File: MD5

package info (click to toggle)
r-cran-phangorn 2.5.5-1
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, sid
  • size: 4,112 kB
  • sloc: ansic: 2,892; cpp: 143; sh: 10; makefile: 4
file content (222 lines) | stat: -rw-r--r-- 12,612 bytes parent folder | download
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
0b3c033721da054576533f1ed4ceaef3 *DESCRIPTION
e4cb286961c23c16719db099d464f713 *NAMESPACE
978cccef6ece31ca36dc581864c42864 *NEWS
d7288c3406b83d0c79f4e8e2d60fc185 *R/Coalescent.R
6d58a2e5e2941218589f7d3ab8204684 *R/Densi.R
06535d25890633c4c2bbd6815c693c48 *R/F3X4.R
711891f7f5be42f22e90457c795e1210 *R/RcppExports.R
6ba080a88b3312de5a48a5bfaefb5c01 *R/SH.R
c03b06289fa093d49bb4b4d871e534e7 *R/SOWH.R
a27248b0e800ddc9b52139ac8c361f4d *R/ancestral_pml.R
5e4912b3d028ff3496d80e1850fbf678 *R/bootstrap.R
1fd6372119ccbd9c843422ee8d09a65a *R/cladePar.R
aa093860dd55cf8464453e408452d0a8 *R/clanistic.R
f2bad0514bbe4a4c25c52878e4ae7335 *R/codonTest.R
8d35028ef5cc61b0a73b24cb1a78ea09 *R/delta.score.R
08dede1f02c4453f625be2338b526432 *R/discrete.gamma.R
61a7a7f8eb2a6ee0015ab4ca51af3203 *R/dist.p.R
2af56f7a275c427c9e7a2eedbc71f0cd *R/distSeq.R
a188c3928c43698a6e5659af8d8d1285 *R/distTree.R
6982ae856359fd2ae7f5a417b5c92825 *R/fitch.R
c589e33b0cb18f00c67a6918c7f8a70e *R/hadamard.R
7d5eee6139bb3b1463f024749e01a96a *R/lento.R
cb753a89f68f765b66820c52a0b47503 *R/mast.R
488f7ad8ed15283f2322af6a8b351eb9 *R/modelTest.R
a2458d0d2dd621406e44e92643ad381e *R/neighborNet.R
8a3b75ccf5951d1b4b81fb1ab8a96225 *R/networx.R
2c54a991b44de58ade583ca501e5694c *R/parsimony.R
88ba447ccac28112890bf14e9b765192 *R/phangorn-package.R
468204866217ac5a5e9c609186fa0871 *R/phyDat.R
642618af182a0432a09051a97488af08 *R/phylo.R
3489a5d70886219ecb34a8c80e3e1b25 *R/pmlMix.R
fdb961e7a3bc4d6bfddb9fc3989614a5 *R/pmlPart.R
08eefc8b3f70e1c127afa95d5e0be591 *R/pmlPen.R
fae7b1eacf4ede471e8574ea6de8e533 *R/read.nexus.splits.R
ce0260294a971a95b34dfd4b6af2a8b0 *R/sankoff.R
496fbf2df131ae4640d68effc24ba124 *R/simSeq.R
2574991b0eab1534ccdb5a39d2aeb671 *R/splits.R
70d76b235e08eea12df1058aff3e45a8 *R/splitsNetwork.R
4860ccf1969d0c2b59ba109f418da250 *R/superTree.R
2b4d6884b4ee2b92e617cea76f79d3da *R/sysdata.rda
502906de444f64fa49c83310e12ec199 *R/treeManipulation.R
6fc32685b0335bcb3549112cc5cfc26b *R/treeRearrangement.R
d3b90d224b7bae2344ff487412338a32 *R/treedist.R
ce5494d235612451a31e5d8cfc108391 *R/utils.R
35bc7f55e7ea2657130f3d12078798a9 *R/zzz.R
fd2336b55b5d508ecd0124169dafe60f *README.md
503bc01d75f0bcef25f3a145e6b73eaf *build/vignette.rds
4a92b07bcd170e85bd237e460acafa93 *data/Laurasiatherian.RData
