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add prototype #754

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ba3d3db
add prototype
BFalquet Jun 4, 2024
3b7f2cc
Merge remote-tracking branch 'origin/main' into ael04@main
BFalquet Jun 5, 2024
f9ff7b3
add cpp
BFalquet Jun 5, 2024
61205db
update snaps
BFalquet Jun 5, 2024
b2dd537
Merge branch 'main' into ael04@main
BFalquet Jul 3, 2024
45c0c34
update roxygen2
BFalquet Jul 3, 2024
544d37c
Merge branch 'main' into ael04@main
BFalquet Sep 12, 2024
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -86,6 +86,7 @@ Collate:
'ael01_nollt.R'
'ael02.R'
'ael03.R'
'ael04.R'
'aet01.R'
'aet01_aesi.R'
'aet02.R'
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3 changes: 3 additions & 0 deletions NAMESPACE
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Expand Up @@ -22,6 +22,9 @@ export(ael02_pre)
export(ael03)
export(ael03_main)
export(ael03_pre)
export(ael04)
export(ael04_main)
export(ael04_pre)
export(aet01)
export(aet01_aesi)
export(aet01_aesi_main)
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2 changes: 1 addition & 1 deletion NEWS.md
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@@ -1,6 +1,6 @@
# chevron 0.2.6.9006

* Add `AEL02`, `AEL03` templates.
* Add `AEL02`, `AEL03`, `AEL04` templates.
* Modify the post processing of `MHT01` to allow multiple `row_split_var`.

# chevron 0.2.6
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64 changes: 64 additions & 0 deletions R/ael04.R
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# ael04_main ----

#' @describeIn ael04 Main TLG function
#'
#' @inheritParams gen_args
#' @returns the main function returns an `rlistings` or a `list` object.
#' @export
#'
ael04_main <- modify_default_args(
std_listing,
dataset = "adsl",
key_cols = "ID",
disp_cols = c("ASR", "TRTSDTM", "EOSDY", "DTHADY", "DTHCAUS", "ADTHAUT"),
split_into_pages_by_var = "ACTARM"
)


#' @describeIn ael04 Preprocessing
#'
#' @inheritParams ael04_main
#' @inheritParams gen_args
#'
#' @export
#'
ael04_pre <- function(adam_db,
dataset = "adsl",
arm_var = "ACTARM",
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...) {
adam_db[[dataset]] <- adam_db[[dataset]] %>%
filter(!is.na(.data$DTHADY)) %>%
mutate(
across(
all_of(c(arm_var, "DTHCAUS", "ADTHAUT")),
~ reformat(.x, missing_rule)
)
) %>%
mutate(
ID = create_id_listings(.data$SITEID, .data$SUBJID),
ASR = with_label(paste(.data$AGE, .data$SEX, .data$RACE, sep = "/"), "Age/Sex/Race"),
TRTSDTM = with_label(
.data$TRTSDTM,
"Date of\nFirst Study\nDrug\nAdministration"
),
!!arm_var := with_label(.data[[arm_var]], "Treatment"),
EOSDY = with_label(.data$EOSDY, "Day of Last\nStudy Drug\nAdministration"),
DTHADY = with_label(.data$DTHADY, "Day of\nDeath"),
DTHCAUS = with_label(.data$DTHCAUS, "Cause of Death"),
ADTHAUT = with_label(.data$ADTHAUT, "Autopsy\nPerformed?")
)

adam_db
}

#' `AEL04` Listing 1 (Default) Listing of Patient Deaths.
#'
#' @include chevron_tlg-S4class.R
#' @export
#'
#' @examples
#' res <- run(ael04, syn_data)
ael04 <- chevron_l(
main = ael04_main,
preprocess = ael04_pre
)
1 change: 1 addition & 0 deletions _pkgdown.yaml
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Expand Up @@ -53,6 +53,7 @@ reference:
- ael01_nollt
- ael02
- ael03
- ael04
- aet01
- aet01_aesi
- aet02
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4 changes: 4 additions & 0 deletions data-raw/syn_data_creation.R
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Expand Up @@ -150,6 +150,10 @@ syn_test_data <- function() {
sd$adsl$ETHNIC <- factor(trimws(sd$adsl$ETHNIC), levels = trimws(levels(sd$adsl$ETHNIC)))
attr(sd$adsl$ETHNIC, "label") <- "Ethnicity"

