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issue with pre functions #491

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merged 14 commits into from
Apr 26, 2023
Merged

issue with pre functions #491

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e0f2a37
export checks
clarkliming Apr 17, 2023
80475b9
fix ext01_1_pre
clarkliming Apr 17, 2023
034410a
update docs
clarkliming Apr 17, 2023
29046c7
fix issue
clarkliming Apr 17, 2023
4748308
export assert_colnames
clarkliming Apr 17, 2023
a50d239
minor update
clarkliming Apr 17, 2023
e3b6aba
Merge branch 'main' into 476_pre@main
clarkliming Apr 25, 2023
df9642d
update according to main
clarkliming Apr 25, 2023
2c6a821
add grade_groups to argument
clarkliming Apr 25, 2023
44aa092
update docs
clarkliming Apr 25, 2023
811ce71
style update
clarkliming Apr 25, 2023
94d0c0e
Update R/aet01_aesi.R
clarkliming Apr 25, 2023
8c49c6e
fix aet01_aesi issue
clarkliming Apr 26, 2023
6d13c28
fix issue
clarkliming Apr 26, 2023
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2 changes: 2 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,9 @@ export(aet10_1_main)
export(aet10_1_post)
export(aet10_1_pre)
export(args_ls)
export(assert_all_tablenames)
export(assert_colnames)
export(assert_only_one_paramcd)
export(check_col_contains)
export(chevron_g)
export(chevron_l)
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18 changes: 9 additions & 9 deletions R/aet01.R
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Expand Up @@ -436,9 +436,12 @@ aet01_2_lyt <- function(arm_var,
#'
#' @export
#'
aet01_2_pre <- function(adam_db, arm_var, safety_var, medconcept_var, ...) {
checkmate::assert_class(adam_db, "dm")

aet01_2_pre <- function(adam_db, arm_var = "ACTARM", safety_var = list(
"FATAL", "SER", "SERWD", "SERDSM",
"RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"
),
medconcept_var = list("SMQ01", "SMQ02", "CQ01"), ...) {
assert_all_tablenames(adam_db, c("adsl", "adae"))
aet01_2_check(adam_db, arm_var = arm_var, safety_var = safety_var, medconcept_var = medconcept_var)

labs <- formatters::var_labels(adam_db$adae)
Expand Down Expand Up @@ -514,12 +517,9 @@ aet01_2_pre <- function(adam_db, arm_var, safety_var, medconcept_var, ...) {
#' @export
aet01_2_check <- function(adam_db,
req_tables = c("adsl", "adae"),
arm_var = "ACTARM",
safety_var = list(
"FATAL", "SER", "SERWD", "SERDSM",
"RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"
),
medconcept_var = list("SMQ01", "SMQ02", "CQ01")) {
arm_var,
safety_var,
medconcept_var) {
assert_all_tablenames(adam_db, req_tables)
checkmate::assert_list(safety_var, types = "character")
safety_var <- unlist(safety_var)
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33 changes: 20 additions & 13 deletions R/aet01_aesi.R
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Expand Up @@ -4,7 +4,7 @@
#'
#' @inheritParams gen_args
#' @param aesi_vars (`list`) the AESI variables to be included in the summary. Defaults to `NA`.
#'
#' @param grade_groups (`list`) the grade groups to be displayed.
#' @details
#' * Does not remove rows with zero counts by default.
#'
Expand Down Expand Up @@ -34,8 +34,19 @@ aet01_aesi_1_main <- function(adam_db,
arm_var = "ACTARM",
aesi_vars = list(NA_character_),
deco = std_deco("AET01_AESI"),
grade_groups = NULL,
...) {
checkmate::assert_list(aesi_vars, types = "character")
checkmate::assert_list(grade_groups, null.ok = TRUE)
if (is.null(grade_groups)) {
grade_groups <- list(
"Grade 1" = "1",
"Grade 2" = "2",
"Grade 3" = "3",
"Grade 4" = "4",
"Grade 5" = "5"
)
}
aesi_vars <- unlist(aesi_vars)
if ("ALL" %in% aesi_vars) aesi_vars <- c("ALL_ALLRES", "ALL_NOTRES", "ALL_SER", "ALL_REL")
if (any(grepl("^ALL_", aesi_vars))) {
Expand All @@ -58,7 +69,8 @@ aet01_aesi_1_main <- function(adam_db,
arm_var = arm_var,
aesi_vars = all_aesi_vars,
deco = deco,
lbl_aesi_vars = lbl_aesi_vars
lbl_aesi_vars = lbl_aesi_vars,
grade_groups
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)

