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Closes #2501-general-issue-make-subject-keys-flexible-in-all-functions #2516

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Closes #2501-general-issue-make-subject-keys-flexible-in-all-functions #2516

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3ba3590
Updated the derive_vars and create_single_dose_dataset function by_va…
ProfessorP-beep Sep 28, 2024
d358fa0
Removed a duplicate of the admiral code within the admiral package I …
ProfessorP-beep Sep 29, 2024
ecd2500
I tried to address the failure in package building by changing bds_ex…
ProfessorP-beep Oct 1, 2024
d10123a
Merge branch 'main' of https://github.com/pharmaverse/admiral into 25…
ProfessorP-beep Oct 1, 2024
808f9de
ran lintr again, styler, and roxygen.
ProfessorP-beep Oct 1, 2024
e1ce1b6
test changes to derive_vars_atc
ProfessorP-beep Oct 1, 2024
c8922f3
changed derive_vars_atc by_vars to exprs(!!!get_admiral_option("subje…
ProfessorP-beep Oct 2, 2024
e908b48
Added STUDYID column to fix error with derive_vars_atc after correcti…
ProfessorP-beep Oct 2, 2024
6ff41a3
Ran devtools::test() and corrected errors that required a STUDYID col…
ProfessorP-beep Oct 2, 2024
fa79598
spellcheck and styler run
ProfessorP-beep Oct 2, 2024
9369763
spellcheck fix again
ProfessorP-beep Oct 2, 2024
9694ee5
moved updates under admiral development version in News.md
ProfessorP-beep Oct 3, 2024
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5 changes: 3 additions & 2 deletions R/create_single_dose_dataset.R
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Original file line number Diff line number Diff line change
Expand Up @@ -397,7 +397,7 @@ dose_freq_lookup <- tribble(
#' # Select valid dose records, non-missing `EXSTDTC` and `EXDOSE`.
#' ex_mod <- ex %>%
#' filter(!is.na(EXSTDTC) & !is.na(EXDOSE)) %>%
#' derive_vars_merged(adsl_death, by_vars = exprs(STUDYID, USUBJID)) %>%
#' derive_vars_merged(adsl_death, by_vars = get_admiral_option("subject_keys")) %>%
#' # Example, set up missing `EXDOSFRQ` as QD daily dosing regime.
#' # Replace with study dosing regime per trial treatment.
#' mutate(EXDOSFRQ = if_else(is.na(EXDOSFRQ), "QD", EXDOSFRQ)) %>%
Expand Down Expand Up @@ -450,7 +450,8 @@ create_single_dose_dataset <- function(dataset,
lookup_column = CDISC_VALUE,
nominal_time = NULL,
keep_source_vars = expr_c(
exprs(USUBJID), dose_freq, start_date, start_datetime,
get_admiral_option("subject_keys"), dose_freq,
start_date, start_datetime,
end_date, end_datetime
)) {
dose_freq <- assert_symbol(enexpr(dose_freq))
Expand Down
4 changes: 2 additions & 2 deletions R/derive_vars_transposed.R
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Expand Up @@ -258,8 +258,8 @@ derive_vars_transposed <- function(dataset,
#' derive_vars_atc(cm, facm)
derive_vars_atc <- function(dataset,
dataset_facm,
by_vars = exprs(USUBJID, CMREFID = FAREFID),
id_vars = NULL,
by_vars = c(get_admiral_option("subject_keys"),
exprs(CMREFID = FAREFID)),
value_var = FASTRESC) {
value_var <- assert_symbol(enexpr(value_var))
assert_vars(by_vars)
Expand Down
6 changes: 3 additions & 3 deletions man/create_single_dose_dataset.Rd
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3 changes: 1 addition & 2 deletions man/derive_vars_atc.Rd
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6 changes: 3 additions & 3 deletions vignettes/bds_exposure.Rmd
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Expand Up @@ -361,7 +361,7 @@ For example, to calculate the total dose by subject and treatment,
adex <- derive_param_exposure(
adex,
dataset_add = adex,
by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars),
by_vars = c(get_admiral_option("subject_keys"), adsl_vars),
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Either we should update all calls in the vignette or none.

@bms63 , did we reach a decision regarding updating vignettes and templates?

input_code = "DOSE",
set_values_to = exprs(
PARAMCD = "TDOSE",
Expand Down Expand Up @@ -441,7 +441,7 @@ adex <- adex %>%
)
),
dataset_add = adex,
by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars)
by_vars = c(get_admiral_option("subject_keys"), adsl_vars)
)

count(adex, PARAMCD, PARCAT1)
Expand All @@ -465,7 +465,7 @@ specified in the `by_vars` argument will be populated in this new record.
```{r eval=TRUE, echo=TRUE}
adex <- adex %>%
derive_param_doseint(
by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars),
by_vars = c(get_admiral_option("subject_keys"), adsl_vars),
set_values_to = exprs(PARAMCD = "TNDOSINT"),
tadm_code = "TDOSE",
tpadm_code = "TPDOSE"
Expand Down
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