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
|
# output-format helper -------------------------
# this function does the main composition of columns for the output.
# it's used by "compare_parameters()", where users can choose between
# different pre-sets of "print-layouts"
.format_output_style <- function(x, style, format, modelname) {
if (identical(format, "html")) {
linesep <- "<br>"
} else {
linesep <- " "
}
if (!is.null(style) && style %in% c("se", "ci")) {
x$p_stars <- ""
}
# find columns
coef_column <- colnames(x)[1]
ci_column <- colnames(x)[endsWith(colnames(x), " CI") | colnames(x) == "CI"]
# make sure we have a glue-like syntax
style <- .convert_to_glue_syntax(style, linesep)
# "|" indicates cell split
style <- unlist(strsplit(style, split = "|", fixed = TRUE))
# define column names
if (length(style) == 1) {
column_names <- modelname
} else {
column_names <- .style_pattern_to_name(style)
}
# paste glue together
formatted_columns <- lapply(seq_along(style), function(i) {
.format_glue_output(x, coef_column, ci_column, style[i], format, column_names[i])
})
out <- do.call(cbind, formatted_columns)
# add modelname to column names; for single column layout per model, we just
# need the column name. If the layout contains more than one column per model,
# add modelname in parenthesis.
if (!is.null(modelname) && nzchar(modelname, keepNA = TRUE)) {
if (ncol(out) > 1) {
colnames(out) <- paste0(colnames(out), " (", modelname, ")")
} else {
colnames(out) <- modelname
}
}
# remove empty parenthesis
out[] <- lapply(out, function(i) {
# here we either have "<br>" or " " as line breaks, followed by empty "()"
i <- gsub("<br>()", "", i, fixed = TRUE)
i <- gsub(" ()", "", i, fixed = TRUE)
i <- gsub("<br>(, )", "", i, fixed = TRUE)
i <- gsub(" (, )", "", i, fixed = TRUE)
i[i == "()"] <- ""
i[i == "(, )"] <- ""
# remove other non-matched patterns
i <- gsub("{stars}", "", i, fixed = TRUE)
i <- gsub("{rhat}", "", i, fixed = TRUE)
i <- gsub("{ess}", "", i, fixed = TRUE)
i <- gsub("{pd}", "", i, fixed = TRUE)
i <- gsub("{rope}", "", i, fixed = TRUE)
i
})
out
}
.convert_to_glue_syntax <- function(style, linesep = NULL) {
# set default
if (is.null(linesep)) {
linesep <- " "
}
# default
if (is.null(style)) {
style <- paste0("{estimate}", linesep, "({ci})|{p}")
# style: estimate and CI, p-value in separate column (currently identical to "ci_p2")
} else if (style %in% c("minimal", "ci_p2")) {
style <- paste0("{estimate}", linesep, "({ci})|{p}")
# style: estimate and CI, no p
} else if (style == "ci") {
style <- paste0("{estimate}", linesep, "({ci})")
# style: estimate, p-stars and CI
} else if (style == "ci_p") {
style <- paste0("{estimate}{stars}", linesep, "({ci})")
# style: estimate and SE, no p
} else if (style == "se") {
style <- paste0("{estimate}", linesep, "({se})")
# style: estimate, p-stars and SE
} else if (style == "se_p") {
style <- paste0("{estimate}{stars}", linesep, "({se})")
# style: estimate and SE, p-value in separate column
} else if (style %in% c("short", "se_p2")) {
style <- paste0("{estimate}", linesep, "({se})|{p}")
# style: only estimate
} else if (style %in% c("est", "coef")) {
style <- "{estimate}"
}
# replace \n for now with default line-separators
gsub("\n", linesep, style, fixed = TRUE)
}
.format_glue_output <- function(x, coef_column, ci_column, style, format, column_names) {
# separate CI columns, for custom layout
ci <- ci_low <- ci_high <- NULL
if (!insight::is_empty_object(ci_column)) {
ci <- x[[ci_column[1]]]
ci_low <- insight::trim_ws(gsub("(\\(|\\[)(.*),(.*)(\\)|\\])", "\\2", ci))
ci_high <- insight::trim_ws(gsub("(\\(|\\[)(.*),(.*)(\\)|\\])", "\\3", ci))
}
# fix p-layout
if ("p" %in% colnames(x)) {
x[["p"]] <- insight::trim_ws(x[["p"]])
x[["p"]] <- gsub("< .", "<0.", x[["p"]], fixed = TRUE)
}
# handle aliases
style <- tolower(style)
style <- gsub("{coef}", "{estimate}", style, fixed = TRUE)
style <- gsub("{coefficient}", "{estimate}", style, fixed = TRUE)
style <- gsub("{std.error}", "{se}", style, fixed = TRUE)
style <- gsub("{standard error}", "{se}", style, fixed = TRUE)
style <- gsub("{pval}", "{p}", style, fixed = TRUE)
style <- gsub("{p.value}", "{p}", style, fixed = TRUE)
style <- gsub("{ci}", "{ci_low}, {ci_high}", style, fixed = TRUE)
# align columns width for text format
.align_values <- function(i) {
if (!is.null(i)) {
non_empty <- !is.na(i) & nzchar(i, keepNA = TRUE)
i[non_empty] <- format(insight::trim_ws(i[non_empty]), justify = "right")