tbl <- build_table(lyt, adam_db$adae, alt_counts_df = adam_db$adsl)
Expand All @@ -76,7 +88,8 @@ aet01_aesi_1_main <- function(adam_db,
aet01_aesi_1_lyt <- function(arm_var,
aesi_vars,
deco,
lbl_aesi_vars) {
lbl_aesi_vars,
grade_groups) {
names(lbl_aesi_vars) <- aesi_vars
basic_table_deco(deco, show_colcounts = TRUE) %>%
split_cols_by(var = arm_var) %>%
Expand All @@ -96,7 +109,8 @@ aet01_aesi_1_lyt <- function(arm_var,
count_occurrences_by_grade(
var = "ATOXGR",
var_labels = "Total number of patients with at least one AE by worst grade",
show_labels = "visible"
show_labels = "visible",
grade_groups = grade_groups
) %>%
count_patients_with_flags(
"USUBJID",
Expand Down Expand Up @@ -206,16 +220,9 @@ aet01_aesi_1_pre <- function(adam_db,
)
) %>%
mutate(
ATOXGR = reformat(
ATOXGR = dunlin::reformat(
.data$ATOXGR,
dunlin::rule(
"Missing" = c("", NA_character_),
"Grade 1" = "1",
"Grade 2" = "2",
"Grade 3" = "3",
"Grade 4" = "4",
"Grade 5 (fatal outcome)" = "5"
)
dunlin::rule("Missing" = c("", NA_character_))
)
)

Expand Down
6 changes: 2 additions & 4 deletions R/aet02.R
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Original file line number Diff line number Diff line change
Expand Up @@ -95,11 +95,9 @@ aet02_1_lyt <- function(arm_var,
#'
#' @export
#'
aet02_1_pre <- function(adam_db, arm_var, ...) {
checkmate::assert_class(adam_db, "dm")

aet02_1_pre <- function(adam_db, arm_var = "ACTARM", ...) {
assert_all_tablenames(adam_db, c("adsl", "adae"))
aet02_1_check(adam_db, arm_var = arm_var)

new_format <- list(
adae = list(
AEBODSYS = rule("No Coding available" = c("", NA, "<Missing>")),
Expand Down
4 changes: 1 addition & 3 deletions R/aet10.R
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Original file line number Diff line number Diff line change
Expand Up @@ -67,9 +67,7 @@ aet10_1_lyt <- function(arm_var,
#'
#' @export
#'
aet10_1_pre <- function(adam_db, arm_var, ...) {
checkmate::assert_class(adam_db, "dm")

aet10_1_pre <- function(adam_db, arm_var = "ACTARM", ...) {
aet10_1_check(adam_db, arm_var = arm_var)

adam_db$adae <- adam_db$adae %>%
Expand Down
1 change: 0 additions & 1 deletion R/assertions.R
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Expand Up @@ -8,7 +8,6 @@
#' @param x (`character`) the names of the columns to be checked.
#' @param null_ok (`logical`) can `x` be NULL.
#'
#' @keywords internal
#' @export
#'
#' @examples
Expand Down
13 changes: 5 additions & 8 deletions R/ext01.R
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Expand Up @@ -82,18 +82,15 @@ ext01_1_lyt <- function(arm_var,
ext01_1_pre <- function(adam_db,
paramcd_order = list("TNDOSE", "DOSE", "NDOSE", "TDOSE"),
...) {
checkmate::assert_class(adam_db, "dm")
checkmate::assert_list(paramcd_order)
paramcd_order <- unlist(paramcd_order)
db <- adam_db %>%
dm_zoom_to("adex") %>%
filter(.data$PARCAT1 == "OVERALL") %>%
dm_update_zoomed()
assert_all_tablenames(adam_db, c("adsl", "adex"))

