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Add test case for baseline_timepoints in derive_blfl function #95

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merged 5 commits into from
Sep 12, 2024
Merged

Add test case for baseline_timepoints in derive_blfl function #95

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a88cd78
Modified test case
ShiyuC Aug 28, 2024
42dd3c5
style file
ShiyuC Sep 6, 2024
64312d9
Add examples to function
ShiyuC Sep 11, 2024
93e2af9
Merge main updates
ShiyuC Sep 11, 2024
a869acd
Empty commit, trigger CI jobs
galachad Sep 12, 2024
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22 changes: 22 additions & 0 deletions R/derive_blfl.R
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Original file line number Diff line number Diff line change
Expand Up @@ -260,6 +260,7 @@ dtc_timepart <- function(dtc, partial_as_na = TRUE, ignore_seconds = TRUE) {
#'
#' sdtm_in
#'
#' # Example 1:
#' observed_output <- derive_blfl(
#' sdtm_in = sdtm_in,
#' dm_domain = dm,
Expand All @@ -269,6 +270,27 @@ dtc_timepart <- function(dtc, partial_as_na = TRUE, ignore_seconds = TRUE) {
#' )
#' observed_output
#'
#' # Example 2:
#' observed_output2 <- derive_blfl(
#' sdtm_in = sdtm_in,
#' dm_domain = dm,
#' tgt_var = "VSLOBXFL",
#' ref_var = "RFXSTDTC",
#' baseline_timepoints = c("PRE-DOSE")
#' )
#' observed_output2
#'
#' # Example 3: Output is the same as Example 2
#' observed_output3 <- derive_blfl(
#' sdtm_in = sdtm_in,
#' dm_domain = dm,
#' tgt_var = "VSLOBXFL",
#' ref_var = "RFXSTDTC",
#' baseline_visits = c("SCREENING"),
#' baseline_timepoints = c("PRE-DOSE")
#' )
#' observed_output3
#'
derive_blfl <- function(sdtm_in,
dm_domain,
tgt_var,
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22 changes: 22 additions & 0 deletions man/derive_blfl.Rd
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10 changes: 8 additions & 2 deletions tests/testthat/_snaps/derive_blfl.md
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Expand Up @@ -16,7 +16,7 @@
"names": {
"type": "character",
"attributes": {},
"value": ["DOMAIN", "oak_id", "raw_source", "patient_number", "USUBJID", "VSDTC", "VSTESTCD", "VSORRES", "VSSTAT", "VISIT", "VSLOBXFL"]
"value": ["DOMAIN", "oak_id", "raw_source", "patient_number", "USUBJID", "VSDTC", "VSTESTCD", "VSORRES", "VSSTAT", "VISIT", "VSTPT", "VSLOBXFL"]
}
},
"value": [
Expand Down Expand Up @@ -73,7 +73,13 @@
{
"type": "character",
"attributes": {},
"value": ["Y", null, null, null, "Y", null, "Y", null, "Y", "Y", null]
"value": ["PRE-DOSE", "30 DAY POST-DOSE", "28 DAY POST-DOSE", "30 DAY POST-DOSE", "28 DAY POST-DOSE", "28 DAY POST-DOSE",
"PRE-DOSE", "PRE-DOSE", "PRE-DOSE", "PRE-DOSE", "1 DAY POST-DOSE"]
},
{
"type": "character",
"attributes": {},
"value": ["Y", null, null, null, null, "Y", "Y", null, "Y", "Y", null]
}
]
}
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27 changes: 14 additions & 13 deletions tests/testthat/test-derive_blfl.R
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Expand Up @@ -9,18 +9,18 @@ dm <- tibble::tribble(

sdtm_in <-
tibble::tribble(
~DOMAIN, ~oak_id, ~raw_source, ~patient_number, ~USUBJID, ~VSDTC, ~VSTESTCD, ~VSORRES, ~VSSTAT, ~VISIT,
"VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-01T13:31", "DIABP", "90", NA, "SCREENING",
"VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T11:20", "DIABP", "90", NA, "SCREENING",
"VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-28T10:10", "PULSE", "ND", NA, "SCREENING",
"VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T13:31", "PULSE", "85", NA, "SCREENING",
"VS", 1L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:10", "SYSBP", "120", NA, "SCREENING",
"VS", 2L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:05", "SYSBP", "120", NA, "SCREENING",
"VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "DIABP", "75", NA, "SCREENING",
"VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", NA, "NOT DONE", "SCREENING", # nolint
"VS", 2L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", "110", NA, "SCREENING",
"VS", 2L, "VTLS1", 378L, "test_study-378", "2020-01-20T10:00", "PULSE", "110", NA, "SCREENING",
"VS", 3L, "VTLS1", 378L, "test_study-378", "2020-01-21T11:00", "PULSE", "105", NA, "SCREENING"
~DOMAIN, ~oak_id, ~raw_source, ~patient_number, ~USUBJID, ~VSDTC, ~VSTESTCD, ~VSORRES, ~VSSTAT, ~VISIT, ~VSTPT,
"VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-01T13:31", "DIABP", "90", NA, "SCREENING", "PRE-DOSE",
"VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T11:20", "DIABP", "90", NA, "SCREENING", "30 DAY POST-DOSE",
"VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-28T10:10", "PULSE", "ND", NA, "SCREENING", "28 DAY POST-DOSE",
"VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T13:31", "PULSE", "85", NA, "SCREENING", "30 DAY POST-DOSE",
"VS", 1L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:10", "SYSBP", "120", NA, "SCREENING", "28 DAY POST-DOSE",
"VS", 2L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:05", "SYSBP", "120", NA, "SCREENING", "28 DAY POST-DOSE",
"VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "DIABP", "75", NA, "SCREENING", "PRE-DOSE",
"VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", NA, "NOT DONE", "SCREENING", "PRE-DOSE", # nolint
"VS", 2L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", "110", NA, "SCREENING", "PRE-DOSE",
"VS", 2L, "VTLS1", 378L, "test_study-378", "2020-01-20T10:00", "PULSE", "110", NA, "SCREENING", "PRE-DOSE",
"VS", 3L, "VTLS1", 378L, "test_study-378", "2020-01-21T11:00", "PULSE", "105", NA, "SCREENING", "1 DAY POST-DOSE"
)

d <- list(sdtm_in = sdtm_in, dm = dm)
Expand All @@ -32,7 +32,8 @@ test_that("derive_blfl example works", {
dm_domain = d$dm,
tgt_var = "VSLOBXFL",
ref_var = "RFXSTDTC",
baseline_visits = c("SCREENING")
baseline_visits = c("SCREENING"),
baseline_timepoints = c("PRE-DOSE")
)
observed_output

Expand Down
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