}
i
}
# we put all elements (coefficient, SE, CI, p, ...) in one column.
# for text format, where columns are not center aligned, this can result in
# misaligned columns, which looks ugly. So we try to ensure that each element
# is formatted and justified to the same width
if (identical(format, "text") || is.null(format)) {
x[[coef_column]] <- .align_values(x[[coef_column]])
x$SE <- .align_values(x$SE)
x[["p"]] <- .align_values(x[["p"]])
x$p_stars <- .align_values(x$p_stars)
ci_low <- .align_values(ci_low)
ci_high <- .align_values(ci_high)
x$pd <- .align_values(x$pd)
x$Rhat <- .align_values(x$Rhat)
x$ESS <- .align_values(x$ESS)
x$ROPE_Percentage <- .align_values(x$ROPE_Percentage)
}
# create new string
table_row <- rep(style, times = nrow(x))
for (r in seq_along(table_row)) {
table_row[r] <- gsub("{estimate}", x[[coef_column]][r], table_row[r], fixed = TRUE)
if (!is.null(ci_low) && !is.null(ci_high)) {
table_row[r] <- gsub("{ci_low}", ci_low[r], table_row[r], fixed = TRUE)
table_row[r] <- gsub("{ci_high}", ci_high[r], table_row[r], fixed = TRUE)
}
if ("SE" %in% colnames(x)) {
table_row[r] <- gsub("{se}", x[["SE"]][r], table_row[r], fixed = TRUE)
}
if ("p" %in% colnames(x)) {
table_row[r] <- gsub("{p}", x[["p"]][r], table_row[r], fixed = TRUE)
}
if ("p_stars" %in% colnames(x)) {
table_row[r] <- gsub("{stars}", x[["p_stars"]][r], table_row[r], fixed = TRUE)
}
if ("pd" %in% colnames(x)) {
table_row[r] <- gsub("{pd}", x[["pd"]][r], table_row[r], fixed = TRUE)
}
if ("Rhat" %in% colnames(x)) {
table_row[r] <- gsub("{rhat}", x[["Rhat"]][r], table_row[r], fixed = TRUE)
}
if ("ESS" %in% colnames(x)) {
table_row[r] <- gsub("{ess}", x[["ESS"]][r], table_row[r], fixed = TRUE)
}
if ("ROPE_Percentage" %in% colnames(x)) {
table_row[r] <- gsub("{rope}", x[["ROPE_Percentage"]][r], table_row[r], fixed = TRUE)
}
}
# some cleaning: columns w/o coefficient are empty
table_row[x[[coef_column]] == "" | is.na(x[[coef_column]])] <- "" # nolint
# fix some p-value stuff, e.g. if pattern is "p={p]}",
# we may have "p= <0.001", which we want to be "p<0.001"
table_row <- gsub("=<", "<", table_row, fixed = TRUE)
table_row <- gsub("= <", "<", table_row, fixed = TRUE)
table_row <- gsub("= ", "=", table_row, fixed = TRUE)
# final output
x <- data.frame(table_row)
colnames(x) <- column_names
x
}
.style_pattern_to_name <- function(style) {
column_names <- tolower(style)
# completely remove these patterns
column_names <- gsub("{stars}", "", column_names, fixed = TRUE)
# remove curlys
column_names <- gsub("{", "", column_names, fixed = TRUE)
column_names <- gsub("}", "", column_names, fixed = TRUE)
# manual renaming
column_names <- gsub("\\Qrope\\E", "% in ROPE", column_names)
column_names <- gsub("(estimate|coefficient|coef)", "Estimate", column_names)
column_names <- gsub("\\Qse\\E", "SE", column_names)
column_names <- gsub("<br>", "", column_names, fixed = TRUE)
column_names
}
# global definition of valid "style" shortcuts
.style_shortcuts <- c("ci_p2", "ci", "ci_p", "se", "se_p", "se_p2", "est", "coef")
.select_shortcuts <- c("minimal", "short")
.add_obs_row <- function(x, att, style) {
observations <- unlist(lapply(att, function(i) {
if (is.null(i$n_obs)) {
NA
} else {
i$n_obs
}
}))
weighted_observations <- unlist(lapply(att, function(i) {
if (is.null(i$weighted_nobs)) {
NA
} else {
i$weighted_nobs
}
}))
# check if model had weights, and if due to missing values n of weighted
# observations differs from "raw" observations
if (!all(is.na(weighted_observations)) && !all(is.na(observations))) {
if (!isTRUE(all.equal(as.vector(weighted_observations), as.vector(observations)))) {
insight::format_alert("Number of weighted observations differs from number of unweighted observations.")
}
observations <- weighted_observations
}
if (!all(is.na(observations))) {
# add empty row, as separator
empty_row <- do.call(data.frame, as.list(rep(NA, ncol(x))))
colnames(empty_row) <- colnames(x)
x <- rbind(x, empty_row)
# add observations
steps <- (ncol(x) - 1) / length(observations)
empty_row[[1]] <- "Observations"
insert_at <- seq(2, ncol(x), by = steps)
for (i in seq_along(insert_at)) {
empty_row[[insert_at[i]]] <- observations[i]
}
x <- rbind(x, empty_row)
}
x
}
# other helper ------------------------
.format_columns_single_component <- function(x,
pretty_names,
digits = 2,
ci_digits = digits,
p_digits = 3,
ci_width = "auto",
ci_brackets = TRUE,
format = NULL,
coef_name = NULL,
zap_small = FALSE,
include_reference = FALSE,
...) {
# default brackets are parenthesis for HTML / MD
if ((is.null(ci_brackets) || isTRUE(ci_brackets)) && (identical(format, "html") || identical(format, "markdown"))) {
brackets <- c("(", ")")
} else if (is.null(ci_brackets) || isTRUE(ci_brackets)) {
brackets <- c("[", "]")
} else {
brackets <- ci_brackets
}
# fix coefficient column name for random effects
if (!is.null(x$Effects) && all(x$Effects == "random") && any(colnames(x) %in% .all_coefficient_types)) {
colnames(x)[colnames(x) %in% .all_coefficient_types] <- "Coefficient"
}
# fix coefficient column name for mixed count and zi pars
if (!is.null(x$Component) &&
sum(c("conditional", "zero_inflated", "dispersion") %in% x$Component) >= 2 &&
any(colnames(x) %in% .all_coefficient_types)) {
colnames(x)[colnames(x) %in% .all_coefficient_types] <- "Coefficient"
}
# random pars with level? combine into parameter column
if (all(c("Parameter", "Level") %in% colnames(x))) {
x$Parameter <- paste0(x$Parameter, " ", brackets[1], x$Level, brackets[2])
x$Level <- NULL
}
# add the coefficient for the base-(reference)-level of factors?
if (include_reference) {
x <- .add_reference_level(x)
}
insight::format_table(
x,
pretty_names = pretty_names,
digits = digits,
ci_width = ci_width,
ci_brackets = ci_brackets,
ci_digits = ci_digits,
p_digits = p_digits,
zap_small = zap_small,
...
