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clarklimingBFalquet
clarkliming
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BFalquet
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issue with pre functions (#491)
export checks and use `::` in pre functions part of #476 --------- Signed-off-by: Liming <[email protected]> Co-authored-by: b_falquet <[email protected]>
1 parent abc287f commit f34bbbd

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+78
-81
lines changed

‎NAMESPACE

+13
Original file line numberDiff line numberDiff line change
@@ -5,23 +5,28 @@ export("main<-")
55
export("postprocess<-")
66
export("preprocess<-")
77
export(ael01_nollt_1)
8+
export(ael01_nollt_1_check)
89
export(ael01_nollt_1_main)
910
export(ael01_nollt_1_pre)
1011
export(aet01_1)
12+
export(aet01_1_check)
1113
export(aet01_1_lyt)
1214
export(aet01_1_main)
1315
export(aet01_1_pre)
1416
export(aet01_2)
17+
export(aet01_2_check)
1518
export(aet01_2_lyt)
1619
export(aet01_2_main)
1720
export(aet01_2_pre)
1821
export(aet01_aesi_1)
22+
export(aet01_aesi_1_check)
1923
export(aet01_aesi_1_lyt)
2024
export(aet01_aesi_1_main)
2125
export(aet01_aesi_1_pre)
2226
export(aet01_aesi_post)
2327
export(aet01_post)
2428
export(aet02_1)
29+
export(aet02_1_check)
2530
export(aet02_1_lyt)
2631
export(aet02_1_main)
2732
export(aet02_1_post)
@@ -47,6 +52,7 @@ export(aet04_1_main)
4752
export(aet04_1_post)
4853
export(aet04_1_pre)
4954
export(aet10_1)
55+
export(aet10_1_check)
5056
export(aet10_1_lyt)
5157
export(aet10_1_main)
5258
export(aet10_1_post)
@@ -55,6 +61,7 @@ export(args_ls)
5561
export(assert_all_tablenames)
5662
export(assert_colnames)
5763
export(assert_only_one_paramcd)
64+
export(check_col_contains)
5865
export(chevron_g)
5966
export(chevron_l)
6067
export(chevron_t)
@@ -120,6 +127,7 @@ export(egt02_2_main)
120127
export(egt02_2_post)
121128
export(egt02_2_pre)
122129
export(egt03_1)
130+
export(egt03_1_check)
123131
export(egt03_1_lyt)
124132
export(egt03_1_main)
125133
export(egt03_1_post)
@@ -161,26 +169,31 @@ export(lbt01_1_main)
161169
export(lbt01_1_post)
162170
export(lbt01_1_pre)
163171
export(lbt04_1)
172+
export(lbt04_1_check)
164173
export(lbt04_1_lyt)
165174
export(lbt04_1_main)
166175
export(lbt04_1_post)
167176
export(lbt04_1_pre)
168177
export(lbt05_1)
178+
export(lbt05_1_check)
169179
export(lbt05_1_lyt)
170180
export(lbt05_1_main)
171181
export(lbt05_1_post)
172182
export(lbt05_1_pre)
173183
export(lbt07_1)
184+
export(lbt07_1_check)
174185
export(lbt07_1_lyt)
175186
export(lbt07_1_main)
176187
export(lbt07_1_post)
177188
export(lbt07_1_pre)
178189
export(lbt14_1)
190+
export(lbt14_1_check)
179191
export(lbt14_1_lyt)
180192
export(lbt14_1_main)
181193
export(lbt14_1_post)
182194
export(lbt14_1_pre)
183195
export(lbt14_2)
196+
export(lbt14_2_check)
184197
export(lbt14_2_lyt)
185198
export(lbt14_2_main)
186199
export(lbt14_2_post)

‎R/ael01_nollt.R

+1-1
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ ael01_nollt_1_pre <- function(adam_db,
6969
#'
7070
#' @inheritParams gen_args
7171
#' @param vars (`character`) variables to be included in the listing.
72-
#'
72+
#' @export
7373
ael01_nollt_1_check <- function(adam_db,
7474
dataset,
7575
vars) {

