@@ -15141,21 +15141,21 @@
tern coverage - 94.66%
| 53 |
- 405x |
+ 407x |
checkmate::assert_character(method_groups)
|
| 54 |
- 405x |
+ 407x |
checkmate::assert_character(stats_in, null.ok = TRUE)
|
| 55 |
- 405x |
+ 407x |
checkmate::assert_flag(add_pval)
|
@@ -15176,7 +15176,7 @@ tern coverage - 94.66%
| 58 |
- 405x |
+ 407x |
if (any(method_groups == "analyze_vars")) {
|
@@ -15204,7 +15204,7 @@ tern coverage - 94.66%
| 62 |
- 405x |
+ 407x |
type_tmp <- ifelse(any(grepl("counts", method_groups)), "counts", "numeric") # for pval checks
|
@@ -15225,7 +15225,7 @@ tern coverage - 94.66%
| 65 |
- 405x |
+ 407x |
out <- NULL
|
@@ -15246,21 +15246,21 @@ tern coverage - 94.66%
| 68 |
- 405x |
+ 407x |
for (mgi in method_groups) {
|
| 69 |
- 415x |
+ 417x |
out_tmp <- if (mgi %in% names(tern_default_stats)) {
|
| 70 |
- 415x |
+ 417x |
tern_default_stats[[mgi]]
|
@@ -15288,7 +15288,7 @@ tern coverage - 94.66%
| 74 |
- 415x |
+ 417x |
out <- unique(c(out, out_tmp))
|
@@ -15316,7 +15316,7 @@ tern coverage - 94.66%
| 78 |
- 405x |
+ 407x |
if (!is.null(stats_in) && any(grepl("^pval", stats_in))) {
|
@@ -15463,7 +15463,7 @@ tern coverage - 94.66%
| 99 |
- 402x |
+ 404x |
if (isTRUE(add_pval)) {
|
@@ -15526,7 +15526,7 @@ tern coverage - 94.66%
| 108 |
- 402x |
+ 404x |
if (!is.null(stats_in)) {
|
@@ -15561,7 +15561,7 @@ tern coverage - 94.66%
| 113 |
- 402x |
+ 404x |
if (length(out) == 0) {
|
@@ -15617,7 +15617,7 @@ tern coverage - 94.66%
| 121 |
- 400x |
+ 402x |
out
|
@@ -15834,7 +15834,7 @@ tern coverage - 94.66%
| 152 |
- 403x |
+ 405x |
checkmate::assert_character(stats, min.len = 1)
|
@@ -15848,7 +15848,7 @@ tern coverage - 94.66%
| 154 |
- 403x |
+ 405x |
if (checkmate::test_list(formats_in, null.ok = TRUE)) {
|
@@ -15876,7 +15876,7 @@ tern coverage - 94.66%
| 158 |
- 42x |
+ 44x |
checkmate::assert_character(formats_in, null.ok = TRUE)
|
@@ -15904,7 +15904,7 @@ tern coverage - 94.66%
| 162 |
- 403x |
+ 405x |
which_fmt <- match(stats, names(tern_default_formats))
|
@@ -15925,14 +15925,14 @@ tern coverage - 94.66%
| 165 |
- 403x |
+ 405x |
ret <- vector("list", length = length(stats)) # Returning a list is simpler
|
| 166 |
- 403x |
+ 405x |
ret[!is.na(which_fmt)] <- tern_default_formats[which_fmt[!is.na(which_fmt)]]
|
@@ -15946,7 +15946,7 @@ tern coverage - 94.66%
| 168 |
- 403x |
+ 405x |
out <- setNames(ret, stats)
|
@@ -15967,7 +15967,7 @@ tern coverage - 94.66%
| 171 |
- 403x |
+ 405x |
if (!is.null(formats_in)) {
|
@@ -15981,14 +15981,14 @@ tern coverage - 94.66%
| 173 |
- 44x |
+ 46x |
common_names <- intersect(names(out), names(formats_in))
|
| 174 |
- 44x |
+ 46x |
out[common_names] <- formats_in[common_names]
|
@@ -16009,7 +16009,7 @@ tern coverage - 94.66%
| 177 |
- 403x |
+ 405x |
out
|
@@ -16212,14 +16212,14 @@ tern coverage - 94.66%
| 206 |
- 387x |
+ 389x |
checkmate::assert_character(stats, min.len = 1, null.ok = TRUE)
|
| 207 |
- 387x |
+ 389x |
checkmate::assert_character(row_nms, null.ok = TRUE)
|
@@ -16233,7 +16233,7 @@ tern coverage - 94.66%
| 209 |
- 387x |
+ 389x |
