 files changed, 26 insertions(+), 29 deletions(-)
* 2013-04-06(Tal Galili) count.terminal.nodes function added |cbcab99|
| DESCRIPTION | 8 +++----
| NAMESPACE | 1 +
| NEWS | 6 ++++++
| R/dendextend.r | 50 +++++++++++++++++++++++++++++++++++++++++--
| R/labels.r | 36 -------------------------------
| README.md | 5 +++--
| man/count.terminal.nodes.Rd | 48 +++++++++++++++++++++++++++++++++++++++++
| 7 files changed, 110 insertions(+), 44 deletions(-)
* 2013-04-06(Tal Galili) Merged "labels<-" help files |8a55439|
| DESCRIPTION | 2 +-
| NAMESPACE | 10 ++--
| NEWS | 3 +-
| R/labels.r | 126 +++++++++++++++++++++++++++----------------------
| man/labels-set.Rd | 48 ++++++++++++++++---
| man/labels.matrix.Rd | 47 ------------------
| 6 files changed, 119 insertions(+), 117 deletions(-)
* 2013-04-05(Tal Galili) NEWS and README.md files added |0a117ae|
| NAMESPACE | 8 +++++++-
| NEWS | 18 ++++++++++++++++++
| R/labels.r | 4 ++--
| README.md | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 4 files changed, 86 insertions(+), 3 deletions(-)
* 2013-04-05(Tal Galili) labels assignment operators for matrix added |25d9c1c|
| DESCRIPTION | 8 +++--
| R/dendextend.r | 3 ++
| R/labels.r | 96 +++++++++++++++++++++++++++++++++++++++++++++++++-
| dendextend.Rproj | 1 +
| man/labels-set.Rd | 57 ++++++++++++++++++++++++++++++
| man/labels.matrix.Rd | 47 ++++++++++++++++++++++++
| 6 files changed, 209 insertions(+), 3 deletions(-)
* 2013-04-05(Tal Galili) labels.r added |2e4a497|
| R/labels.r | 120 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 1 file changed, 120 insertions(+)
* 2013-04-05(Tal Galili) minor edit to DESCRIPTION |8479c64|
| DESCRIPTION | 2 +-
| 1 file changed, 1 insertion(+), 1 deletion(-)
* 2013-04-05(Tal Galili) Package shell |05eb3f9
.Rbuildignore | 2 ++
.gitignore | 3 +++
DESCRIPTION | 9 +++++++++
NAMESPACE | 1 +
R/dendextend.r | 0
dendextend.Rproj | 16 ++++++++++++++++
6 files changed, 31 insertions(+)
|