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rebase to end of 1325
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@shajoezhu
shajoezhu committed Oct 22, 2024
1 parent 22936ca commit 17047d3
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1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -3,6 +3,7 @@
### Enhancements
* Added the `denom` parameter to `s_count_cumulative()`, `s_count_missed_doses()`, and `s_count_occurrences_by_grade()`.
* Added `"N_row"` as an optional input to `denom` in `s_count_occurrences()`.
* Refactored `a_count_occurrences_by_grade()` to no longer use `make_afun()`.

### Bug Fixes
* Fixed bug in `a_summary()` causing non-unique `row_name` values to occur when multiple statistics are selected for count variables.
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127 changes: 90 additions & 37 deletions R/count_occurrences_by_grade.R
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Expand Up @@ -235,10 +235,7 @@ s_count_occurrences_by_grade <- function(df,
#' * `a_count_occurrences_by_grade()` returns the corresponding list with formatted [rtables::CellValue()].
#'
#' @examples
#' # We need to ungroup `count_fraction` first so that the `rtables` formatting
#' # function `format_count_fraction()` can be applied correctly.
#' afun <- make_afun(a_count_occurrences_by_grade, .ungroup_stats = "count_fraction")
#' afun(
#' a_count_occurrences_by_grade(
#' df,
#' .N_col = 10L,
#' .N_row = 10L,
Expand All @@ -248,10 +245,62 @@ s_count_occurrences_by_grade <- function(df,
#' )
#'
#' @export
a_count_occurrences_by_grade <- make_afun(
s_count_occurrences_by_grade,
.formats = c("count_fraction" = format_count_fraction_fixed_dp)
)
a_count_occurrences_by_grade <- function(df,
labelstr = "",
id = "USUBJID",
grade_groups = list(),
remove_single = TRUE,
only_grade_groups = FALSE,
denom = c("N_col", "n", "N_row"),
.N_col, # nolint
.N_row, # nolint
.df_row,
.var = NULL,
.stats = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL,
na_str = default_na_str()) {
x_stats <- s_count_occurrences_by_grade(
df = df, .var = .var, .N_row = .N_row, .N_col = .N_col, id = id,
grade_groups = grade_groups, remove_single = remove_single, only_grade_groups = only_grade_groups,
denom = denom, labelstr = labelstr
)

if (is.null(unlist(x_stats))) {
return(NULL)
}
x_lvls <- names(x_stats[[1]])

# Fill in with formatting defaults if needed
.stats <- get_stats("count_occurrences_by_grade", stats_in = .stats)
if (length(.formats) == 1 && is.null(names(.formats))) {
.formats <- rep(.formats, length(.stats)) %>% setNames(.stats)
}
.formats <- get_formats_from_stats(.stats, .formats)
.labels <- get_labels_from_stats(.stats, .labels, row_nms = x_lvls)
.indent_mods <- get_indents_from_stats(.stats, .indent_mods, row_nms = x_lvls)

if ("count_fraction_fixed_dp" %in% .stats) x_stats[["count_fraction_fixed_dp"]] <- x_stats[["count_fraction"]]
x_stats <- x_stats[.stats]

# Ungroup statistics with values for each level of x
x_ungrp <- ungroup_stats(x_stats, .formats, .labels, list())
x_stats <- x_ungrp[["x"]]
.formats <- x_ungrp[[".formats"]]

# Auto format handling
.formats <- apply_auto_formatting(.formats, x_stats, .df_row, .var)

in_rows(
.list = x_stats,
.formats = .formats,
.names = unlist(.labels),
.labels = unlist(.labels),
.indent_mods = .indent_mods,
.format_na_strs = na_str
)
}

#' @describeIn count_occurrences_by_grade Layout-creating function which can take statistics function
#' arguments and additional format arguments. This function is a wrapper for [rtables::analyze()].
Expand Down Expand Up @@ -321,40 +370,36 @@ count_occurrences_by_grade <- function(lyt,
nested = TRUE,
...,
table_names = var,
.stats = NULL,
.formats = NULL,
.stats = "count_fraction",
.formats = list(count_fraction = format_count_fraction_fixed_dp),
.indent_mods = NULL,
.labels = NULL) {
checkmate::assert_flag(riskdiff)
extra_args <- list(
.stats = .stats, .formats = .formats, .labels = .labels, .indent_mods = .indent_mods, na_str = na_str
)
s_args <- list(
id = id, grade_groups = grade_groups, remove_single = remove_single, only_grade_groups = only_grade_groups, ...
)

afun <- make_afun(
a_count_occurrences_by_grade,
.stats = .stats,
.formats = .formats,
.indent_mods = .indent_mods,
.ungroup_stats = "count_fraction"
)

extra_args <- if (isFALSE(riskdiff)) {
s_args
if (isFALSE(riskdiff)) {
extra_args <- c(extra_args, s_args)
} else {
list(
afun = list("s_count_occurrences_by_grade" = afun),
.stats = .stats,
.indent_mods = .indent_mods,
s_args = s_args
extra_args <- c(
extra_args,
list(
afun = list("s_count_occurrences_by_grade" = a_count_occurrences_by_grade),
s_args = s_args
)
)
}