# useful for ael04
sd$adsl$TRTSDTM <- lubridate::force_tz(sd$adsl$TRTSDTM, tzone = "UTC")


adsub <- sd$adsub
adsub_wide_ls <- dunlin::poly_pivot_wider(
adsub,
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58 changes: 58 additions & 0 deletions man/ael04.Rd
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143 changes: 143 additions & 0 deletions tests/testthat/_snaps/ael04.md
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# ael04 works with adsl dataset

Code
cat(export_as_txt(res, lpp = 100, cpp = 110))
Output
ACTARM: C: Combination

——————————————————————————————————————————————————————————————————————————————————————————————————
Date of
First Study Day of Last
Drug Study Drug Day of
Center/Patients ID Age/Sex/Race Administration Administration Death Cause of Death
——————————————————————————————————————————————————————————————————————————————————————————————————
BRA-11/9 40/M/ASIAN 26MAR2019 1056 1091 DISEASE PROGRESSION
CHN-15/201 49/M/ASIAN 05MAR2019 1082 1085 ADVERSE EVENT
CHN-15/245 34/F/WHITE 29MAR2019 1057 1057 DISEASE PROGRESSION
\s\nACTARM: C: Combination

———————————————————————————————


Autopsy
Center/Patients ID Performed?
———————————————————————————————
BRA-11/9 Yes
CHN-15/201 Yes
CHN-15/245 Yes
\s\nACTARM: B: Placebo

—————————————————————————————————————————————————————————————————————————————————————————————————————————————
Date of
First Study Day of Last
Drug Study Drug Day of Autopsy
Center/Patients ID Age/Sex/Race Administration Administration Death Cause of Death Performed?
—————————————————————————————————————————————————————————————————————————————————————————————————————————————
CAN-1/341 43/F/ASIAN 23MAY2019 998 1014 SUICIDE Yes
CHN-1/307 24/M/ASIAN 11MAR2019 1076 1122 LOST TO FOLLOW UP <Missing>
CHN-13/240 42/M/ASIAN 08APR2019 1044 1087 ADVERSE EVENT Yes
CHN-7/126 27/M/WHITE 02MAY2019 1025 1066 ADVERSE EVENT Yes
\s\nACTARM: A: Drug X

——————————————————————————————————————————————————————————————————————————————————————————————————
Date of
First Study Day of Last
Drug Study Drug Day of
Center/Patients ID Age/Sex/Race Administration Administration Death Cause of Death
——————————————————————————————————————————————————————————————————————————————————————————————————
CHN-3/128 32/M/ASIAN 24FEB2019 1084 1106 ADVERSE EVENT
RUS-1/52 40/F/ASIAN 18MAR2019 1064 1070 DISEASE PROGRESSION
\s\nACTARM: A: Drug X

———————————————————————————————


Autopsy
Center/Patients ID Performed?
———————————————————————————————
CHN-3/128 Yes
RUS-1/52 Yes

