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Closes #2109 ADPP template program has x and y variables #2110

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merged 5 commits into from
Sep 22, 2023
Merged

Closes #2109 ADPP template program has x and y variables #2110

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c2a9795
#2109 ADPP template program has x and y variables: Update to use `der…
jeffreyad Sep 19, 2023
544b042
#2109 Doc: update NEWS for ADPP template change
jeffreyad Sep 20, 2023
29006a3
ignore notes r cmd checks (#2114)
dgrassellyb Sep 21, 2023
a3e87b6
Merge branch 'main' into 2109_ADPP_template_program_has_xy_variables
bms63 Sep 21, 2023
49b50ee
Merge branch 'patch' into 2109_ADPP_template_program_has_xy_variables
bms63 Sep 22, 2023
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20 changes: 11 additions & 9 deletions inst/templates/ad_adpp.R
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Original file line number Diff line number Diff line change
Expand Up @@ -80,11 +80,12 @@ format_avalcat1n <- function(param, aval) {
# Get list of ADSL vars required for derivations
adsl_vars <- exprs(TRTSDT, TRTEDT, DTHDT, EOSDT, TRT01P, TRT01A)

adpp <- pp %>%
adpp_pp <- pp %>%
# Join ADSL with PP (need TRTSDT for ADY derivation)
left_join(
select(admiral_adsl, STUDYID, USUBJID, !!!adsl_vars),
by = c("STUDYID", "USUBJID")
derive_vars_merged(
dataset_add = admiral_adsl,
new_vars = adsl_vars,
by_vars = exprs(STUDYID, USUBJID)
) %>%
## Calculate ADT, ADY ----
derive_vars_dt(
Expand All @@ -93,7 +94,7 @@ adpp <- pp %>%
) %>%
derive_vars_dy(reference_date = TRTSDT, source_vars = exprs(ADT))

adpp <- adpp %>%
adpp_aval <- adpp_pp %>%
## Add PARAMCD only - add PARAM etc later ----
left_join(
select(param_lookup, PPTESTCD, PARAMCD),
Expand All @@ -117,7 +118,7 @@ adpp <- adpp %>%
## Get visit info ----
# See also the "Visit and Period Variables" vignette
# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#visit_bds)
adpp <- adpp %>%
adpp_avisit <- adpp_aval %>%
# Derive Timing
mutate(
VISIT = "", # /!\ To remove
Expand All @@ -141,9 +142,10 @@ adpp <- adpp %>%
derive_vars_merged(dataset_add = avalcat_lookup, by_vars = exprs(PARAMCD, AVALCA1N))

# Add all ADSL variables
adpp <- adpp %>%
left_join(admiral_adsl,
by = c("STUDYID", "USUBJID")
adpp <- adpp_avisit %>%
derive_vars_merged(
dataset_add = select(admiral_adsl, !!!negate_vars(adsl_vars)),
by_vars = exprs(STUDYID, USUBJID)
)

# Final Steps, Select final variables and Add labels
Expand Down