analyze(
lyt = lyt,
vars = var,
afun = ifelse(isFALSE(riskdiff), a_count_occurrences_by_grade, afun_riskdiff),
var_labels = var_labels,
show_labels = show_labels,
afun = ifelse(isFALSE(riskdiff), afun, afun_riskdiff),
table_names = table_names,
na_str = na_str,
nested = nested,
Expand Down Expand Up @@ -398,29 +443,37 @@ summarize_occurrences_by_grade <- function(lyt,
grade_groups = list(),
remove_single = TRUE,
only_grade_groups = FALSE,
riskdiff = FALSE,
na_str = default_na_str(),
...,
.stats = NULL,
.formats = NULL,
.stats = "count_fraction",
.formats = list(count_fraction = format_count_fraction_fixed_dp),
.indent_mods = NULL,
.labels = NULL) {
checkmate::assert_flag(riskdiff)
extra_args <- list(
.stats = .stats, .formats = .formats, .labels = .labels, .indent_mods = .indent_mods, na_str = na_str
)
s_args <- list(
id = id, grade_groups = grade_groups, remove_single = remove_single, only_grade_groups = only_grade_groups, ...
)

cfun <- make_afun(
a_count_occurrences_by_grade,
.stats = .stats,
.formats = .formats,
.labels = .labels,
.indent_mods = .indent_mods,
.ungroup_stats = "count_fraction"
)
if (isFALSE(riskdiff)) {
extra_args <- c(extra_args, s_args)
} else {
extra_args <- c(
extra_args,
list(
afun = list("s_count_occurrences_by_grade" = a_count_occurrences_by_grade),
s_args = s_args
)
)
}

summarize_row_groups(
lyt = lyt,
var = var,
cfun = cfun,
cfun = ifelse(isFALSE(riskdiff), a_count_occurrences_by_grade, afun_riskdiff),
na_str = na_str,
extra_args = extra_args
)
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30 changes: 18 additions & 12 deletions man/count_occurrences_by_grade.Rd
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4 changes: 2 additions & 2 deletions man/try_car_anova.Rd
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69 changes: 69 additions & 0 deletions tests/testthat/_snaps/count_occurrences_by_grade.md
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Expand Up @@ -228,6 +228,39 @@

# a_count_occurrences_by_grade works with healthy input.

Code
res
Output
RowsVerticalSection (in_rows) object print method:
----------------------------
row_name formatted_cell indent_mod row_label
1 1 2 (20%) 0 1
2 2 2 (20%) 0 2
3 3 2 (20%) 0 3
4 4 0 0 4
5 5 0 0 5
6 1 2 (20.0%) 0 1
7 2 2 (20.0%) 0 2
8 3 2 (20.0%) 0 3
9 4 0 0 4
10 5 0 0 5

# a_count_occurrences_by_grade works with custom input.

Code
res
Output
RowsVerticalSection (in_rows) object print method:
----------------------------
row_name formatted_cell indent_mod row_label
1 Level: 1 2 (20%) 1 Level: 1
2 LVL 2 2 (20%) 2 LVL 2
3 Count of 3 2 (20%) 0 Count of 3
4 Missing 4 0 (0%) 3 Missing 4
5 5 0 (0%) 0 5

# count_occurrences_by_grade works with default arguments for intensity

Code
Expand Down Expand Up @@ -416,3 +449,39 @@
MODERATE 1 (100%) 1 (50.0%)
SEVERE 0 0

# summarize_occurrences works as expected with risk difference column

Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
————————————————————————————————————————————————————————————————————————————————————
F
MILD 3 (1.5%) 4 (2.3%) 1 (0.6%) -0.8 (-3.5 - 2.0)
MODERATE 8 (4.0%) 6 (3.4%) 6 (3.7%) 0.6 (-3.2 - 4.4)
SEVERE 22 (10.9%) 21 (11.9%) 20 (12.3%) -1.0 (-7.4 - 5.4)
M
MILD 3 (1.5%) 0 1 (0.6%) 1.5 (-0.2 - 3.2)
MODERATE 11 (5.4%) 9 (5.1%) 8 (4.9%) 0.4 (-4.1 - 4.9)
SEVERE 12 (5.9%) 17 (9.6%) 12 (7.4%) -3.7 (-9.1 - 1.8)

---

Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
—————————————————————————————————————————————————————————————————————————————————————
F
-Any- 20 (9.9%) 19 (10.7%) 19 (11.7%) -0.8 (-7.0 - 5.3)
MILD 2 (1.0%) 2 (1.1%) 0 -0.1 (-2.2 - 1.9)
MODERATE 4 (2.0%) 3 (1.7%) 3 (1.9%) 0.3 (-2.4 - 3.0)
SEVERE 14 (6.9%) 14 (7.9%) 16 (9.9%) -1.0 (-6.3 - 4.3)
M
-Any- 14 (6.9%) 21 (11.9%) 17 (10.5%) -4.9 (-10.8 - 1.0)
MILD 1 (0.5%) 0 1 (0.6%) 0.5 (-0.5 - 1.5)
MODERATE 4 (2.0%) 7 (4.0%) 5 (3.1%) -2.0 (-5.4 - 1.5)
SEVERE 9 (4.5%) 14 (7.9%) 11 (6.8%) -3.5 (-8.3 - 1.4)

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