if (checkmate::test_list(labels_in, null.ok = TRUE)) {
|
@@ -16261,7 +16261,7 @@ tern coverage - 94.66%
| 213 |
- 49x |
+ 51x |
checkmate::assert_character(labels_in, null.ok = TRUE)
|
@@ -16282,7 +16282,7 @@ tern coverage - 94.66%
| 216 |
- 387x |
+ 389x |
if (!is.null(row_nms)) {
|
@@ -16345,7 +16345,7 @@ tern coverage - 94.66%
| 225 |
- 344x |
+ 346x |
which_lbl <- match(stats, names(tern_default_labels))
|
@@ -16359,14 +16359,14 @@ tern coverage - 94.66%
| 227 |
- 344x |
+ 346x |
ret <- vector("character", length = length(stats)) # it needs to be a character vector
|
| 228 |
- 344x |
+ 346x |
ret[!is.na(which_lbl)] <- tern_default_labels[which_lbl[!is.na(which_lbl)]]
|
@@ -16380,7 +16380,7 @@ tern coverage - 94.66%
| 230 |
- 344x |
+ 346x |
out <- setNames(ret, stats)
|
@@ -16408,7 +16408,7 @@ tern coverage - 94.66%
| 234 |
- 387x |
+ 389x |
if (!is.null(labels_in)) {
|
@@ -16422,14 +16422,14 @@ tern coverage - 94.66%
| 236 |
- 49x |
+ 51x |
common_names <- intersect(names(out), names(labels_in))
|
| 237 |
- 49x |
+ 51x |
out[common_names] <- labels_in[common_names]
|
@@ -16450,7 +16450,7 @@ tern coverage - 94.66%
| 240 |
- 387x |
+ 389x |
out
|
@@ -16597,14 +16597,14 @@ tern coverage - 94.66%
| 261 |
- 367x |
+ 369x |
checkmate::assert_character(stats, min.len = 1)
|
| 262 |
- 367x |
+ 369x |
checkmate::assert_character(row_nms, null.ok = TRUE)
|
@@ -16618,14 +16618,14 @@ tern coverage - 94.66%
| 264 |
- 367x |
+ 369x |
if (checkmate::test_list(indents_in, null.ok = TRUE)) {
|
| 265 |
- 336x |
+ 338x |
checkmate::assert_list(indents_in, null.ok = TRUE)
|
@@ -16667,7 +16667,7 @@ tern coverage - 94.66%
| 271 |
- 367x |
+ 369x |
if (is.null(names(indents_in)) && length(indents_in) == 1) {
|
@@ -16702,7 +16702,7 @@ tern coverage - 94.66%
| 276 |
- 359x |
+ 361x |
if (!is.null(row_nms)) {
|
@@ -16765,14 +16765,14 @@ tern coverage - 94.66%
| 285 |
- 322x |
+ 324x |
ret <- rep(0L, length(stats))
|
| 286 |
- 322x |
+ 324x |
out <- setNames(ret, stats)
|
@@ -16800,7 +16800,7 @@ tern coverage - 94.66%
| 290 |
- 359x |
+ 361x |
if (!is.null(indents_in)) {
|
@@ -16842,7 +16842,7 @@ tern coverage - 94.66%
| 296 |
- 359x |
+ 361x |
out
|
@@ -17038,42 +17038,42 @@ tern coverage - 94.66%
| 324 |
- 18x |
+ 20x |
if ("conf_level" %in% names(control)) {
|
| 325 |
- 18x |
+ 20x |
labels_default <- sapply(
|
| 326 |
- 18x |
+ 20x |
names(labels_default),
|
| 327 |
- 18x |
+ 20x |
function(x) {
|
| 328 |
- 74x |
+ 86x |
if (!x %in% names(labels_custom)) {
|
| 329 |
- 73x |
+ 85x |
gsub(labels_default[[x]], pattern = "[0-9]+% CI", replacement = f_conf_level(control[["conf_level"]]))
|
@@ -17122,35 +17122,35 @@ tern coverage - 94.66%
| 336 |
- 18x |
+ 20x |
if ("quantiles" %in% names(control) && "quantiles" %in% names(labels_default) &&
|
| 337 |
- 18x |
+ 20x |
!"quantiles" %in% names(labels_custom)) { # nolint
|
| 338 |
- 14x |
+ 16x |
labels_default["quantiles"] <- gsub(
|
| 339 |
- 14x |
+ 16x |
"[0-9]+% and [0-9]+", paste0(control[["quantiles"]][1] * 100, "% and ", control[["quantiles"]][2] * 100, ""),
|
| 340 |
- 14x |
+ 16x |