)
}
.format_ranef_parameters <- function(x) {
if (!is.null(x$Group) && !is.null(x$Effects)) {
ran_pars <- which(x$Effects == "random")
stddevs <- startsWith(x$Parameter[ran_pars], "SD (")
x$Parameter[ran_pars[stddevs]] <- paste0(
gsub("(.*)\\)", "\\1", x$Parameter[ran_pars[stddevs]]),
": ",
x$Group[ran_pars[stddevs]],
")"
)
corrs <- startsWith(x$Parameter[ran_pars], "Cor (")
x$Parameter[ran_pars[corrs]] <- paste0(
gsub("(.*)\\)", "\\1", x$Parameter[ran_pars[corrs]]),
": ",
x$Group[ran_pars[corrs]],
")"
)
x$Parameter[x$Parameter == "SD (Observations: Residual)"] <- "SD (Residual)"
x$Group <- NULL
}
x
}
.add_reference_level <- function(params, model = NULL) {
if (is.null(model)) {
# check if we have a model object, if not provided by user
model <- .get_object(params)
}
# no model object provided? Try to get data from model call
if (is.null(model)) {
# get data from model call
model_data <- .safe(eval(attributes(params)$model_call$data))
} else {
# get data from model object
model_data <- insight::get_data(model, verbose = FALSE)
}
# check if we have model data, else return parameter table
if (is.null(model_data)) {
return(params)
}
# find factors and factor levels and check if we have any factors in the data
factors <- .find_factor_levels(model_data, model, model_call = attributes(params)$model_call)
if (!length(factors)) {
# in case of "on-the-fly" factors, e.g.:
# m <- lm(mpg ~ cut(wt, c(0, 2.5, 3, 5)), data = mtcars)
# we need to receive the data from the model frame, in order to find factors
model_data <- insight::get_data(model, source = "mf", verbose = FALSE)
if (!is.null(model_data)) {
factors <- .find_factor_levels(model_data, model, model_call = attributes(params)$model_call)
}
# if we still didn't find anything, quit...
if (!length(factors)) {
return(params)
}
}
# next, check contrasts of factors. including the reference level makes
# only sense if there are contrasts that are all zeros, which means that
# the reference level is not included in the model matrix
remove_contrasts <- .remove_reference_contrasts(model)
# keep only factors with valid contrasts
if (!is.null(remove_contrasts) && length(remove_contrasts)) {
factors <- factors[setdiff(names(factors), remove_contrasts)]
}
# we need some more information about prettified labels etc.
pretty_names <- attributes(params)$pretty_names
coef_name <- attributes(params)$coefficient_name
if (is.null(coef_name)) {
coef_name <- "Coefficient"
}
zi_coef_name <- attributes(params)$zi_coefficient_name
if (is.null(zi_coef_name)) {
zi_coef_name <- "Coefficient"
}
# copy object, so we save original data
out <- params
# sanity check - is pretty_names NULL? If so, use Parameters as pretty_names
if (is.null(pretty_names)) {
pretty_names <- stats::setNames(params$Parameter, params$Parameter)
}
# if we use "include_reference" and set "pretty_names = FALSE", pretty_names
# is no named vector. So we need to make sure we have a named vector
if (is.null(names(pretty_names))) {
pretty_names <- stats::setNames(pretty_names, params$Parameter)
}
# if we use "keep" or "drop", we have less parameters in our data frame,
# so we need to make sure we only have those pretty_names, which names match
# the parameters in the data frame
pretty_names <- pretty_names[names(pretty_names) %in% params$Parameter]
# iterate all factors in the data and check if any factor was used in the model
for (fn in names(factors)) {
f <- factors[[fn]]
# "f" contains all combinations of factor name and levels from the data,
# which we can match with the names of the pretty_names vector
found <- which(names(pretty_names) %in% f)
# if we have a match, we add the reference level to the pretty_names vector
if (length(found)) {
# the reference level is *not* in the pretty names yet
reference_level <- f[!f %in% names(pretty_names)]
# for on-the-fly conversion of factors, the names of the factors can
# can also contain "factor()" or "as.factor()" - we need to remove these
if (any(grepl("(as\\.factor|factor|as\\.character)", fn))) {
fn_clean <- gsub("(as\\.factor|factor|as\\.character)\\((.*)\\)", "\\2", fn)
} else {
fn_clean <- fn
}
# create a pretty level for the reference category
pretty_level <- paste0(fn_clean, " [", sub(fn, "", reference_level, fixed = TRUE), "]")
pretty_level <- gsub("_", " ", pretty_level, fixed = TRUE)
# special handling for "cut()"
pattern_cut_right <- "(.*)\\((.*),(.*)\\]\\]$"
pattern_cut_left <- "(.*)\\[(.*),(.*)\\)\\]$"
if (all(grepl(pattern_cut_right, pretty_level))) {
lower_bounds <- gsub(pattern_cut_right, "\\2", pretty_level)
upper_bounds <- gsub(pattern_cut_right, "\\3", pretty_level)
pretty_level <- gsub(pattern_cut_right, paste0("\\1>", as.numeric(lower_bounds), "-", upper_bounds, "]"), pretty_level)
} else if (all(grepl(pattern_cut_left, pretty_level))) {
lower_bounds <- gsub(pattern_cut_left, "\\2", pretty_level)
upper_bounds <- gsub(pattern_cut_left, "\\3", pretty_level)
pretty_level <- gsub(pattern_cut_left, paste0("\\1", as.numeric(lower_bounds), "-<", upper_bounds, "]"), pretty_level)
}
# insert new pretty level at the correct position in "pretty_names"
pretty_names <- .insert_element_at(
pretty_names,
stats::setNames(pretty_level, reference_level),
min(found)
)
# now we need to update the data as well (i.e. the parameters table)
row_data <- data.frame(
Parameter = reference_level,
Coefficient = as.numeric(attributes(params)$exponentiate),
stringsAsFactors = FALSE
)
# coefficient name can also be "Odds Ratio" etc., so make sure we
# have the correct column name in the data row we want to insert
if (coef_name %in% colnames(out)) {
colnames(row_data)[2] <- coef_name
} else if (zi_coef_name %in% colnames(out)) {
colnames(row_data)[2] <- zi_coef_name
}
out <- .insert_row_at(out, row_data, min(found))
}
}
# update pretty_names attribute
attr(out, "pretty_names") <- pretty_names
# update pretty_labels attribute
pretty_names[match(names(attr(out, "pretty_labels")), names(pretty_names))] <- attr(out, "pretty_labels")