‎R/aet01.R

+11-11
Original file line numberDiff line numberDiff line change
@@ -196,7 +196,7 @@ aet01_1_pre <- function(adam_db,
196196
#' @describeIn aet01_1 Checks
197197
#'
198198
#' @inheritParams gen_args
199-
#'
199+
#' @export
200200
aet01_1_check <- function(adam_db,
201201
req_tables = c("adsl", "adae"),
202202
arm_var = "ACTARM",
@@ -436,10 +436,13 @@ aet01_2_lyt <- function(arm_var,
436436
#'
437437
#' @export
438438
#'
439-
aet01_2_pre <- function(adam_db, ...) {
439+
aet01_2_pre <- function(adam_db, arm_var = "ACTARM", safety_var = list(
440+
"FATAL", "SER", "SERWD", "SERDSM",
441+
"RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"
442+
),
443+
medconcept_var = list("SMQ01", "SMQ02", "CQ01"), ...) {
440444
assert_all_tablenames(adam_db, c("adsl", "adae"))
441-
442-
aet01_2_check(adam_db)
445+
aet01_2_check(adam_db, arm_var = arm_var, safety_var = safety_var, medconcept_var = medconcept_var)
443446

444447
labs <- formatters::var_labels(adam_db$adae)
445448

@@ -511,15 +514,12 @@ aet01_2_pre <- function(adam_db, ...) {
511514
#' @describeIn aet01_2 Checks
512515
#'
513516
#' @inheritParams gen_args
514-
#'
517+
#' @export
515518
aet01_2_check <- function(adam_db,
516519
req_tables = c("adsl", "adae"),
517-
arm_var = "ACTARM",
518-
safety_var = list(
519-
"FATAL", "SER", "SERWD", "SERDSM",
520-
"RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"
521-
),
522-
medconcept_var = list("SMQ01", "SMQ02", "CQ01")) {
520+
arm_var,
521+
safety_var,
522+
medconcept_var) {
523523
assert_all_tablenames(adam_db, req_tables)
524524
checkmate::assert_list(safety_var, types = "character")
525525
safety_var <- unlist(safety_var)

‎R/aet01_aesi.R

+20-13
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
#'
55
#' @inheritParams gen_args
66
#' @param aesi_vars (`list`) the AESI variables to be included in the summary. Defaults to `NA`.
7-
#'
7+
#' @param grade_groups (`list`) the grade groups to be displayed.
88
#' @details
99
#' * Does not remove rows with zero counts by default.
1010
#'
@@ -34,8 +34,19 @@ aet01_aesi_1_main <- function(adam_db,
3434
arm_var = "ACTARM",
3535
aesi_vars = list(NA_character_),
3636
deco = std_deco("AET01_AESI"),
37+
grade_groups = NULL,
3738
...) {
3839
checkmate::assert_list(aesi_vars, types = "character")
40+
checkmate::assert_list(grade_groups, null.ok = TRUE)
41+
if (is.null(grade_groups)) {
42+
grade_groups <- list(
43+
"Grade 1" = "1",
44+
"Grade 2" = "2",
45+
"Grade 3" = "3",
46+
"Grade 4" = "4",
47+
"Grade 5 (fatal outcome)" = "5"
48+
)
49+
}
3950
aesi_vars <- unlist(aesi_vars)
4051
if ("ALL" %in% aesi_vars) aesi_vars <- c("ALL_ALLRES", "ALL_NOTRES", "ALL_SER", "ALL_REL")
4152
if (any(grepl("^ALL_", aesi_vars))) {
@@ -58,7 +69,8 @@ aet01_aesi_1_main <- function(adam_db,
5869
arm_var = arm_var,
5970
aesi_vars = all_aesi_vars,
6071
deco = deco,
61-
lbl_aesi_vars = lbl_aesi_vars
72+
lbl_aesi_vars = lbl_aesi_vars,
73+
grade_groups = grade_groups
6274
)
6375