labels_default["quantiles"]
|
@@ -17171,14 +17171,14 @@ tern coverage - 94.66%
| 343 |
- 18x |
+ 20x |
if ("test_mean" %in% names(control) && "mean_pval" %in% names(labels_default) &&
|
| 344 |
- 18x |
+ 20x |
!"mean_pval" %in% names(labels_custom)) { # nolint
|
@@ -17220,7 +17220,7 @@ tern coverage - 94.66%
| 350 |
- 18x |
+ 20x |
labels_default
|
@@ -27319,14 +27319,14 @@ tern coverage - 94.66%
| 570 |
- 366x |
+ 368x |
is_auto_fmt <- vapply(.formats, function(ii) is.character(ii) && ii == "auto", logical(1))
|
| 571 |
- 366x |
+ 368x |
if (any(is_auto_fmt)) {
|
@@ -27361,7 +27361,7 @@ tern coverage - 94.66%
| 576 |
- 366x |
+ 368x |
.formats
|
@@ -44878,7 +44878,7 @@ tern coverage - 94.66%
| 456 |
- 230x |
+ 232x |
getOption("tern_default_na_str", default = NA_character_)
|
@@ -70256,7 +70256,7 @@ tern coverage - 94.66%
| 15 |
- 1291x |
+ 1297x |
checkmate::assert_numeric(x)
|
@@ -70270,7 +70270,7 @@ tern coverage - 94.66%
| 17 |
- 1291x |
+ 1297x |
if (finite) {
|
@@ -70284,14 +70284,14 @@ tern coverage - 94.66%
| 19 |
- 1267x |
+ 1273x |
} else if (na.rm) {
|
| 20 |
- 630x |
+ 636x |
x <- x[!is.na(x)]
|
@@ -70312,21 +70312,21 @@ tern coverage - 94.66%
| 23 |
- 1291x |
+ 1297x |
if (length(x) == 0) {
|
| 24 |
- 85x |
+ 87x |
rval <- c(NA, NA)
|
| 25 |
- 85x |
+ 87x |
mode(rval) <- typeof(x)
|
@@ -70340,7 +70340,7 @@ tern coverage - 94.66%
| 27 |
- 1206x |
+ 1210x |
rval <- c(min(x, na.rm = FALSE), max(x, na.rm = FALSE))
|
@@ -70361,7 +70361,7 @@ tern coverage - 94.66%
| 30 |
- 1291x |
+ 1297x |
return(rval)
|
@@ -70452,14 +70452,14 @@ tern coverage - 94.66%
| 43 |
- 2365x |
+ 2379x |
assert_proportion_value(conf_level)
|
| 44 |
- 2363x |
+ 2377x |
paste0(conf_level * 100, "% CI")
|
@@ -111931,35 +111931,35 @@ tern coverage - 94.66%
| 45 |
- 203x |
+ 205x |
conf_type <- match.arg(conf_type)
|
| 46 |
- 202x |
+ 204x |
checkmate::assert_numeric(quantiles, lower = 0, upper = 1, len = 2, unique = TRUE, sorted = TRUE)
|
| 47 |
- 201x |
+ 203x |
nullo <- lapply(quantiles, assert_proportion_value)
|
| 48 |
- 201x |
+ 203x |
assert_proportion_value(conf_level)
|
| 49 |
- 200x |
+ 202x |
list(conf_level = conf_level, conf_type = conf_type, quantiles = quantiles)
|
@@ -136677,28 +136677,28 @@ tern coverage - 94.66%
| 54 |
- 206x |
+ 208x |
checkmate::assert_string(.var)
|
| 55 |
- 206x |
+ 208x |
assert_df_with_variables(df, list(tte = .var, is_event = is_event))
|
| 56 |
- 206x |
+ 208x |
checkmate::assert_numeric(df[[.var]], min.len = 1, any.missing = FALSE)
|
| 57 |
- 206x |
+ 208x |
checkmate::assert_logical(df[[is_event]], min.len = 1, any.missing = FALSE)
|
@@ -136712,21 +136712,21 @@ tern coverage - 94.66%
| 59 |
- 206x |
+ 208x |
conf_type <- control$conf_type
|
| 60 |
- 206x |
+ 208x |
conf_level <- control$conf_level
|
| 61 |
- 206x |
+ 208x |
quantiles <- control$quantiles
|
@@ -136740,42 +136740,42 @@ tern coverage - 94.66%
| 63 |
- 206x |
+ 208x |
formula <- stats::as.formula(paste0("survival::Surv(", .var, ", ", is_event, ") ~ 1"))
|
| 64 |
- 206x |
+ 208x |
srv_fit <- survival::survfit(
|
| 65 |
- 206x |
