Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Open
wants to merge 14 commits into
base: main
Choose a base branch
from
Open

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

Show file tree
Hide file tree
Changes from 11 commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
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
c389dd9
Aligned tables and changed the STUDYID, USUBJID to get_admiral_option…
ProfessorP-beep Oct 30, 2024
ee9a029
ran styler on requested files from last push
ProfessorP-beep Oct 30, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,8 @@
</details>

# admiral 1.1.1

- `derive_vars_atc()` and `create_single_dose_dataset()` `by_vars` argument updated to use `get_admiral_option("subject_keys")` instead of `USUBJID` or `STUDYID`.
ProfessorP-beep marked this conversation as resolved.
Show resolved Hide resolved
- test scripts, R, and markdown files for `create_single_dose_dataset` and `occds.Rmd` updated to include a `STUDYID` column because of `get_admiral_option("subject_keys")` update above.
- `derive_extreme_event()` was fixed such that `check_type = "none"` is accepted
again. (#2462)

Expand Down
27 changes: 14 additions & 13 deletions R/create_single_dose_dataset.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -287,12 +287,12 @@ dose_freq_lookup <- tribble(
#' library(dplyr)
#'
#' data <- tribble(
#' ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
#' "P01", "Q2D", ymd("2021-01-01"), ymd_hms("2021-01-01 10:30:00"),
#' ~STUDYID, ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
#' "STUDY01", "P01", "Q2D", ymd("2021-01-01"), ymd_hms("2021-01-01 10:30:00"),
#' ymd("2021-01-07"), ymd_hms("2021-01-07 11:30:00"),
#' "P01", "Q3D", ymd("2021-01-08"), ymd_hms("2021-01-08 12:00:00"),
#' "STUDY01", "P01", "Q3D", ymd("2021-01-08"), ymd_hms("2021-01-08 12:00:00"),
#' ymd("2021-01-14"), ymd_hms("2021-01-14 14:00:00"),
#' "P01", "EVERY 2 WEEKS", ymd("2021-01-15"), ymd_hms("2021-01-15 09:57:00"),
#' "STUDY01", "P01", "EVERY 2 WEEKS", ymd("2021-01-15"), ymd_hms("2021-01-15 09:57:00"),
#' ymd("2021-01-29"), ymd_hms("2021-01-29 10:57:00")
#' )
#'
Expand All @@ -307,10 +307,10 @@ dose_freq_lookup <- tribble(
#' )
#'
#' data <- tribble(
#' ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
#' "P01", "Q30MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"),
#' ~STUDYID, ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
#' "STUDY01", "P01", "Q30MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"),
#' ymd("2021-01-01"), ymd_hms("2021-01-01T07:00:00"),
#' "P02", "Q90MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"),
#' "STUDY02", "P02", "Q90MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"),
#' ymd("2021-01-01"), ymd_hms("2021-01-01T09:00:00")
#' )
#'
Expand All @@ -323,12 +323,12 @@ dose_freq_lookup <- tribble(
#' # Example with nominal time
#'
#' data <- tribble(
#' ~USUBJID, ~EXDOSFRQ, ~NFRLT, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
#' "P01", "BID", 0, ymd("2021-01-01"), ymd_hms("2021-01-01 08:00:00"),
#' ~STUDYID, ~USUBJID, ~EXDOSFRQ, ~NFRLT, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
#' "STUDY01", "P01", "BID", 0, ymd("2021-01-01"), ymd_hms("2021-01-01 08:00:00"),
#' ymd("2021-01-07"), ymd_hms("2021-01-07 20:00:00"),
#' "P01", "BID", 168, ymd("2021-01-08"), ymd_hms("2021-01-08 08:00:00"),
#' "STUDY01", "P01", "BID", 168, ymd("2021-01-08"), ymd_hms("2021-01-08 08:00:00"),
#' ymd("2021-01-14"), ymd_hms("2021-01-14 20:00:00"),
#' "P01", "BID", 336, ymd("2021-01-15"), ymd_hms("2021-01-15 08:00:00"),
#' "STUDY01", "P01", "BID", 336, ymd("2021-01-15"), ymd_hms("2021-01-15 08:00:00"),
#' ymd("2021-01-29"), ymd_hms("2021-01-29 20:00:00")
#' )
#'
Expand Down 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
55 changes: 29 additions & 26 deletions R/derive_vars_transposed.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -226,39 +226,42 @@ derive_vars_transposed <- function(dataset,
#' library(tibble)
#'
#' cm <- tribble(
#' ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD,
#' "BP40257-1001", "14", "1192056", "PARACETAMOL",
#' "BP40257-1001", "18", "2007001", "SOLUMEDROL",
#' "BP40257-1002", "19", "2791596", "SPIRONOLACTONE"
#' ~STUDYID, ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD,
#' "STUDY01", "BP40257-1001", "14", "1192056", "PARACETAMOL",
#' "STUDY01", "BP40257-1001", "18", "2007001", "SOLUMEDROL",
#' "STUDY01", "BP40257-1002", "19", "2791596", "SPIRONOLACTONE"
ProfessorP-beep marked this conversation as resolved.
Show resolved Hide resolved
#' )
#' facm <- tribble(
#' ~USUBJID, ~FAGRPID, ~FAREFID, ~FATESTCD, ~FASTRESC,
#' "BP40257-1001", "1", "1192056", "CMATC1CD", "N",
#' "BP40257-1001", "1", "1192056", "CMATC2CD", "N02",
#' "BP40257-1001", "1", "1192056", "CMATC3CD", "N02B",
#' "BP40257-1001", "1", "1192056", "CMATC4CD", "N02BE",
#' "BP40257-1001", "1", "2007001", "CMATC1CD", "D",
#' "BP40257-1001", "1", "2007001", "CMATC2CD", "D10",
#' "BP40257-1001", "1", "2007001", "CMATC3CD", "D10A",
#' "BP40257-1001", "1", "2007001", "CMATC4CD", "D10AA",
#' "BP40257-1001", "2", "2007001", "CMATC1CD", "D",
#' "BP40257-1001", "2", "2007001", "CMATC2CD", "D07",
#' "BP40257-1001", "2", "2007001", "CMATC3CD", "D07A",
#' "BP40257-1001", "2", "2007001", "CMATC4CD", "D07AA",
#' "BP40257-1001", "3", "2007001", "CMATC1CD", "H",
#' "BP40257-1001", "3", "2007001", "CMATC2CD", "H02",
#' "BP40257-1001", "3", "2007001", "CMATC3CD", "H02A",
#' "BP40257-1001", "3", "2007001", "CMATC4CD", "H02AB",
#' "BP40257-1002", "1", "2791596", "CMATC1CD", "C",
#' "BP40257-1002", "1", "2791596", "CMATC2CD", "C03",
#' "BP40257-1002", "1", "2791596", "CMATC3CD", "C03D",
#' "BP40257-1002", "1", "2791596", "CMATC4CD", "C03DA"
#' ~STUDYID, ~USUBJID, ~FAGRPID, ~FAREFID, ~FATESTCD, ~FASTRESC,
#' "STUDY01", "BP40257-1001", "1", "1192056", "CMATC1CD", "N",
#' "STUDY01", "BP40257-1001", "1", "1192056", "CMATC2CD", "N02",
#' "STUDY01", "BP40257-1001", "1", "1192056", "CMATC3CD", "N02B",
#' "STUDY01", "BP40257-1001", "1", "1192056", "CMATC4CD", "N02BE",
#' "STUDY01", "BP40257-1001", "1", "2007001", "CMATC1CD", "D",
#' "STUDY01", "BP40257-1001", "1", "2007001", "CMATC2CD", "D10",
#' "STUDY01", "BP40257-1001", "1", "2007001", "CMATC3CD", "D10A",
#' "STUDY01", "BP40257-1001", "1", "2007001", "CMATC4CD", "D10AA",
#' "STUDY01", "BP40257-1001", "2", "2007001", "CMATC1CD", "D",
#' "STUDY01", "BP40257-1001", "2", "2007001", "CMATC2CD", "D07",
#' "STUDY01", "BP40257-1001", "2", "2007001", "CMATC3CD", "D07A",
#' "STUDY01", "BP40257-1001", "2", "2007001", "CMATC4CD", "D07AA",
#' "STUDY01", "BP40257-1001", "3", "2007001", "CMATC1CD", "H",
#' "STUDY01", "BP40257-1001", "3", "2007001", "CMATC2CD", "H02",
#' "STUDY01", "BP40257-1001", "3", "2007001", "CMATC3CD", "H02A",
#' "STUDY01", "BP40257-1001", "3", "2007001", "CMATC4CD", "H02AB",
#' "STUDY01", "BP40257-1002", "1", "2791596", "CMATC1CD", "C",
#' "STUDY01", "BP40257-1002", "1", "2791596", "CMATC2CD", "C03",
#' "STUDY01", "BP40257-1002", "1", "2791596", "CMATC3CD", "C03D",
#' "STUDY01", "BP40257-1002", "1", "2791596", "CMATC4CD", "C03DA"
ProfessorP-beep marked this conversation as resolved.
Show resolved Hide resolved
#' )
#'
#' derive_vars_atc(cm, facm)
derive_vars_atc <- function(dataset,
dataset_facm,
by_vars = exprs(USUBJID, CMREFID = FAREFID),
by_vars = exprs(
!!!get_admiral_option("subject_keys"),
CMREFID = FAREFID
),
id_vars = NULL,
value_var = FASTRESC) {
value_var <- assert_symbol(enexpr(value_var))
Expand Down
28 changes: 14 additions & 14 deletions man/create_single_dose_dataset.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