6476
tbl <- build_table(lyt, adam_db$adae, alt_counts_df = adam_db$adsl)
@@ -76,7 +88,8 @@ aet01_aesi_1_main <- function(adam_db,
7688
aet01_aesi_1_lyt <- function(arm_var,
7789
aesi_vars,
7890
deco,
79-
lbl_aesi_vars) {
91+
lbl_aesi_vars,
92+
grade_groups) {
8093
names(lbl_aesi_vars) <- aesi_vars
8194
basic_table_deco(deco, show_colcounts = TRUE) %>%
8295
split_cols_by(var = arm_var) %>%
@@ -96,7 +109,8 @@ aet01_aesi_1_lyt <- function(arm_var,
96109
count_occurrences_by_grade(
97110
var = "ATOXGR",
98111
var_labels = "Total number of patients with at least one AE by worst grade",
99-
show_labels = "visible"
112+
show_labels = "visible",
113+
grade_groups = grade_groups
100114
) %>%
101115
count_patients_with_flags(
102116
"USUBJID",
@@ -206,14 +220,7 @@ aet01_aesi_1_pre <- function(adam_db,
206220
)
207221
) %>%
208222
mutate(
209-
ATOXGR = forcats::fct_recode(
210-
.data$ATOXGR,
211-
"Grade 1" = "1",
212-
"Grade 2" = "2",
213-
"Grade 3" = "3",
214-
"Grade 4" = "4",
215-
"Grade 5 (fatal outcome)" = "5"
216-
)
223+
ATOXGR = factor(ATOXGR, levels = 1:5)
217224
)
218225

219226
adam_db
@@ -222,7 +229,7 @@ aet01_aesi_1_pre <- function(adam_db,
222229
#' @describeIn aet01_aesi_1 Checks
223230
#'
224231
#' @inheritParams gen_args
225-
#'
232+
#' @export
226233
aet01_aesi_1_check <- function(adam_db,
227234
req_tables = c("adsl", "adae"),
228235
arm_var = "ACTARM") {

‎R/aet02.R

+3-4
Original file line numberDiff line numberDiff line change
@@ -95,10 +95,9 @@ aet02_1_lyt <- function(arm_var,
9595
#'
9696
#' @export
9797
#'
98-
aet02_1_pre <- function(adam_db, ...) {
98+
aet02_1_pre <- function(adam_db, arm_var = "ACTARM", ...) {
9999
assert_all_tablenames(adam_db, c("adsl", "adae"))
100-
aet02_1_check(adam_db)
101-
100+
aet02_1_check(adam_db, arm_var = arm_var)
102101
new_format <- list(
103102
adae = list(
104103
AEBODSYS = rule("No Coding available" = c("", NA, "<Missing>")),
@@ -116,7 +115,7 @@ aet02_1_pre <- function(adam_db, ...) {
116115
#' @describeIn aet02_1 Checks
117116
#'
118117
#' @inheritParams gen_args
119-
#'
118+
#' @export
120119
aet02_1_check <- function(adam_db,
121120
req_tables = c("adsl", "adae"),
122121
arm_var = "ACTARM") {

‎R/aet10.R

+3-3
Original file line numberDiff line numberDiff line change
@@ -67,8 +67,8 @@ aet10_1_lyt <- function(arm_var,
6767
#'
6868
#' @export
6969
#'
70-
aet10_1_pre <- function(adam_db, ...) {
71-
aet10_1_check(adam_db)
70+
aet10_1_pre <- function(adam_db, arm_var = "ACTARM", ...) {
71+
aet10_1_check(adam_db, arm_var = arm_var)
7272

7373
adam_db$adae <- adam_db$adae %>%
7474
filter(.data$ANL01FL == "Y")
@@ -86,7 +86,7 @@ aet10_1_pre <- function(adam_db, ...) {
8686
#' @describeIn aet10_1 Checks
8787
#'
8888
#' @inheritParams gen_args
89-
#'
89+
#' @export
9090
aet10_1_check <- function(adam_db,
9191
req_tables = c("adsl", "adae"),
9292
arm_var = "ACTARM") {

‎R/checks.R

+1
Original file line numberDiff line numberDiff line change
@@ -60,6 +60,7 @@ check_one_colnames <- function(df, x, null_ok = TRUE, qualifier = NULL) {
6060
#' @param df_name (`string`) name of the data frame
6161
#'
6262
#' @keywords internal
63+
#' @export
6364
#'
6465
#' @examples
6566
#' \dontrun{