attr(out, "pretty_labels") <- pretty_names
out
}
# The coefficient column in the printed output is renamed, based on the model.
# But for instance, for random effects, however, which are on a different scale,
# we want a different name for this column. Since print.parameters_model() splits
# components into different tables, we change the column name for those "tables"
# that contain the random effects or zero-inflation parameters
.all_coefficient_types <- c(
"Odds Ratio", "Risk Ratio", "Prevalence Ratio", "IRR", "Log-Odds",
"Log-Mean", "Log-Ratio", "Log-Prevalence", "Probability", "Marginal Means",
"Estimated Counts", "Ratio"
)
.all_coefficient_names <- c("Coefficient", "Std_Coefficient", "Estimate", "Median", "Mean", "MAP")
.format_stan_parameters <- function(out) {
has_component <- !is.null(out$Component)
# brms random intercepts or random slope variances
ran_sd <- startsWith(out$Parameter, "sd_") & out$Effects == "random"
if (any(ran_sd)) {
out$Parameter[ran_sd] <- gsub("^sd_(.*?)__(.*)", "SD \\(\\2\\)", out$Parameter[ran_sd])
if (has_component) {
ran_zi_sd <- ran_sd & out$Component == "zero_inflated"
if (any(ran_zi_sd)) {
out$Parameter[ran_zi_sd] <- gsub("zi_", "", out$Parameter[ran_zi_sd], fixed = TRUE)
}
}
}
# brms random slope-intercepts correlation
ran_cor <- startsWith(out$Parameter, "cor_") & out$Effects == "random"
if (any(ran_cor)) {
out$Parameter[ran_cor] <- gsub("^cor_(.*?)__(.*)__(.*)", "Cor \\(\\2~\\3\\)", out$Parameter[ran_cor])
if (has_component) {
ran_zi_cor <- ran_cor & out$Component == "zero_inflated"
if (any(ran_zi_cor)) {
out$Parameter[ran_zi_cor] <- gsub("zi_", "", out$Parameter[ran_zi_cor], fixed = TRUE)
}
}
}
# stanreg random effects variances
ran_sd_cor <- startsWith(out$Parameter, "Sigma[")
if (any(ran_sd_cor)) {
out$Parameter[ran_sd_cor] <- gsub("(Intercept)", "Intercept", out$Parameter[ran_sd_cor], fixed = TRUE)
parm1 <- gsub("^Sigma\\[(.*):(.*),(.*)\\]", "\\2", out$Parameter[ran_sd_cor])
parm2 <- gsub("^Sigma\\[(.*):(.*),(.*)\\]", "\\3", out$Parameter[ran_sd_cor])
# for random intercept or slopes, parm1 and parm2 are identical
ran_sd <- parm1 == parm2
ran_cor <- parm1 != parm2
if (any(ran_sd)) {
out$Parameter[which(ran_sd_cor)[ran_sd]] <- paste0("Sigma (", parm1[ran_sd], ")")
}
if (any(ran_cor)) {
out$Parameter[which(ran_sd_cor)[ran_cor]] <- paste0("Sigma (", parm1[ran_cor], "~", parm2[ran_cor], ")")
}
}
out
}
# helper to format the header / subheader of different model components --------------
.format_model_component_header <- function(x,
type,
split_column,
is_zero_inflated,
is_ordinal_model,
is_multivariate = FALSE,
ran_pars, # nolint
formatted_table = NULL) {
# prepare component names
.conditional_fixed_text <- if (is_zero_inflated) {
"Fixed Effects (Count Model)"
} else {
"Fixed Effects"
}
.conditional_random_text <- if (ran_pars) {
"Random Effects Variances"
} else if (is_zero_inflated) {
"Random Effects (Count Model)"
} else {
"Random Effects"
}
component_name <- switch(type,
mu = ,
fixed = ,
fixed. = ,
conditional = ,
conditional. = "Fixed Effects",
random. = ,
random = "Random Effects",
conditional.fixed = ,
conditional.fixed. = .conditional_fixed_text,
conditional.random = .conditional_random_text,
zero_inflated = "Zero-Inflation",
zero_inflated.fixed = ,
zero_inflated.fixed. = "Fixed Effects (Zero-Inflation Component)",
zero_inflated.random = "Random Effects (Zero-Inflation Component)",
survival = ,
survival.fixed = "Survival",
dispersion.fixed = ,
dispersion.fixed. = ,
dispersion = "Dispersion",
marginal = "Marginal Effects",
emmeans = "Estimated Marginal Means",
contrasts = "Contrasts",
simplex.fixed = ,
simplex = "Monotonic Effects",
smooth_sd = "Smooth Terms (SD)",
smooth_terms = "Smooth Terms",
sigma.fixed = ,
sigma.fixed. = ,
sigma = "Sigma",
thresholds = "Thresholds",
correlation = "Correlation",
`SD/Cor` = "SD / Correlation",
Loading = "Loading",
location = ,
location.fixed = ,
location.fixed. = "Location Parameters",
scale = ,
scale.fixed = ,
scale.fixed. = "Scale Parameters",
extra = ,
extra.fixed = ,
extra.fixed. = "Extra Parameters",
nu = "Nu",
tau = "Tau",
meta = "Meta-Parameters",
studies = "Studies",
within = "Within-Effects",
between = "Between-Effects",
interactions = "(Cross-Level) Interactions",
precision = ,
precision. = "Precision",