4b269c2e640293341b9b1c04d4dd7f4e *data/chloroplast.RData
19f84425e8caaf9f605490cdff17dd81 *data/yeast.RData
82c44d6919bfb89935a2aaf44893f750 *inst/CITATION
61b3722df2ead748e0db8595428412a1 *inst/README
0bb98666442df10c578c5e44ef55a594 *inst/doc/Ancestral.R
c9f68393038b1593f83d26226c24a166 *inst/doc/Ancestral.Rnw
513e52ec4371ddf4fbda1b799d86e338 *inst/doc/Ancestral.pdf
ded9d871b4e54387c14340167f196a93 *inst/doc/IntertwiningTreesAndNetworks.R
9364f4bdf1689f43b2c202c9511515f9 *inst/doc/IntertwiningTreesAndNetworks.Rmd
7b63659e612e65db4213d5a17dba897a *inst/doc/IntertwiningTreesAndNetworks.html
d24a83a2803108ede87eff4de3c13ae8 *inst/doc/Networx.R
fe641c0b4c7aac7aabf24c47ed6cde40 *inst/doc/Networx.Rmd
bf3ceddfab47bf675ed7babcf5a76f78 *inst/doc/Networx.html
7ad7cef59361223e74d8e163035f9085 *inst/doc/Trees.R
38b0e3b2f528a536cdedde4af745739f *inst/doc/Trees.Rnw
89d9220d2157a23341a4def6797749a4 *inst/doc/Trees.pdf
619064ee07b658cfa503a016d7b0aa99 *inst/doc/phangorn-specials.R
6b1a8f46dcada22e6a3f118fd5b8ca4e *inst/doc/phangorn-specials.Rnw
30c4ee5b7b3339df44ad0f7ee3e4300b *inst/doc/phangorn-specials.pdf
3009f9da02a198cb557d435cc5ad8c7f *inst/extdata/Blosum62.dat
72f496d4c6e937ffe744d25bd8891313 *inst/extdata/Dayhoff.dat
5aa357dab0e72b27023e4302bc37dbad *inst/extdata/FLU.dat
7f63f617d5d29421b0bd90ab8511feb7 *inst/extdata/HIVb.dat
29e1aa10906a86bb9bca6d9c7f98a6cb *inst/extdata/HIVw.dat
ca86e539345fa57de5c77a60308bed09 *inst/extdata/JTT.dat
fdc1176d0c0f2db3de1c9dfd83d3c070 *inst/extdata/MtZoa.dat
106715eba35efc2743ccad7923ac13ce *inst/extdata/RtREV.dat
e05f5a0ca507e4e15e7b95d1ce93b9fa *inst/extdata/VT.dat
fc090d051ce4f18b937448a254e2764e *inst/extdata/cpREV.dat
50c707c26bf9015b37670f15d5e1c14b *inst/extdata/dayhoff-dcmut.dat
6da24109959f0c7a7db50c8db78d5d42 *inst/extdata/jtt-dcmut.dat
ddc4bd45521cd72848aaf2f79b90ac6e *inst/extdata/lg.dat
917303a3df098f9137c651de0afa78fa *inst/extdata/mtArt.dat
1cd5e39670b86d32b5fe5c27dcc79648 *inst/extdata/mtREV24.dat
0ca0d0e987fcebf847a876779eddd934 *inst/extdata/mtmam.dat
20be734137b889e34006f8b8bd969054 *inst/extdata/trees/RAxML_bestTree.3moles
384aa1b8d633aa8c9f533396bd6798cb *inst/extdata/trees/RAxML_bestTree.AIs
757e4718b72d7829b5ceb34f765dc626 *inst/extdata/trees/RAxML_bestTree.Wang.out
5c7b80221c2dc93d4e6a6b857ccb62e8 *inst/extdata/trees/RAxML_bestTree.YCh
0e77d8f9386ddaee1de2f6678530c823 *inst/extdata/trees/RAxML_bestTree.mtG
2f7670326d5ff9235ecd0943944b6d59 *inst/extdata/trees/RAxML_bipartitions.3moles
959bc9ea585c21ab89b3f32a5bb49d25 *inst/extdata/trees/RAxML_bipartitions.AIs
