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Tests subsetCohort argument in conceptCohort #418

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Dec 20, 2024
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Tests subsetCohort argument in conceptCohort #418

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22 changes: 17 additions & 5 deletions R/conceptCohort.R
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Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,9 @@
#' @param useSourceFields If TRUE, the source concept_id fields will also be
#' used when identifying relevant clinical records. If FALSE, only the standard
#' concept_id fields will be used.
#' @param subsetCohort A cohort table containing individuals for whom cohorts
#' will be generated. Only individuals in this table will appear in the
#' generated cohort.
#' @param subsetCohort A character refering to a cohort table containing
#' individuals for whom cohorts will be generated. Only individuals in this
#' table will appear in the generated cohort.
#' @param subsetCohortId Optional. Specifies cohort IDs from the `subsetCohort`
#' table to include. If none are provided, all cohorts from the `subsetCohort`
#' are included.
Expand Down Expand Up @@ -77,7 +77,7 @@ conceptCohort <- function(cdm,
omopgenerics::assertCharacter(subsetCohort, length = 1, null = TRUE)
if (!is.null(subsetCohort)) {
subsetCohort <- omopgenerics::validateCohortArgument(cdm[[subsetCohort]])
subsetCohortId <- omopgenerics::validateCohortIdArgument({{subsetCohortId}}, subsetCohort)
subsetCohortId <- omopgenerics::validateCohortIdArgument({{subsetCohortId}}, subsetCohort, validation = "warning")
}

useIndexes <- getOption("CohortConstructor.use_indexes")
Expand Down Expand Up @@ -120,7 +120,19 @@ conceptCohort <- function(cdm,
dplyr::compute(name = subsetName, temporary = FALSE)
if (omopgenerics::isTableEmpty(subsetIndividuals)) {
omopgenerics::dropTable(cdm = cdm, name = subsetName)
cli::cli_abort("There are no individuals in the `subsetCohort` and `subsetCohortId` provided.")
cli::cli_warn("There are no individuals in the `subsetCohort` and `subsetCohortId` provided. Returning empty cohort.")
cdm <- omopgenerics::emptyCohortTable(cdm = cdm, name = name)
cdm[[name]] <- cdm[[name]] |>
omopgenerics::newCohortTable(
cohortSetRef = cohortSet,
cohortAttritionRef = dplyr::tibble(
"cohort_definition_id" = cohortSet$cohort_definition_id,
"number_records" = 0L, "number_subjects" = 0L,
"reason_id" = 1L, "reason" = "Qualifying initial events",
"excluded_records" = NA_integer_, "excluded_subjects" = NA_integer_
)
)
return(cdm[[name]])
}
if (!isFALSE(useIndexes)) {
addIndex(
Expand Down
6 changes: 3 additions & 3 deletions man/conceptCohort.Rd
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103 changes: 52 additions & 51 deletions tests/testthat/test-conceptCohort.R
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Original file line number Diff line number Diff line change
Expand Up @@ -101,8 +101,8 @@ test_that("simple example", {
cdm = cdm, name = "cohort", table = dplyr::tibble(
"cohort_definition_id" = c(1, 1, 2) |> as.integer(),
"subject_id" = c(1, 2, 3) |> as.integer(),
"cohort_start_date" = c(0, 300, 1500) |> as.Date(origin = "2020-01-01"),
"cohort_end_date" = c(400, 800, 1600) |> as.Date(origin = "2020-01-01")
"cohort_start_date" = c(0, 300, 1400) |> as.Date(origin = "2020-01-01"),
"cohort_end_date" = c(400, 800, 1420) |> as.Date(origin = "2020-01-01")
)
)

Expand Down Expand Up @@ -180,33 +180,34 @@ test_that("simple example", {
)

# subsetCohort ----
# cdm$cohort <- cdm$cohort |> omopgenerics::newCohortTable()
# cdm$cohort <- cdm$cohort |>
# omopgenerics::newCohortTable(
# cohortSetRef = dplyr::tibble(
# "cohort_definition_id" = c(1L, 2L, 3L),
# "cohort_name" = paste0("cohort", 1:3),
# ),
# cohortAttritionRef = dplyr::bind_rows(
# attrition(cdm$cohort),attrition(cdm$cohort)[1] |> dplyr::mutate("cohort_definition_id" = 3L)
# )
# )
# cohort2 <- conceptCohort(cdm = cdm,
# conceptSet = list(a = 1L),
# name = "my_cohort2",
# subsetCohort = cdm$cohort)
# expect_equal(collectCohort(cohort2, 1), collectCohort(cohort, 1))
# cohort3 <- conceptCohort(cdm = cdm,
# conceptSet = list(a = 1L),
# name = "my_cohort3",
# subsetCohort = cdm$cohort,
# subsetCohortId = 2)
# expect_true(nrow(collectCohort(cohort3, 1)) == 0)
# expect_error(conceptCohort(cdm = cdm,
# conceptSet = list(a = 1L),
# name = "my_cohort3",
# subsetCohort = cdm$cohort,
# subsetCohortId = 3))
cdm$cohort <- cdm$cohort |> omopgenerics::newCohortTable()
cdm$cohort <- cdm$cohort |>
omopgenerics::newCohortTable(
cohortSetRef = dplyr::tibble(
"cohort_definition_id" = c(1L, 2L, 3L),
"cohort_name" = paste0("cohort", 1:3),
),
cohortAttritionRef = dplyr::bind_rows(
attrition(cdm$cohort),attrition(cdm$cohort)[1] |> dplyr::mutate("cohort_definition_id" = 3L)
)
)
cohort2 <- conceptCohort(cdm = cdm,
conceptSet = list(a = 1L),
name = "my_cohort2",
subsetCohort = "cohort")
expect_equal(collectCohort(cohort2, 1), collectCohort(cohort, 1))
cohort3 <- conceptCohort(cdm = cdm,
conceptSet = list(a = 1L),
name = "my_cohort3",
subsetCohort = "cohort",
subsetCohortId = 2)
expect_true(nrow(collectCohort(cohort3, 1)) == 0)
expect_warning(c <- conceptCohort(cdm = cdm,
conceptSet = list(a = 1L),
name = "my_cohort3",
subsetCohort = "cohort",
subsetCohortId = 3))
expect_true(dplyr::pull(dplyr::tally(c)) == 0)