52 changes: 26 additions & 26 deletions man/derive_vars_atc.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

3 changes: 2 additions & 1 deletion tests/testthat/_snaps/create_single_dose_dataset.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@

Code
create_single_dose_dataset(input, start_date = ADTSTD, keep_source_vars = exprs(
USUBJID, EXDOSFRQ, ADTSTD, ASTDTM, AENDT, AENDTM))
!!!get_admiral_option("subject_keys"), EXDOSFRQ, ADTSTD, ASTDTM, AENDT,
AENDTM))
Condition
Error in `create_single_dose_dataset()`:
! The argument `start_date` is expected to have a name ending with "---DT".
Expand Down
17 changes: 9 additions & 8 deletions tests/testthat/_snaps/derive_vars_transposed.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,13 +1,14 @@
# derive_vars_transposed Test 3: filter merge dataset 'many-to-one'

Code
derive_vars_transposed(dataset, dataset_merge, by_vars = exprs(USUBJID),
key_var = TESTCD, value_var = VALUE, filter = TESTCD == "T01", relationship = "many-to-one")
derive_vars_transposed(dataset, dataset_merge, by_vars = get_admiral_option(
"subject_keys"), key_var = TESTCD, value_var = VALUE, filter = TESTCD ==
"T01", relationship = "many-to-one")
Output
# A tibble: 3 x 3
USUBJID VAR1 T01
<chr> <dbl> <dbl>
1 P01 3 31
2 P02 31 3
3 P03 42 NA
# A tibble: 3 x 4
STUDYID USUBJID VAR1 T01
<chr> <chr> <dbl> <dbl>
1 STUDY01 P01 3 31
2 STUDY01 P02 31 3
3 STUDY01 P03 42 NA

Loading
Loading