infrequent_purchase = "Infrequent Purchase",
auxiliary = "Auxiliary",
residual = "Residual",
intercept = "Intercept",
regression = "Regression",
latent = "Latent",
time_dummies = "Time Dummies",
type
)
if (grepl("^conditional\\.(r|R)andom_variances", component_name)) {
component_name <- insight::trim_ws(gsub("^conditional\\.(r|R)andom_variances(\\.)*", "", component_name))
if (nzchar(component_name, keepNA = TRUE)) {
component_name <- paste0("Random Effects Variances: ", component_name)
} else {
component_name <- "Random Effects Variances"
}
}
if (grepl("^conditional\\.(r|R)andom", component_name)) {
component_name <- insight::trim_ws(gsub("^conditional\\.(r|R)andom(\\.)*", "", component_name))
if (nzchar(component_name, keepNA = TRUE)) {
component_name <- paste0("Random Effects (Count Model): ", component_name)
} else {
component_name <- ifelse(ran_pars, "Random Effects Variances", "Random Effects (Count Model)")
}
}
if (grepl("^zero_inflated\\.(r|R)andom", component_name)) {
component_name <- insight::trim_ws(gsub("^zero_inflated\\.(r|R)andom(\\.)*", "", component_name))
if (nzchar(component_name, keepNA = TRUE)) {
component_name <- paste0("Random Effects (Zero-Inflation Component): ", component_name)
} else {
component_name <- "Random Effects (Zero-Inflation Component)"
}
}
if (startsWith(component_name, "random.")) {
component_name <- paste0("Random Effects: ", gsub("^random\\.", "", component_name))
}
# if we show ZI component only, make sure this appears in header
if (!grepl("(Zero-Inflation Component)", component_name, fixed = TRUE) &&
!is.null(formatted_table$Component) &&
all(formatted_table$Component == "zero_inflated")) {
component_name <- paste0(component_name, " (Zero-Inflation Component)")
}
# tweaking of sub headers
if (isTRUE(attributes(x)$is_ggeffects)) {
s1 <- gsub("(.*)\\.(.*) = (.*)", "\\1 (\\2 = \\3)", component_name)
s2 <- ""
} else if ("DirichletRegModel" %in% attributes(x)$model_class) {
if (startsWith(component_name, "conditional.") || split_column == "Response") {
s1 <- "Response level:"
s2 <- gsub("^conditional\\.(.*)", "\\1", component_name)
} else {
s1 <- component_name
s2 <- ""
}
} else if (length(split_column) > 1 && "Response" %in% split_column && is_multivariate) {
# This here only applies to brms multivariate response models
component_name <- gsub("^conditional\\.(.*)", "Response level: \\1", component_name)
component_name <- gsub("^sigma\\.(.*)", "Auxilliary parameters, response level: \\1", component_name)
component_name <- gsub("(.*)fixed\\.(.*)", "\\1\\2", component_name)
component_name <- gsub("(.*)random\\.(.*)", "Random effects, \\1\\2", component_name)
s1 <- component_name
s2 <- ""
} else if (length(split_column) > 1 ||
split_column %in% c("Subgroup", "Type", "Group") ||
grepl(tolower(split_column), tolower(component_name), fixed = TRUE) ||
component_name %in% c("Within-Effects", "Between-Effects", "(Cross-Level) Interactions")) {
s1 <- component_name
s2 <- ""
} else if (split_column == "Response" && is_ordinal_model) {
s1 <- "Response level:"
s2 <- component_name
} else {
s1 <- component_name
if (tolower(split_column) == "component") {
s2 <- ""
} else {
s2 <- split_column
}
}
list(name = component_name, subheader1 = s1, subheader2 = s2)
}
# helper grouping parameters -------------------
.parameter_groups <- function(x, groups) {
# only apply to conditional component for now
if ("Component" %in% colnames(x) && !any(x$Component == "conditional")) {
return(x)
}
if ("Component" %in% colnames(x)) {
row_index <- which(x$Component == "conditional")
} else {
row_index <- seq_len(nrow(x))
}
x_other <- x[-row_index, ]
x <- x[row_index, ]
att <- attributes(x)
indent_rows <- NULL
indent_parameters <- NULL
if (is.list(groups)) {
# find parameter names and replace by rowindex
group_rows <- lapply(groups, function(i) {
if (is.character(i)) {
i <- match(i, x$Parameter)
}
i
})
# validation check - check if all parameter names in the
# group list are spelled correctly
misspelled <- vapply(group_rows, anyNA, TRUE)
if (any(misspelled)) {
# remove invalid groups
group_rows[misspelled] <- NULL
# tell user
insight::format_alert(
"Couldn't find one or more parameters specified in following groups:",
toString(names(misspelled[misspelled])),
"Maybe you misspelled parameter names?"