# ael04 can handle all missing values

Code
cat(export_as_txt(res, lpp = 100, cpp = 110))
Output
ACTARM: <Missing>

——————————————————————————————————————————————————————————————————————————————————————————————————————————
Date of
First Study Day of Last
Drug Study Drug Day of Autopsy
Center/Patients ID Age/Sex/Race Administration Administration Death Cause of Death Performed?
——————————————————————————————————————————————————————————————————————————————————————————————————————————
BRA-11/9 40/M/ASIAN 26MAR2019 1056 1091 <Missing> Yes
CAN-1/341 43/F/ASIAN 23MAY2019 998 1014 <Missing> Yes
CHN-1/307 24/M/ASIAN 11MAR2019 1076 1122 <Missing> <Missing>
CHN-13/240 42/M/ASIAN 08APR2019 1044 1087 <Missing> Yes
CHN-15/201 49/M/ASIAN 05MAR2019 1082 1085 <Missing> Yes
CHN-15/245 34/F/WHITE 29MAR2019 1057 1057 <Missing> Yes
CHN-3/128 32/M/ASIAN 24FEB2019 1084 1106 <Missing> Yes
CHN-7/126 27/M/WHITE 02MAY2019 1025 1066 <Missing> Yes
RUS-1/52 40/F/ASIAN 18MAR2019 1064 1070 <Missing> Yes

# ael04 functions work as expected

Code
cat(export_as_txt(res, lpp = 100, cpp = 110))
Output
ACTARM: C: Combination

——————————————————————————————————————————————————————————————————————————————————————————————————
Date of
First Study Day of Last
Drug Study Drug Day of
Center/Patients ID Age/Sex/Race Administration Administration Death Cause of Death
——————————————————————————————————————————————————————————————————————————————————————————————————
BRA-11/9 40/M/ASIAN 26MAR2019 1056 1091 DISEASE PROGRESSION
CHN-15/201 49/M/ASIAN 05MAR2019 1082 1085 ADVERSE EVENT
CHN-15/245 34/F/WHITE 29MAR2019 1057 1057 DISEASE PROGRESSION
\s\nACTARM: C: Combination

———————————————————————————————


Autopsy
Center/Patients ID Performed?
———————————————————————————————
BRA-11/9 Yes
CHN-15/201 Yes
CHN-15/245 Yes
\s\nACTARM: B: Placebo

—————————————————————————————————————————————————————————————————————————————————————————————————————————————
Date of
First Study Day of Last
Drug Study Drug Day of Autopsy
Center/Patients ID Age/Sex/Race Administration Administration Death Cause of Death Performed?
—————————————————————————————————————————————————————————————————————————————————————————————————————————————
CAN-1/341 43/F/ASIAN 23MAY2019 998 1014 SUICIDE Yes
CHN-1/307 24/M/ASIAN 11MAR2019 1076 1122 LOST TO FOLLOW UP <Missing>
CHN-13/240 42/M/ASIAN 08APR2019 1044 1087 ADVERSE EVENT Yes
CHN-7/126 27/M/WHITE 02MAY2019 1025 1066 ADVERSE EVENT Yes
\s\nACTARM: A: Drug X

——————————————————————————————————————————————————————————————————————————————————————————————————
Date of
First Study Day of Last
Drug Study Drug Day of
Center/Patients ID Age/Sex/Race Administration Administration Death Cause of Death
——————————————————————————————————————————————————————————————————————————————————————————————————
CHN-3/128 32/M/ASIAN 24FEB2019 1084 1106 ADVERSE EVENT
RUS-1/52 40/F/ASIAN 18MAR2019 1064 1070 DISEASE PROGRESSION
\s\nACTARM: A: Drug X

———————————————————————————————


Autopsy
Center/Patients ID Performed?
———————————————————————————————
CHN-3/128 Yes
RUS-1/52 Yes

27 changes: 27 additions & 0 deletions tests/testthat/test-ael04.R
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# ael04 ----

test_that("ael04 works with adsl dataset", {
expect_silent(
res <- run(ael04, syn_data, dataset = "adsl")
)
expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 110)))
})

test_that("ael04 can handle all missing values", {
proc_data <- syn_data
proc_data$adsl <- proc_data$adsl %>%
mutate(
ACTARM = NA_character_,
DTHCAUS = NA_character_
)

expect_silent(res <- run(ael04, proc_data))
expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 110)))
})

# ael04 functions ----

test_that("ael04 functions work as expected", {
expect_silent(res <- ael04_pre(syn_data) %>% ael04_main())
expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 110)))
})
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