46c172becde7e1d90ab68820b0c48822 *inst/extdata/trees/RAxML_bipartitions.YCh
75061d3e313e19632dcbce0ef48e9cdc *inst/extdata/trees/RAxML_bipartitions.mtG
2212d49c7269978890887be3686c12f9 *inst/extdata/trees/RAxML_bipartitions.woodmouse
b1b3ceb83427c63fed23790fd563ef6e *inst/extdata/trees/RAxML_bipartitionsBranchLabels.3moles
41fd855853c4ceb7e28d5212b1c72d9b *inst/extdata/trees/RAxML_bipartitionsBranchLabels.AIs
0d8694f8ea078f981819be215fb724ba *inst/extdata/trees/RAxML_bipartitionsBranchLabels.YCh
abcfbaf31212288e26a67c5b6c30ae70 *inst/extdata/trees/RAxML_bipartitionsBranchLabels.mtG
25077ff0b9f822583f5ae13d8bbc181a *inst/extdata/trees/RAxML_bootstrap.3moles
bd830645e73afa0ee2cb121c22c4d2f2 *inst/extdata/trees/RAxML_bootstrap.AIs
086fb65b6bd2d40f09fff513b86d55cc *inst/extdata/trees/RAxML_bootstrap.Wang.out
49ade6ade3f8f08033b887a001243c86 *inst/extdata/trees/RAxML_bootstrap.YCh
d2016de5a6926dd0b62c49502ec2d6b9 *inst/extdata/trees/RAxML_bootstrap.mtG
000df141b844795d38e5a755aa360f97 *inst/extdata/trees/RAxML_bootstrap.woodmouse
6cd945acf5464dce8e10c350097e2c20 *inst/extdata/trees/RAxML_distances.Wang.nxs
02888c45178001387b7a5397a3a17d3c *inst/extdata/trees/Splits.txt
d3069d1eff9e70bed655b8962bf4ee2b *inst/extdata/trees/primates.dna
129e8c41182f3557b1b9911625e100b9 *inst/extdata/trees/woodmouse.fasta
421488c1ce8687879f64a350fca6d055 *inst/extdata/trees/woodmouse.mrbayes.nex.con
d83fc4958acba1f1d0ca4092393c5b3d *inst/extdata/trees/woodmouse.mrbayes.nex.run1.t
e185a8c9c7aed17a3e216cb78d517fd4 *inst/extdata/trees/woodmouse.mrbayes.nex.run2.t
01399608c5cc2927ebed0659ac78863d *inst/extdata/trees/woodmouse.nxs
87fa1533c4dfe7074237cfa2196bcbeb *inst/extdata/wag.dat
5e5c9da6e7ba15b472b9ea3958876662 *inst/phangorn_sticker.png
308cc143865b25766c9577650b87f5c0 *man/Ancestors.Rd
884ef49b5b15c34a389046336d547b94 *man/CI.Rd
e72793e4e3e08c49156b1357a9291a01 *man/Laurasiatherian.Rd
f0c375eb726b230fdd114f0b3bb1b96b *man/NJ.Rd
ebaa7cd9dab35f7e83ca9edb2294a1f4 *man/SH.test.Rd
3e3918b52c25ea2f1764ab6a3a55349b *man/SOWH.test.Rd
99d52e574dc6a5b0520aeaa49944bd04 *man/add.tips.Rd
6cef4523dc9eea44b06bc15e173111b7 *man/addConfidences.Rd
c04c9432a573eb46abf88a4168eaa19e *man/allTrees.Rd
ef41c0200fa24d56c318f79d931e3e98 *man/ancestral.pml.Rd
5cc9ca1ee5b6b029581149a2a70612c9 *man/as.networx.Rd
4de98194f5b83d4ee658ece09cec905b *man/as.splits.Rd
085934af2215731061cbe4f246c812cb *man/bab.Rd
b8a8f6b11e1e2642bbc192a45dfb3786 *man/bootstrap.pml.Rd
84449bdbd0b2adefb75bd71de6be5d8d *man/chloroplast.Rd
3cd568b4891d8b8668e6c32baa89ddb8 *man/cladePar.Rd
7f22c4b1e1385b67ce4f53b86461bd5e *man/coalSpeciesTree.Rd
