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Merge branch 'dev-current'
Deprecation of na.rm in tb()
2 parents e3aa026 + af830bd commit c663fed

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-48
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4 files changed

+24
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‎NEWS.md‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@
99
- In `tb()`
1010
+ Fix for broken proportions in freq tables
1111
+ New parameters `fct.to.chr` and `recalculate` for freq tables
12+
+ Parameter `na.rm` deprecated
1213
- In `dfSummary()`:
1314
+ New parameter `class` allows switching off class reporting in *Variable*
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column.

‎R/args_validation.R‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -399,17 +399,17 @@ check_args_tb <- function(mc) {
399399
!isTRUE(test_choice(pf$order, c(1, 2, 3)))) {
400400
errmsg %+=% "'order' must be one of 1, 2, or 3"
401401
}
402-
403-
if ("na.rm" %in% names(mc) &&
404-
!isTRUE(test_logical(pf$na.rm, len = 1, any.missing = FALSE))) {
405-
errmsg %+=% "'na.rm' must be either TRUE or FALSE"
406-
}
407402

408403
if ("drop.val.col" %in% names(mc) &&
409404
!isTRUE(test_logical(pf$drop.val.col, len = 1, any.missing = FALSE))) {
410405
errmsg %+=% "'drop.val.col' must be either TRUE or FALSE"
411406
}
412407

408+
if ("na.rm" %in% names(mc)) {
409+
message("parameter na.rm is deprecated; use ",
410+
"freq(..., report.nas = FALSE) instead")
411+
}
412+
413413
return(errmsg)
414414
}
415415

‎R/tb.R‎

Lines changed: 18 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -11,11 +11,6 @@
1111
#' as with \code{2} is used, but the analytical variable is placed in
1212
#' first position. Depending on what function was used for grouping,
1313
#' the results will be different in subtle ways. See \emph{Details}.
14-
#' @param na.rm Logical. Affects grouped \code{\link{freq}} objects only.
15-
#' Discard rows with \code{NA} values on at least one of the grouping
16-
#' variables. \code{FALSE} by default. (To exclude NA values on the main
17-
#' variable as well as \emph{pct_valid} & \emph{pct_valid_cum} columns, use
18-
#' \code{freq()}'s `report.nas` and `cumul` arguments.)
1914
#' @param drop.var.col Logical. For \code{\link{descr}} objects, drop the
2015
#' \code{variable} column. This is possible only when statistics are
2116
#' produced for a single variable; when multiple variables are present,
@@ -61,7 +56,7 @@
6156
#' @importFrom tibble tibble as_tibble
6257
#' @importFrom dplyr bind_rows bind_cols
6358
#' @export
64-
tb <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
59+
tb <- function(x, order = 1, drop.var.col = FALSE,
6560
recalculate = TRUE, fct.to.chr = FALSE, ...) {
6661

6762
# For dispatched list elements having a NULL group
@@ -88,7 +83,7 @@ tb <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
8883
}
8984

9085
#' @exportS3Method tb default
91-
tb.default <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
86+
tb.default <- function(x, order = 1, drop.var.col = FALSE,
9287
recalculate = TRUE, fct.to.chr = FALSE, ...) {
9388

9489
st_type <- attr(x, "st_type")
@@ -100,13 +95,13 @@ tb.default <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
10095

10196
do.call(
10297
method,
103-
list(x = x, order = order, na.rm = na.rm, drop.var.col = drop.var.col,
98+
list(x = x, order = order, drop.var.col = drop.var.col,
10499
recalculate = recalculate, fct.to.chr = fct.to.chr, ...)
105100
)
106101
}
107102

108103
#' @exportS3Method tb summarytools
109-
tb.summarytools <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
104+
tb.summarytools <- function(x, order = 1, drop.var.col = FALSE,
110105
recalculate = TRUE, fct.to.chr = FALSE, ...) {
111106

112107
st_type <- attr(x, "st_type")
@@ -118,24 +113,24 @@ tb.summarytools <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
118113

119114
do.call(
120115
method,
121-
list(x = x, order = order, na.rm = na.rm, drop.var.col = drop.var.col,
116+
list(x = x, order = order, drop.var.col = drop.var.col,
122117
recalculate = recalculate, fct.to.chr = fct.to.chr, ...)
123118
)
124119
}
125120

126121

127122
#' @exportS3Method tb by
128-
tb.by <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
123+
tb.by <- function(x, order = 1, drop.var.col = FALSE,
129124
recalculate = TRUE, fct.to.chr = FALSE, ...) {
130125
do.call(
131126
tb.stby,
132-
list(x = x, order = order, na.rm = na.rm, drop.var.col = drop.var.col,
127+
list(x = x, order = order, drop.var.col = drop.var.col,
133128
recalculate = recalculate, fct.to.chr = fct.to.chr, ...)
134129
)
135130
}
136131