‎R/egt03.R

+1-1
Original file line numberDiff line numberDiff line change
@@ -92,7 +92,7 @@ egt03_1_lyt <- function(arm_var,
9292
#' @describeIn egt03_1 Checks
9393
#'
9494
#' @inheritParams gen_args
95-
#'
95+
#' @export
9696
egt03_1_check <- function(adam_db,
9797
req_tables,
9898
visit_var,

‎R/ext01.R

+2-2
Original file line numberDiff line numberDiff line change
@@ -80,7 +80,7 @@ ext01_1_lyt <- function(arm_var,
8080
#' @export
8181
#'
8282
ext01_1_pre <- function(adam_db,
83-
paramcd_order = c("TNDOSE", "DOSE", "NDOSE", "TDOSE"),
83+
paramcd_order = list("TNDOSE", "DOSE", "NDOSE", "TDOSE"),
8484
...) {
8585
assert_all_tablenames(adam_db, c("adsl", "adex"))
8686

@@ -90,7 +90,7 @@ ext01_1_pre <- function(adam_db,
9090
if (nrow(adam_db$adex) > 0L) {
9191
param_vars <- adam_db$adex %>%
9292
dplyr::select("PARAM", "PARAMCD") %>%
93-
dunlin::co_relevels("PARAMCD", "PARAM", paramcd_order)
93+
dunlin::co_relevels("PARAMCD", "PARAM", unlist(paramcd_order))
9494

9595
adam_db$adex <- adam_db$adex %>%
9696
mutate(PARAM = param_vars$PARAM, PARAMCD = param_vars$PARAMCD)

‎R/lbt04.R

+1-1
Original file line numberDiff line numberDiff line change
@@ -99,7 +99,7 @@ lbt04_1_pre <- function(adam_db, req_tables = c("adsl", "adlb"), arm_var = "ACTA
9999
#' @describeIn lbt04_1 Checks
100100
#'
101101
#' @inheritParams gen_args
102-
#'
102+
#' @export
103103
lbt04_1_check <- function(adam_db,
104104
req_tables = c("adsl", "adlb"),
105105
arm_var = "ACTARM") {

‎R/lbt05.R

+1-1
Original file line numberDiff line numberDiff line change
@@ -116,7 +116,7 @@ lbt05_1_pre <- function(adam_db, arm_var = "ACTARM", ...) {
116116
#' @describeIn lbt05_1 Checks
117117
#'
118118
#' @inheritParams gen_args
119-
#'
119+
#' @export
120120
lbt05_1_check <- function(adam_db,
121121
req_tables,
122122
arm_var) {

‎R/lbt07.R

+1-1
Original file line numberDiff line numberDiff line change
@@ -151,7 +151,7 @@ lbt07_1_pre <- function(adam_db, ...) {
151151
#' @describeIn lbt07_1 Checks
152152
#'
153153
#' @inheritParams gen_args
154-
#'
154+
#' @export
155155
lbt07_1_check <- function(adam_db,
156156
req_tables = c("adsl", "adlb"),
157157
arm_var = "ACTARM") {

‎R/lbt14.R

+2-2
Original file line numberDiff line numberDiff line change
@@ -154,7 +154,7 @@ lbt14_1_pre <- function(adam_db,
154154
#' @describeIn lbt14_1 Checks
155155
#'
156156
#' @inheritParams gen_args
157-
#'
157+
#' @export
158158
lbt14_1_check <- function(adam_db,
159159
req_tables = c("adsl", "adlb"),
160160
arm_var = "ACTARM") {
@@ -357,7 +357,7 @@ lbt14_2_pre <- function(adam_db,
357357
#' @describeIn lbt14_2 Checks
358358
#'
359359
#' @inheritParams gen_args
360-
#'
360+
#' @export
361361
lbt14_2_check <- function(adam_db,
362362
req_tables = c("adsl", "adlb"),
363363
arm_var = "ACTARM") {

‎man/aet01_2.Rd

+11-5
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‎man/aet01_aesi_1.Rd

+4-1
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