d346d6fb6d2e0936ee778d7841aa7ce8 *man/codonTest.Rd
3857b55e9f2676785716c811811b89ac *man/consensusNet.Rd
9a6059134efdbcae3f438ef949806bfd *man/cophenetic.networx.Rd
5173eb8e2f87b21391e5c49c0927e905 *man/delta.score.Rd
bc5176475146d24e35d3149f14add4ee *man/densiTree.Rd
10e2f903c59378d66b0b364413db9a52 *man/designTree.Rd
dfbc54435ddc425192da2b8de37a90fe *man/dfactorial.Rd
30388d37deba2942db54bec505357f9a *man/discrete.gamma.Rd
822a653d8577af85801dbfc6d7c7d39d *man/dist.hamming.Rd
dfde0d7dfca8bd88d8fb9075d4c1c66f *man/dist.p.Rd
13e311418f4e1eaf9c0f23f83a708324 *man/distanceHadamard.Rd
d092f8360372abe2b4fcde6d1b9e3605 *man/getClans.Rd
f87e9235742f659511655e25a9911b3e *man/hadamard.Rd
88d5f40a3251082914b398fe2c0706cd *man/identify.networx.Rd
fc3e5a6fd08cb98b6300c04cd81c771d *man/lento.Rd
828f11eb12db139a86bd3d65bd316baa *man/mast.Rd
766fdd9eb0cf1adf18d7f2c695c161e7 *man/maxCladeCred.Rd
feb54260f92f9e1d27248eb2d91b1a8f *man/midpoint.Rd
47a039b94655fe0f0985630f64035a5f *man/modelTest.Rd
cc7c4671f631780dfdf621343998d6d0 *man/neighborNet.Rd
214b9849369866569e980e7be0bb387a *man/nni.Rd
df634b3d70c4a882f249359879fae853 *man/parsimony.Rd
653842f0e6847be2675a74ca27f7ca90 *man/phangorn-internal.Rd
868acc3c4940b61304ddc3907a9e6448 *man/phangorn-package.Rd
cfee40b1573ed873dd2d09d0f24a7f39 *man/phyDat.Rd
5abb2e5f0ef8fc4165353c7827150359 *man/plot.networx.Rd
194aed8c3145206e91b8585b1e4a5c7f *man/pml.Rd
e5d391d06fd29761adbae6f342ca7535 *man/pml.fit.Rd
d0db98616ba12dfe7b0dda1a6d741241 *man/pmlCluster.Rd
5af01d5bfcd32d28844254b1a1e30df4 *man/pmlMix.Rd
8094fb42c593515dbfe46a4ac515f13d *man/pmlPart.Rd
331cc7b9328ef3de64da631bacb4dcf7 *man/read.aa.Rd
ec69858f15ab64abd2995d57aa959e59 *man/read.nexus.splits.Rd
02bf46e94e692fccaaba2db6d66a7e06 *man/reexports.Rd
e2f18b4e16f29f77cda6b6fa00e86caf *man/simSeq.Rd
b4d04e2166b7169e9756f6b79c054bec *man/splitsNetwork.Rd
fbaee3a67e1cf235a3916889c5638abe *man/superTree.Rd
fa767d27a6444f7fa246620d3b4e67e0 *man/treedist.Rd
73308bbdef266b537f9a6aa413f539b7 *man/upgma.Rd
8d1ad5757e44f5318adabe5b0d94a2e1 *man/writeDist.Rd
7b4fdcfc85bc945a86723f094057dbcb *man/yeast.Rd
a1e86627020c43852446a8e2c2141b3f *src/Makevars
a745fb77d5e9d2039ca304e8fe934603 *src/RcppExports.cpp
1e590763e414b57667f2eff67e4499ed *src/dist.c
45db6d1427387ba1ce497ee11818e1a6 *src/fitch.c
da6ac928ad23fb7c53dfe537fc491a52 *src/init.c
924b123a88291cf9c3148c47abb9d6b2 *src/ml.c
0266fb499e415e17da7cc31b8ea0650f *src/phangorn.c
13542b1e1396af8f7b9cc5021a6288d4 *src/phangorn_help.cpp
65522949b14d564f53a90ac438de6afc *src/sankoff.c
918df7ea8eb9b43ba5b24fafa1f6953c *src/sprdist.c