)
}
# sort parameters according to grouping
selected_rows <- unlist(group_rows)
indent_parameters <- x$Parameter[selected_rows]
x <- rbind(x[selected_rows, ], x[-selected_rows, ])
# set back correct indices
groups <- 1
for (i in 2:length(group_rows)) {
groups <- c(groups, groups[i - 1] + length(group_rows[[i - 1]]))
}
names(groups) <- names(group_rows)
} else {
# find parameter names and replace by rowindex
group_names <- names(groups)
groups <- match(groups, x$Parameter)
names(groups) <- group_names
# order groups
groups <- sort(groups, na.last = TRUE)
}
empty_row <- x[1, ]
for (i in seq_len(ncol(empty_row))) {
empty_row[[i]] <- NA
}
for (i in rev(seq_along(groups))) {
x[seq(groups[i] + 1, nrow(x) + 1), ] <- x[seq(groups[i], nrow(x)), ]
x[groups[i], ] <- empty_row
x$Parameter[groups[i]] <- paste0("# ", names(groups[i]))
}
# find row indices of indented parameters
if (!is.null(indent_parameters)) {
indent_rows <- match(indent_parameters, x$Parameter)
}
# add other rows back
if (nrow(x_other) > 0) {
x <- rbind(x, x_other)
}
attributes(x) <- utils::modifyList(att, attributes(x))
attr(x, "indent_rows") <- indent_rows
attr(x, "indent_groups") <- "# "
x
}
# .insert_row <- function(x, newrow, r) {
# existingDF[seq(r+1,nrow(existingDF)+1),] <- existingDF[seq(r,nrow(existingDF)),]
# existingDF[r,] <- newrow
# existingDF
# }
.prepare_x_for_print <- function(x, select, coef_name, s_value) {
# minor fix for nested Anovas
if ("Group" %in% colnames(x) && sum(x$Parameter == "Residuals") > 1) {
colnames(x)[which(colnames(x) == "Group")] <- "Subgroup"
}
# check which columns to be printed
if (!is.null(select)) {
if (all(select == "minimal")) {
select <- c("Parameter", "Coefficient", "Std_Coefficient", "CI", "CI_low", "CI_high", "p")
} else if (all(select == "short")) {
select <- c("Parameter", "Coefficient", "Std_Coefficient", "SE", "p")
} else if (is.numeric(select)) {
select <- colnames(x)[select]
}
select <- union(select, c("Parameter", "Component", "Effects", "Response", "Subgroup"))
# for emmGrid objects, we save specific parameter names as attribute
parameter_names <- attributes(x)$parameter_names
if (!is.null(parameter_names)) {
select <- c(parameter_names, select)
}
to_remove <- setdiff(colnames(x), select)
x[to_remove] <- NULL
}
# remove columns that have only NA or Inf
to_remove <- vapply(colnames(x), function(col) {
all(is.na(x[[col]]) | is.infinite(x[[col]])) & !grepl("CI_", col, fixed = TRUE)
}, TRUE)
if (any(to_remove)) x[to_remove] <- NULL
# For Bayesian models, we need to prettify parameter names here...
mc <- attributes(x)$model_class
cp <- attributes(x)$cleaned_parameters
if (!is.null(mc) && !is.null(cp) && any(mc %in% c("stanreg", "stanmvreg", "brmsfit"))) {
match_params <- stats::na.omit(match(names(cp), x$Parameter))
if (any(match_params)) {
x$Parameter[match_params] <- cp[x$Parameter[match_params]]
}
attr(x, "pretty_names") <- FALSE
attr(x, "cleaned_parameters") <- NULL
}
# for bayesian meta, remove ROPE_CI
if (isTRUE(attributes(x)$is_bayes_meta)) {
x$CI <- NULL
x$ROPE_CI <- NULL
x$ROPE_low <- NULL
x$ROPE_high <- NULL
}
if (!is.null(coef_name)) {
colnames(x)[which(colnames(x) == "Coefficient")] <- coef_name
colnames(x)[which(colnames(x) == "Std_Coefficient")] <- paste0("Std_", coef_name)
}
# cpmpute s- instead of p-value?
# see 10.1186/s12874-020-01105-9
if (isTRUE(s_value) && "p" %in% colnames(x)) {
colnames(x)[colnames(x) == "p"] <- "s"
x[["s"]] <- log2(1 / x[["s"]])
}
x
}
.prepare_splitby_for_print <- function(x) {
if (!is.null(attributes(x)$model_class) && any(attributes(x)$model_class == "mvord")) {
x$Response <- NULL
}
split_by <- ""
if ("Component" %in% names(x) && insight::n_unique(x$Component) > 1) {
split_by <- c(split_by, "Component")
}
if ("Effects" %in% names(x) && insight::n_unique(x$Effects) > 1) {
split_by <- c(split_by, "Effects")
}
if ("Response" %in% names(x) && insight::n_unique(x$Response) > 1) {
split_by <- c(split_by, "Response")
}
if ("Group" %in% names(x) && insight::n_unique(x$Group) > 1) {
split_by <- c(split_by, "Group")
}
if ("Subgroup" %in% names(x) && insight::n_unique(x$Subgroup) > 1) {
split_by <- c(split_by, "Subgroup")
}
split_by <- split_by[nzchar(split_by, keepNA = TRUE)]