PatientProfiles::mockDisconnect(cdm)
})
Expand Down Expand Up @@ -482,7 +483,7 @@ test_that("table not present in the cdm", {

test_that("cohort exit as event start date", {
skip_on_cran()
cdm <- omock::mockCdmReference() |>
cdm <- omock::mockCdmReference() |>
omock::mockCdmFromTables(tables = list("cohort" = dplyr::tibble(
"cohort_definition_id" = 1L,
"subject_id" = c(1L, 2L, 3L),
Expand Down Expand Up @@ -554,7 +555,7 @@ test_that("cohort exit as event start date", {

test_that("use source field concepts", {
skip_on_cran()
cdm <- omock::mockCdmReference() |>
cdm <- omock::mockCdmReference() |>
omock::mockCdmFromTables(tables = list("cohort" = dplyr::tibble(
"cohort_definition_id" = 1L,
"subject_id" = c(1L, 2L, 3L),
Expand Down Expand Up @@ -728,11 +729,11 @@ test_that("overlap option", {
expect_true(nrow(cdm$cohort_1 |>
dplyr::collect()) == 4)
expect_true(all(sort(cdm$cohort_1 |>
dplyr::pull("cohort_start_date")) ==
as.Date(c("2020-01-01",
"2020-01-01",
"2020-01-02",
"2020-01-20"))))
dplyr::pull("cohort_start_date")) ==
as.Date(c("2020-01-01",
"2020-01-01",
"2020-01-02",
"2020-01-20"))))
expect_true(all(sort(cdm$cohort_1 |>
dplyr::pull("cohort_end_date")) ==
as.Date(c("2020-01-03",
Expand Down Expand Up @@ -760,7 +761,7 @@ test_that("overlap option", {
"2020-01-21"))))


# only overlapping records
# only overlapping records
cdm <- omopgenerics::insertTable(
cdm = cdm, name = "drug_exposure", table = dplyr::tibble(
"drug_exposure_id" = c(1L, 2L),
Expand Down Expand Up @@ -788,7 +789,7 @@ test_that("overlap option", {
dplyr::pull("cohort_end_date")) ==
as.Date(c("2020-01-10"))))

# no overlapping records
# no overlapping records
cdm <- omopgenerics::insertTable(
cdm = cdm, name = "drug_exposure", table = dplyr::tibble(
"drug_exposure_id" = c(1L, 2L),
Expand Down Expand Up @@ -816,12 +817,12 @@ test_that("overlap option", {
dplyr::pull("cohort_end_date")) ==
as.Date(c("2020-01-03", "2020-01-10"))))

# wrong input
# wrong input
expect_error(cdm$cohort_5 <- conceptCohort(cdm = cdm,
conceptSet = list(a = 1L),
name = "cohort_5",
exit = "event_end_date",
overlap = "another"))
conceptSet = list(a = 1L),
name = "cohort_5",
exit = "event_end_date",
overlap = "another"))



Expand All @@ -836,10 +837,10 @@ test_that("overlap option", {
"drug_type_concept_id" = 1L
))
expect_no_error(cdm$cohort_6 <- conceptCohort(cdm = cdm,
conceptSet = list(a = 1L),
name = "cohort_6",
exit = "event_end_date",
overlap = "extend"))
conceptSet = list(a = 1L),
name = "cohort_6",
exit = "event_end_date",
overlap = "extend"))

expect_true((cdm$cohort_6 |> dplyr::pull("cohort_start_date")) == as.Date("2020-01-01"))
expect_true((cdm$cohort_6 |> dplyr::pull("cohort_end_date")) == as.Date("2020-01-16"))
Expand All @@ -856,10 +857,10 @@ test_that("overlap option", {
))

expect_no_error(cdm$cohort_7 <- conceptCohort(cdm = cdm,
conceptSet = list(a = 1L),
name = "cohort_7",
exit = "event_end_date",
overlap = "extend"))
conceptSet = list(a = 1L),
name = "cohort_7",
exit = "event_end_date",
overlap = "extend"))
expect_true((cdm$cohort_7 |> dplyr::pull("cohort_start_date")) == as.Date("2020-01-15"))
expect_true((cdm$cohort_7 |> dplyr::pull("cohort_end_date")) == as.Date("2020-01-30"))

Expand Down
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