+ 208x |
formula = formula,
|
| 66 |
- 206x |
+ 208x |
data = df,
|
| 67 |
- 206x |
+ 208x |
conf.int = conf_level,
|
| 68 |
- 206x |
+ 208x |
conf.type = conf_type
|
@@ -136789,63 +136789,63 @@ tern coverage - 94.66%
| 70 |
- 206x |
+ 208x |
srv_tab <- summary(srv_fit, extend = TRUE)$table
|
| 71 |
- 206x |
+ 208x |
srv_qt_tab <- stats::quantile(srv_fit, probs = quantiles)$quantile
|
| 72 |
- 206x |
+ 208x |
range_censor <- range_noinf(df[[.var]][!df[[is_event]]], na.rm = TRUE)
|
| 73 |
- 206x |
+ 208x |
range_event <- range_noinf(df[[.var]][df[[is_event]]], na.rm = TRUE)
|
| 74 |
- 206x |
+ 208x |
range <- range_noinf(df[[.var]], na.rm = TRUE)
|
| 75 |
- 206x |
+ 208x |
list(
|
| 76 |
- 206x |
+ 208x |
median = formatters::with_label(unname(srv_tab["median"]), "Median"),
|
| 77 |
- 206x |
+ 208x |
median_ci = formatters::with_label(
|
| 78 |
- 206x |
+ 208x |
unname(srv_tab[paste0(srv_fit$conf.int, c("LCL", "UCL"))]), f_conf_level(conf_level)
|
@@ -136859,14 +136859,14 @@ tern coverage - 94.66%
| 80 |
- 206x |
+ 208x |
quantiles = formatters::with_label(
|
| 81 |
- 206x |
+ 208x |
unname(srv_qt_tab), paste0(quantiles[1] * 100, "% and ", quantiles[2] * 100, "%-ile")
|
@@ -136880,21 +136880,21 @@ tern coverage - 94.66%
| 83 |
- 206x |
+ 208x |
range_censor = formatters::with_label(range_censor, "Range (censored)"),
|
| 84 |
- 206x |
+ 208x |
range_event = formatters::with_label(range_event, "Range (event)"),
|
| 85 |
- 206x |
+ 208x |
range = formatters::with_label(range, "Range")
|
@@ -137104,14 +137104,14 @@ tern coverage - 94.66%
| 115 |
- 12x |
+ 14x |
x_stats <- s_surv_time(
|
| 116 |
- 12x |
+ 14x |
df = df, .var = .var, is_event = is_event, control = control
|
@@ -137125,14 +137125,14 @@ tern coverage - 94.66%
| 118 |
- 12x |
+ 14x |
rng_censor_lwr <- x_stats[["range_censor"]][1]
|
| 119 |
- 12x |
+ 14x |
rng_censor_upr <- x_stats[["range_censor"]][2]
|
@@ -137153,35 +137153,35 @@ tern coverage - 94.66%
| 122 |
- 12x |
+ 14x |
fmts <- c(median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x")
|
| 123 |
- 12x |
+ 14x |
lbls <- c(median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)")
|
| 124 |
- 12x |
+ 14x |
lbls_custom <- .labels
|
| 125 |
- 12x |
+ 14x |
.formats <- c(.formats, fmts[setdiff(names(fmts), names(.formats))])
|
| 126 |
- 12x |
+ 14x |
.labels <- c(.labels, lbls[setdiff(names(lbls), names(lbls_custom))])
|
@@ -137202,28 +137202,28 @@ tern coverage - 94.66%
| 129 |
- 12x |
+ 14x |
.stats <- get_stats("surv_time", stats_in = .stats)
|
| 130 |
- 12x |
+ 14x |
.formats <- get_formats_from_stats(.stats, .formats)
|
| 131 |
- 12x |
+ 14x |
.labels <- get_labels_from_stats(.stats, .labels) %>% labels_use_control(control, lbls_custom)
|
| 132 |
- 12x |
+ 14x |
.indent_mods <- get_indents_from_stats(.stats, .indent_mods)
|
@@ -137237,7 +137237,7 @@ tern coverage - 94.66%
| 134 |
- 12x |
+ 14x |
x_stats <- x_stats[.stats]
|
@@ -137258,7 +137258,7 @@ tern coverage - 94.66%
| 137 |
- 12x |
+ 14x |
.formats <- apply_auto_formatting(.formats, x_stats, .df_row, .var)
|