split_by
}
# this function is actually similar to "insight::print_parameters()", but more
# sophisticated, to ensure nicely outputs even for complicated or complex models,
# or edge cases...
#' @keywords internal
.format_columns_multiple_components <- function(x,
pretty_names,
split_column = "Component",
digits = 2,
ci_digits = digits,
p_digits = 3,
coef_column = NULL,
format = NULL,
ci_width = "auto",
ci_brackets = TRUE,
zap_small = FALSE,
include_reference = FALSE,
...) {
final_table <- list()
ignore_group <- isTRUE(attributes(x)$ignore_group)
ran_pars <- isTRUE(attributes(x)$ran_pars)
is_ggeffects <- isTRUE(attributes(x)$is_ggeffects)
is_fixest_multi <- identical(attributes(x)$model_class, "fixest_multi")
# name of "Parameter" column - usually the first column, however, for
# ggeffects objects, this column has the name of the focal term
if (is_ggeffects) {
parameter_column <- colnames(x)[1]
} else {
parameter_column <- "Parameter"
}
# default brackets are parenthesis for HTML / MD
if ((is.null(ci_brackets) || isTRUE(ci_brackets)) && (identical(format, "html") || identical(format, "markdown"))) {
ci_brackets <- c("(", ")")
} else if (is.null(ci_brackets) || isTRUE(ci_brackets)) {
ci_brackets <- c("[", "]")
}
# check ordinal / multivariate
is_ordinal_model <- isTRUE(attributes(x)$ordinal_model)
is_multivariate <- isTRUE(attributes(x)$multivariate_response)
# zero-inflation stuff
is_zero_inflated <- (!is.null(x$Component) & "zero_inflated" %in% x$Component)
zi_coef_name <- attributes(x)$zi_coefficient_name
# other special model-components, like emm_list
coef_name2 <- attributes(x)$coefficient_name2
# make sure we have correct order of levels from split-factor
if (!is.null(attributes(x)$model_class) && all(attributes(x)$model_class == "mediate")) {
x$Component <- factor(x$Component, levels = c("control", "treated", "average", "Total Effect"))
x$Parameter <- insight::trim_ws(gsub("(.*)\\((.*)\\)$", "\\1", x$Parameter))
} else {
x[split_column] <- lapply(x[split_column], function(i) {
if (!is.factor(i)) i <- factor(i, levels = unique(i))
i
})
}
# fix column output
if (inherits(attributes(x)[["model"]], c("lavaan", "blavaan")) && "Label" %in% colnames(x)) {
x$From <- ifelse(!nzchar(as.character(x$Label), keepNA = TRUE) | x$Label == x$To, x$From, paste0(x$From, " (", x$Label, ")")) # nolint
x$Label <- NULL
}
if (inherits(attributes(x)[["model"]], c("lavaan", "blavaan")) && !"Parameter" %in% colnames(x)) {
parameter_column <- colnames(x)[1]
}
if (inherits(attributes(x)[["model"]], c("lavaan", "blavaan")) && "Defined" %in% x$Component) {
x$From[x$Component == "Defined"] <- ""
x$Operator[x$Component == "Defined"] <- ""
x$To <- ifelse(x$Component == "Defined", paste0("(", x$To, ")"), x$To)
}
# set up split-factor
if (length(split_column) > 1) {
split_by <- lapply(split_column, function(i) x[[i]])
} else {
split_by <- list(x[[split_column]])
}
names(split_by) <- split_column
# make sure we have correct sorting here...
tables <- split(x, f = split_by)
# validation check - only preserve tables with any data in data frames
tables <- tables[vapply(tables, nrow, numeric(1)) > 0]
# fix table names for random effects, when we only have random
# effects. in such cases, the wrong header (fixed effects) is chosen
# to prevent this, we "fake" the name of the splitted components by
# prefixing them with "random."
if (!is.null(x$Effects) && all(x$Effects == "random") && !all(startsWith(names(tables), "random."))) {
wrong_names <- !startsWith(names(tables), "random.")
names(tables)[wrong_names] <- paste0("random.", names(tables)[wrong_names])
}
# fixest_multi models can have a special structure, with multiple responses
# and multiple rhs of formulas. We fix headers here
if (is_fixest_multi && length(split_column) > 1) {
old_names <- unique(paste0(x$Response, ".", x$Group))
new_names <- unique(paste0(x$Response, " ~ ", x$Group))
names(tables) <- new_names[match(names(tables), old_names)]
}
for (type in names(tables)) {
# do we have emmeans emlist? and contrasts?
model_class <- attributes(tables[[type]])$model_class
em_list_coef_name <- (!is.null(model_class) && "emm_list" %in% model_class &&
"contrasts" %in% tables[[type]]$Component)
# Don't print Component column
for (i in split_column) {
tables[[type]][[i]] <- NULL
}
# Smooth terms statistics
if ("t / F" %in% names(tables[[type]])) {
if (type == "smooth_terms") {
names(tables[[type]])[names(tables[[type]]) == "t / F"] <- "F"
}
if (type == "conditional") {
names(tables[[type]])[names(tables[[type]]) == "t / F"] <- "t"
}
} else if (type == "smooth_terms" && "t" %in% names(tables[[type]])) {
names(tables[[type]])[names(tables[[type]]) == "t"] <- "F"
}
if ("z / Chi2" %in% names(tables[[type]])) {
if (type == "smooth_terms") {
names(tables[[type]])[names(tables[[type]]) == "z / Chi2"] <- "Chi2"
}
if (type == "conditional") {
names(tables[[type]])[names(tables[[type]]) == "z / Chi2"] <- "z"
}
}
# Don't print se and ci if all are missing
if (all(is.na(tables[[type]]$SE))) tables[[type]]$SE <- NULL
if (all(is.na(tables[[type]]$CI_low)) && all(is.na(tables[[type]]$CI_high))) {
tables[[type]]$CI_low <- NULL
tables[[type]]$CI_high <- NULL
}
# if (all(is.na(tables[[type]]$CI_low))) tables[[type]]$CI_low <- NULL
# if (all(is.na(tables[[type]]$CI_high))) tables[[type]]$CI_high <- NULL
# Don't print if empty col
tables[[type]][vapply(colnames(tables[[type]]), function(x) {
column <- tables[[type]][[x]]
(!any(nzchar(as.character(column), keepNA = TRUE)) | all(is.na(column))) && !grepl("_CI_(high|low)$", x)
}, logical(1))] <- NULL
attr(tables[[type]], "digits") <- digits
attr(tables[[type]], "ci_digits") <- ci_digits
attr(tables[[type]], "p_digits") <- p_digits
