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issues #23

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merged 2 commits into from
Dec 11, 2023
Merged

issues #23

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65a5456
Merge pull request #22 from oxford-pharmacoepi/main
MimiYuchenGuo Dec 11, 2023
e7305cf
issues 7, 10, 11
MimiYuchenGuo Dec 11, 2023
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25 changes: 18 additions & 7 deletions R/generateCombinationCohorts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@
#' combinations.
#' @param targetCohortId Ids to combine of the target cohort. If NULL all
#' cohort present in the table will be used.
#' @param mutuallyExclusive Wheather the generated cohorts are mutually
#' @param mutuallyExclusive Whether the generated cohorts are mutually
#' exclusive or not.
#'
#' @param returnOnlyComb Whether to only get the combination cohort back
#' @export
#'
#' @return The cdm object with the new generated cohort set
Expand All @@ -36,7 +36,8 @@ generateCombinationCohortSet <- function(cdm,
name,
targetCohortName,
targetCohortId = NULL,
mutuallyExclusive = FALSE) {
mutuallyExclusive = FALSE,
returnOnlyComb = FALSE) {
# initial checks
checkmate::checkClass(cdm, "cdm_reference")
checkmate::checkCharacter(name, len = 1, any.missing = FALSE, min.chars = 1)
Expand Down Expand Up @@ -95,7 +96,7 @@ generateCombinationCohortSet <- function(cdm,
nameStyle = "{cohort_name}"
)

# cretae cohort_definition_id
# create cohort_definition_id
cohortNames <- CDMConnector::cohortSet(cdm[[targetCohortName]]) %>%
dplyr::filter(.data$cohort_definition_id %in% .env$targetCohortId) %>%
dplyr::pull("cohort_name")
Expand All @@ -112,13 +113,22 @@ generateCombinationCohortSet <- function(cdm,
cohSet <- notMutuallyEclusiveCohortSet(cohSet)
}


if (returnOnlyComb) {
cohSet <- cohSet %>%
dplyr::rowwise() %>%
dplyr::mutate(product = prod(dplyr::c_across(-"cohort_definition_id"), na.rm = TRUE)) %>%
dplyr::filter(.data$product == 1) %>%
dplyr::select(-"product")
}


# add cohort definition id
cohort <- cohort %>%
dplyr::inner_join(cohSet, copy = TRUE, by = cohortNames) %>%
dplyr::select(
"cohort_definition_id", "subject_id", "cohort_start_date",
"cohort_end_date"
)
"cohort_end_date")

if (!mutuallyExclusive) {
cohort <- joinOverlap(x = cohort, gap = 1)
Expand All @@ -132,7 +142,8 @@ generateCombinationCohortSet <- function(cdm,
dplyr::distinct()
}

cohort <- cohort %>%

cohort <- cohort %>%
CDMConnector::computeQuery(
name = name,
temporary = FALSE,
Expand Down
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