@@ -137272,37 +137272,37 @@ tern coverage - 94.66%
| 139 |
- 12x |
+ 14x |
cell_fns <- setNames(vector("list", length = length(x_stats)), .labels)
|
| 140 |
- 12x |
+ 14x |
if ("range" %in% names(x_stats) && ref_fn_censor) {
|
| 141 |
- 12x |
+ 14x |
- if (x_stats[["range"]][1] == rng_censor_lwr && x_stats[["range"]][2] == rng_censor_upr) {
+ if (identical(x_stats[["range"]][1], rng_censor_lwr) && identical(x_stats[["range"]][2], rng_censor_upr)) {
|
| 142 |
- 1x |
+ 2x |
cell_fns[[.labels[["range"]]]] <- "Censored observations: range minimum & maximum"
|
| 143 |
- 11x |
+ 12x |
- } else if (x_stats[["range"]][1] == rng_censor_lwr) {
+ } else if (identical(x_stats[["range"]][1], rng_censor_lwr)) {
|
@@ -137314,9 +137314,9 @@ tern coverage - 94.66%
| 145 |
- 9x |
+ 10x |
- } else if (x_stats[["range"]][2] == rng_censor_upr) {
+ } else if (identical(x_stats[["range"]][2], rng_censor_upr)) {
|
@@ -137349,56 +137349,56 @@ tern coverage - 94.66%
| 150 |
- 12x |
+ 14x |
in_rows(
|
| 151 |
- 12x |
+ 14x |
.list = x_stats,
|
| 152 |
- 12x |
+ 14x |
.formats = .formats,
|
| 153 |
- 12x |
+ 14x |
.names = .labels,
|
| 154 |
- 12x |
+ 14x |
.labels = .labels,
|
| 155 |
- 12x |
+ 14x |
.indent_mods = .indent_mods,
|
| 156 |
- 12x |
+ 14x |
.format_na_strs = na_str,
|
| 157 |
- 12x |
+ 14x |
.cell_footnotes = cell_fns
|
@@ -170549,7 +170549,7 @@ tern coverage - 94.66%
| 22 |
- 2455x |
+ 2457x |
x <- Filter(Negate(is.null), x)
|
@@ -170563,35 +170563,35 @@ tern coverage - 94.66%
| 24 |
- 2455x |
+ 2457x |
res <- checkmate::check_list(x,
|
| 25 |
- 2455x |
+ 2457x |
names = "named",
|
| 26 |
- 2455x |
+ 2457x |
min.len = 1,
|
| 27 |
- 2455x |
+ 2457x |
any.missing = FALSE,
|
| 28 |
- 2455x |
+ 2457x |
types = "character"
|
@@ -170612,14 +170612,14 @@ tern coverage - 94.66%
| 31 |
- 2455x |
+ 2457x |
if (isTRUE(res)) {
|
| 32 |
- 2450x |
+ 2452x |
res <- checkmate::check_character(unlist(x), min.chars = 1)
|
@@ -170633,7 +170633,7 @@ tern coverage - 94.66%
| 34 |
- 2455x |
+ 2457x |
return(res)
|
@@ -170696,14 +170696,14 @@ tern coverage - 94.66%
| 43 |
- 2172x |
+ 2174x |
checkmate::assert_data_frame(df)
|
| 44 |
- 2170x |
+ 2172x |
assert_list_of_variables(variables)
|
@@ -170724,14 +170724,14 @@ tern coverage - 94.66%
| 47 |
- 2168x |
+ 2170x |
err_flag <- all(unlist(variables) %in% colnames(df))
|
| 48 |
- 2168x |
+ 2170x |
checkmate::assert_flag(err_flag)
|
@@ -170745,7 +170745,7 @@ tern coverage - 94.66%
| 50 |
- 2168x |
+ 2170x |
if (isFALSE(err_flag)) {
|
@@ -170808,7 +170808,7 @@ tern coverage - 94.66%
| 59 |
- 2163x |
+ 2165x |
if (!is.null(na_level)) {
|
@@ -170892,7 +170892,7 @@ tern coverage - 94.66%
| 71 |
- 2162x |
+ 2164x |
return(TRUE)
|
@@ -171487,35 +171487,35 @@ tern coverage - 94.66%
| 156 |
- 9840x |
+ 9860x |
checkmate::assert_number(x, lower = 0, upper = 1)
|
| 157 |
- 9828x |
+ 9848x |
checkmate::assert_flag(include_boundaries)
|
| 158 |
- 9828x |
+ 9848x |
if (isFALSE(include_boundaries)) {
|
| 159 |
- 5298x |
+ 5318x |
checkmate::assert_true(x > 0)
|
| 160 |
- 5296x |
+ 5316x |
checkmate::assert_true(x < 1)
|