137132
#' @exportS3Method tb stby
138-
tb.stby <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
133+
tb.stby <- function(x, order = 1, drop.var.col = FALSE,
139134
recalculate = TRUE, fct.to.chr = FALSE, ...) {
140135

141136
st_type <- attr(x[[1]], "st_type")
@@ -147,19 +142,16 @@ tb.stby <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
147142

148143
do.call(
149144
method,
150-
list(x = x, order = order, na.rm = na.rm, drop.var.col = drop.var.col,
145+
list(x = x, order = order, drop.var.col = drop.var.col,
151146
recalculate = recalculate, fct.to.chr = fct.to.chr, ...)
152147
)
153148
}
154149

155150
# Handles lists containing freq objects when freq() is called on a df
156151
#' @exportS3Method tb list
157-
tb.list <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
152+
tb.list <- function(x, order = 1, drop.var.col = FALSE,
158153
recalculate = FALSE, fct.to.chr = TRUE, ...) {
159154

160-
if (isTRUE(na.rm))
161-
message("na.rm is only applicable to by-group results")
162-
163155
if (isTRUE(recalculate))
164156
message("recalculate is only applicable to by-group results")
165157

@@ -177,7 +169,7 @@ tb.list <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
177169

178170
# Get first set of results
179171
gr_res <- do.call(tb_freq,
180-
list(x = x[[1]], order = 1, na.rm = FALSE,
172+
list(x = x[[1]], order = 1,
181173
recalculate = FALSE, fct.to.chr = TRUE))
182174

183175
colnames(gr_res)[1] <- "value"
@@ -189,7 +181,7 @@ tb.list <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
189181

190182
for (group in 2:length(x)) {
191183
gr_res <- do.call(tb_freq,
192-
list(x = x[[group]], order = 1, na.rm = FALSE,
184+
list(x = x[[group]], order = 1,
193185
recalculate = FALSE, fct.to.chr = TRUE))
194186

195187
colnames(gr_res)[1] <- "value"
@@ -206,7 +198,7 @@ tb.list <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
206198
return(output)
207199
}
208200

209-
tb_stby_freq <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
201+
tb_stby_freq <- function(x, order = 1, drop.var.col = FALSE,
210202
recalculate = TRUE, fct.to.chr = FALSE, ...) {
211203

212204
# initialise variables relevant only to stby() objects
@@ -239,7 +231,7 @@ tb_stby_freq <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
239231

240232
# Dispatch to tb_freq
241233
grp_stats <- lapply(x, function(group) {
242-
tb(group, fct.to.chr = TRUE)
234+
tb(group, fct.to.chr = fct.to.chr)
243235
})
244236

245237
# Eliminate null groups
@@ -256,13 +248,6 @@ tb_stby_freq <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
256248
output <- dplyr::bind_rows(grp_stats)
257249
var_name <- colnames(output)[nb_gr_var + 1]
258250

259-
# Remove rows having grouping vars = NA when na.rm = TRUE
260-
if (isTRUE(na.rm)) {
261-
na_rows <- which(rowSums(is.na(output[,1:nb_gr_var])) > 0)
262-
if (length(na_rows) > 0)
263-
output <- output[-na_rows,]
264-
}
265-
266251
# Adjust ordering of rows and columns ('order' arg)
267252
if (order %in% c(2,3)) {
268253
output <- output[
@@ -342,7 +327,7 @@ tb_stby_freq <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
342327
return(output)
343328
}
344329

345-
tb_stby_descr <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
330+
tb_stby_descr <- function(x, order = 1, drop.var.col = FALSE,
346331
recalculate = NA, fct.to.chr = FALSE, ...) {
347332

348333
grp_stats <- lapply(x, function(group) {
@@ -412,12 +397,9 @@ tb_stby_descr <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
412397
}
413398

414399
# Single freq object -------------------------------------------------------
415-
tb_freq <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
400+
tb_freq <- function(x, order = 1, drop.var.col = FALSE,
416401
recalculate = FALSE, fct.to.chr = FALSE, ...) {
417-
418-
if (isTRUE(na.rm))
419-
message("na.rm ignored for single results; use freq(x, report.nas = FALSE)")
420-
402+
421403
# Flags for columns to keep in the output
422404
report.nas <- attr(x, "format_info")$report.nas
423405
cumul <- attr(x, "format_info")$cumul
@@ -510,7 +492,7 @@ tb_freq <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
510492
}
511493

512494
# Single descr object ------------------------------------------------------
513-
tb_descr <- function(x, order = 1, na.rm = FALSE, drop.var.col = FALSE,
495+
tb_descr <- function(x, order = 1, drop.var.col = FALSE,
514496
recalculate = FALSE, fct.to.chr = FALSE, ...) {
515497

516498
if (!isTRUE(attr(x, "data_info")$transposed)) {

‎man/tb.Rd‎

Lines changed: 0 additions & 7 deletions
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