# random pars with level? combine into parameter column
if (all(c("Parameter", "Level") %in% colnames(tables[[type]]))) {
tables[[type]]$Parameter <- paste0(
tables[[type]]$Parameter, " ", ci_brackets[1],
tables[[type]]$Level, ci_brackets[2]
)
tables[[type]]$Level <- NULL
}
# rename columns for emmeans contrast part
if (em_list_coef_name && !is.null(coef_column)) {
colnames(tables[[type]])[which(colnames(tables[[type]]) == coef_column)] <- coef_name2
}
# rename columns for zero-inflation part
if (startsWith(type, "zero") && !is.null(zi_coef_name) && !is.null(coef_column)) {
colnames(tables[[type]])[which(colnames(tables[[type]]) == coef_column)] <- zi_coef_name
colnames(tables[[type]])[which(colnames(tables[[type]]) == paste0("Std_", coef_column))] <- paste0("Std_", zi_coef_name) # nolint
}
# rename columns for correlation, location or scale part
if (type %in% c("correlation", "scale", "location") && !is.null(coef_column)) {
colnames(tables[[type]])[which(colnames(tables[[type]]) == coef_column)] <- "Estimate"
}
# rename columns for dispersion part
if (startsWith(type, "dispersion") && !is.null(coef_column)) {
colnames(tables[[type]])[which(colnames(tables[[type]]) == coef_column)] <- "Coefficient"
}
# rename columns for random part
if (grepl("random", type, fixed = TRUE) && any(colnames(tables[[type]]) %in% .all_coefficient_types)) {
colnames(tables[[type]])[colnames(tables[[type]]) %in% .all_coefficient_types] <- "Coefficient"
}
if (grepl("random", type, fixed = TRUE) && isTRUE(ran_pars)) {
tables[[type]]$CI <- NULL
}
# for ggeffects objects, only choose selected lines, to have
# a more compact output
if (is_ggeffects && is.numeric(tables[[type]][[1]])) {
n_rows <- nrow(tables[[type]])
row_steps <- round(sqrt(n_rows))
sample_rows <- round(c(1, stats::quantile(seq_len(n_rows), seq_len(row_steps - 2) / row_steps), n_rows))
tables[[type]] <- tables[[type]][sample_rows, ]
tables[[type]][[1]] <- insight::format_value(tables[[type]][[1]], digits = digits, protect_integers = TRUE)
}
# add the coefficient for the base-(reference)-level of factors?
if (include_reference) {
tables[[type]] <- .add_reference_level(tables[[type]])
}
formatted_table <- insight::format_table(
tables[[type]],
digits = digits, ci_digits = ci_digits,
p_digits = p_digits, pretty_names = pretty_names, ci_width = ci_width,
ci_brackets = ci_brackets, zap_small = zap_small, ...
)
component_header <- .format_model_component_header(
x, type, split_column, is_zero_inflated, is_ordinal_model,
is_multivariate, ran_pars, formatted_table
)
# exceptions for random effects
if (insight::n_unique(formatted_table$Group) == 1) {
component_header$subheader1 <- paste0(component_header$subheader1, " (", formatted_table$Group, ")")
formatted_table$Group <- NULL
}
# remove non-necessary columns
if (insight::n_unique(formatted_table$Component) == 1) {
formatted_table$Component <- NULL
}
# no column with CI-level in output
if (!is.null(formatted_table$CI) && insight::n_unique(formatted_table$CI) == 1) {
formatted_table$CI <- NULL
}
table_caption <- NULL
if (is.null(format) || format %in% c("markdown", "text")) {
# Print
if (component_header$name != "rewb-contextual") {
table_caption <- c(
sprintf("# %s %s", component_header$subheader1, tolower(component_header$subheader2)),
"blue"
)
}
} else if (format %in% c("markdown", "html")) {
# Print
if (component_header$name != "rewb-contextual") {
table_caption <- sprintf("%s %s", component_header$subheader1, tolower(component_header$subheader2))
}
# replace brackets by parenthesis
if (!is.null(parameter_column) && parameter_column %in% colnames(formatted_table)) {
formatted_table[[parameter_column]] <- gsub("[", ci_brackets[1], formatted_table[[parameter_column]], fixed = TRUE) # nolint
formatted_table[[parameter_column]] <- gsub("]", ci_brackets[2], formatted_table[[parameter_column]], fixed = TRUE) # nolint
}
}
if (identical(format, "html")) {
formatted_table$Component <- table_caption
} else {
attr(formatted_table, "table_caption") <- table_caption
}
# remove unique columns
if (insight::n_unique(formatted_table$Effects) == 1) formatted_table$Effects <- NULL
if (insight::n_unique(formatted_table$Group) == 1) formatted_table$Group <- NULL
final_table <- c(final_table, list(formatted_table))
}
if (identical(format, "html")) {
# fix non-equal length of columns
final_table <- .fix_nonmatching_columns(
final_table,
is_lavaan = inherits(attributes(x)[["model"]], c("lavaan", "blavaan"))
)
do.call(rbind, final_table)
} else {
insight::compact_list(final_table)
}
}
# helper to fix unequal number of columns for list of data frames,
# when used for HTML printing
.fix_nonmatching_columns <- function(final_table, is_lavaan = FALSE) {
# fix for lavaan here
if (is_lavaan) {
for (i in seq_along(final_table)) {
if (!is.null(final_table[[i]]$Link) && !is.null(final_table[[i]]$To) && all(is.na(final_table[[i]]$Link))) {
final_table[[i]]$Link <- final_table[[i]]$To
final_table[[i]]$To <- NA
}
colnames(final_table[[i]])[1] <- "Parameter"
if (!is.null(final_table[[i]]$To) && all(is.na(final_table[[i]]$To))) {
final_table[[i]]$To <- NULL
}
}
}
# then check for correct column length
col_len <- vapply(final_table, function(i) length(colnames(i)), numeric(1))
# remove non matching columns
if (!all(col_len == max(col_len))) {
all_columns <- unique(unlist(lapply(final_table, colnames)))
for (i in seq_along(final_table)) {
missing_columns <- setdiff(all_columns, colnames(final_table[[i]]))
if (length(missing_columns)) {
a <- attributes(final_table[[i]])
final_table[[i]][missing_columns] <- NA
final_table[[i]] <- final_table[[i]][match(all_columns, colnames(final_table[[i]]))]
attributes(final_table[[i]]) <- utils::modifyList(a, attributes(final_table[[i]]))
}
}
}
final_table
}
|