c52c864af2efbc706fbd5aa38d1cd394 *tests/figs/densitree/densitree-plot.svg
0f6c7fb7a936f6a1362540ab4635f5fb *tests/figs/deps.txt
00c7ec639c948ec07fe48a27d4404a8e *tests/figs/lento-plot/lento-plot.svg
7d1eaef831fb2372b367f5be1b0a5790 *tests/testthat.R
fe1ae4880f6635b5f750ed9381121ae9 *tests/testthat/test-simSeq.R
434965cace2a3bbd36811d3d6e75cba0 *tests/testthat/test_Clanistics.R
1c58551e18ec17091d9e4eb07dc866ea *tests/testthat/test_SH.R
cb58c4c67f246b5ac1a70426fc311550 *tests/testthat/test_ancestral.R
055161560a7a758f86e2ab44b5d99d57 *tests/testthat/test_codon.R
6a9f749eee99ea6e58ebc49763df0fa7 *tests/testthat/test_densiTree.R
97d94788752f552d019cdaafcf7a66bc *tests/testthat/test_dist_tree.R
1c0d94b362c0c971a061db6008e1e20b *tests/testthat/test_distances.R
276d5ea8b5e180f111b90ab803f4cb3e *tests/testthat/test_hadamard.R
525cf934d948281d5f2b9df2fd9e25b5 *tests/testthat/test_lento.R
d0e85a4256891fa63558b5708e83c69b *tests/testthat/test_mast.R
0de6763f787e9f1a5e9111dece7c098e *tests/testthat/test_modelTest.R
a362d2410e514392501dbf666cef9ee5 *tests/testthat/test_parsimony.R
756ab51f5ad754a45d42131edc025115 *tests/testthat/test_phyDat.R
8b04dafe1258fddd16c7956ae6aa14fc *tests/testthat/test_pml.R
2a071f76d4c2ba4b9c79a7b7e8789883 *tests/testthat/test_pmlCluster.R
05ceb5befd7acf2b32441d1c13a2630d *tests/testthat/test_pmlMix.R
7783367db4fa5fd4933b70cb78844527 *tests/testthat/test_pmlPart.R
dce752eac431d3b11cdb6fb1a9706e35 *tests/testthat/test_pmlPen.R
26bd54252efbc97a9a252ee11469eff7 *tests/testthat/test_speciesTree.R
2a36c9af728102816d8885ca5f9a9a99 *tests/testthat/test_splits.R
20ec41bfea311dd762e984f834a26948 *tests/testthat/test_superTree.R
7a55f09707b95c663e8d03e2a4d59318 *tests/testthat/test_treeManipulation.R
5be434930bfc189bec3ba745b2738d5f *tests/testthat/test_treeRearrangement.R
46c174995f382ef7dd6cec5ef5ac8b90 *tests/testthat/test_treedist.R
c9f68393038b1593f83d26226c24a166 *vignettes/Ancestral.Rnw
9364f4bdf1689f43b2c202c9511515f9 *vignettes/IntertwiningTreesAndNetworks.Rmd
fe641c0b4c7aac7aabf24c47ed6cde40 *vignettes/Networx.Rmd
a8250afd3b341e6c3f889e9454d5bc5f *vignettes/Trees.RData
38b0e3b2f528a536cdedde4af745739f *vignettes/Trees.Rnw
3b1285249eed24e70427c0b56450533a *vignettes/cophylo.png
6af5f4d4c2e93469cc19d46a97ab5d0f *vignettes/exdna.txt
1ca8b1d97a011a9d0ecd9630d548dfb3 *vignettes/movie.gif
6b1a8f46dcada22e6a3f118fd5b8ca4e *vignettes/phangorn-specials.Rnw
927c5b5d25e0aaa54b0b42c0f6919d94 *vignettes/phangorn.bib
d3069d1eff9e70bed655b8962bf4ee2b *vignettes/primates.dna
8f16a94fb418c2e580b92d2d63a05a44 *vignettes/seqLogo.pdf