adam_db$adex <- adam_db$adex %>%
filter(.data$PARCAT1 == "OVERALL")

if (nrow(adam_db$adex) > 0L) {
param_vars <- adam_db$adex %>%
dplyr::select("PARAM", "PARAMCD") %>%
dunlin::co_relevels("PARAMCD", "PARAM", paramcd_order)
dunlin::co_relevels("PARAMCD", "PARAM", unlist(paramcd_order))

adam_db$adex <- adam_db$adex %>%
mutate(PARAM = param_vars$PARAM, PARAMCD = param_vars$PARAMCD)
Expand Down
16 changes: 11 additions & 5 deletions man/aet01_2.Rd
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5 changes: 4 additions & 1 deletion man/aet01_aesi_1.Rd
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2 changes: 1 addition & 1 deletion man/aet02_1.Rd
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2 changes: 1 addition & 1 deletion man/aet10_1.Rd
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11 changes: 7 additions & 4 deletions tests/testthat/_snaps/aet01_aesi.md
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Expand Up @@ -13,7 +13,8 @@
Grade 2 6 (4.5%) 10 (7.5%) 7 (5.3%)
Grade 3 18 (13.4%) 14 (10.4%) 16 (12.1%)
Grade 4 15 (11.2%) 20 (14.9%) 18 (13.6%)
Grade 5 (fatal outcome) 76 (56.7%) 70 (52.2%) 75 (56.8%)
Grade 5 76 (56.7%) 70 (52.2%) 75 (56.8%)
Missing 0 0 0
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Not sure if missing should appear (I dont think so). What do you think @barnett11

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this is a difficult issue. We can expect Missing grade in adae.atoxgr, (even in cleaned adam). We should not filter this out because we also need to count the number of events. But this should not be counted in the count_occurrences_by_grade.

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ok. for ATOXGR, those records are still using NA (not convertet to a level) and then will be discarded.

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another update: ADAE.ATOXGR is a string (character in R's language). in rtables we require ATOXGR to be factor. Then we need to convert it into factor.
so here while we apply reformating, we need to populate NA for empty strings. Very different logic here!

reformat(c('1','2','3','4','5',''), rule('1'='1','2'='2','3'='3','4'='4','5'='5'))

my suggestion is to keep this missing level for now (as this solves many issues) and open another issue to deal with this.

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probably need to evaluate the reformat when it is partial match of the whole set, option 1, keep the rest, option 2, discard the rest levels (use NA to replace) (but this is really contradictory to what we are doing to conver NA to "Missing"!) The logic/design behind this need to be further evaluated.

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issue opened here: #492

Total number of patients with study drug withdrawn due to AE 0 0 0
Total number of patients with dose modified/interrupted due to AE 0 0 0
Total number of patients with treatment received for AE 0 0 0
Expand All @@ -37,7 +38,7 @@
Grade 2 6 (4.5%) 10 (7.5%) 7 (5.3%)
Grade 3 18 (13.4%) 14 (10.4%) 16 (12.1%)
Grade 4 15 (11.2%) 20 (14.9%) 18 (13.6%)
Grade 5 (fatal outcome) 76 (56.7%) 70 (52.2%) 75 (56.8%)
Grade 5 76 (56.7%) 70 (52.2%) 75 (56.8%)
Total number of patients with all non-fatal AEs resolved 84 (62.7%) 92 (68.7%) 97 (73.5%)
Total number of patients with at least one unresolved or ongoing non-fatal AE 102 (76.1%) 110 (82.1%) 107 (81.1%)
Total number of patients with at least one related AE 105 (78.4%) 108 (80.6%) 109 (82.6%)
Expand All @@ -57,7 +58,8 @@
Grade 2 6 (4.5%) 10 (7.5%) 7 (5.3%)
Grade 3 18 (13.4%) 14 (10.4%) 16 (12.1%)
Grade 4 15 (11.2%) 20 (14.9%) 18 (13.6%)
Grade 5 (fatal outcome) 76 (56.7%) 70 (52.2%) 75 (56.8%)
Grade 5 76 (56.7%) 70 (52.2%) 75 (56.8%)
Missing 0 0 0
Total number of patients with study drug withdrawn due to AE 27 (20.1%) 26 (19.4%) 30 (22.7%)
Total number of patients with dose modified/interrupted due to AE 66 (49.3%) 76 (56.7%) 74 (56.1%)
Total number of patients with treatment received for AE 98 (73.1%) 102 (76.1%) 103 (78.0%)
Expand All @@ -81,7 +83,8 @@
Grade 2 6 (4.5%) 10 (7.5%) 7 (5.3%)
Grade 3 18 (13.4%) 14 (10.4%) 16 (12.1%)
Grade 4 15 (11.2%) 20 (14.9%) 18 (13.6%)
Grade 5 (fatal outcome) 76 (56.7%) 70 (52.2%) 75 (56.8%)
Grade 5 76 (56.7%) 70 (52.2%) 75 (56.8%)
Missing 0 0 0
Total number of patients with study drug withdrawn due to AE 27 (20.1%) 26 (19.4%) 30 (22.7%)
Total number of patients with dose modified/interrupted due to AE 66 (49.3%) 76 (56.7%) 74 (56.1%)
Total number of patients with treatment received for AE 98 (73.1%) 102 (76.1%) 103 (78.0%)
Expand Down
32 changes: 0 additions & 32 deletions tests/testthat/_snaps/chevron_tlg-methods.md
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Expand Up @@ -131,38 +131,6 @@

# script_funs works as expected in interactive mode

Code
res
Output
[1] "# Edit Preprocessing Function."
[2] "pre_fun <- function(adam_db, ...) {"
[3] " checkmate::assert_class(adam_db, \"dm\")"
[4] ""
[5] " new_format <- list("
[6] " adae = list("
[7] " AEBODSYS = rule(\"No Coding Available\" = c(\"\", NA, \"<Missing>\")),"
[8] " AEDECOD = rule(\"No Coding Available\" = c(\"\", NA, \"<Missing>\")),"
[9] " ATOXGR = rule(\"No Grading Available\" = c(\"\", NA, \"<Missing>\"))"
[10] " )"
[11] " )"
[12] ""
[13] " adam_db <- dunlin::reformat(adam_db, new_format, na_last = TRUE)"
[14] ""
[15] " adam_db %>%"
[16] " dm_zoom_to(\"adae\") %>%"
[17] " filter(.data$ANL01FL == \"Y\") %>%"
[18] " filter(.data$ATOXGR != \"No Grading Available\") %>%"
[19] " mutate(ATOXGR = factor(.data$ATOXGR,"
[20] " levels = setdiff(levels(.data$ATOXGR), \"No Grading Available\")"
[21] " )) %>%"
[22] " dm_update_zoomed()"
[23] "}"
[24] ""
[25] "# Create TLG"
[26] "tlg_output <- rlang::exec(.fn = pre_fun, adam_db = data, !!!args_ls) %>% \nrlang::exec(.fn = run, object = aet04_1, !!!args_ls, auto_pre = FALSE, check_arg = FALSE)"

# script_funs works as expected in non interactive mode

Code
res
Output
Expand Down
3 changes: 2 additions & 1 deletion tests/testthat/_snaps/default_tlg.md
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,8 @@
Grade 2 6 (4.5%) 10 (7.5%) 7 (5.3%)
Grade 3 18 (13.4%) 14 (10.4%) 16 (12.1%)
Grade 4 15 (11.2%) 20 (14.9%) 18 (13.6%)
Grade 5 (fatal outcome) 76 (56.7%) 70 (52.2%) 75 (56.8%)
Grade 5 76 (56.7%) 70 (52.2%) 75 (56.8%)
Missing 0 0 0
Total number of patients with study drug withdrawn due to AE 27 (20.1%) 26 (19.4%) 30 (22.7%)
Total number of patients with dose modified/interrupted due to AE 66 (49.3%) 76 (56.7%) 74 (56.1%)
Total number of patients with treatment received for AE 98 (73.1%) 102 (76.1%) 103 (78.0%)
Expand Down