test

R/summariseAllConceptCounts.R

@@ -52,6 +52,8 @@ checkFeasibility <- function(omopTable, tableName, conceptId){
 #' @param sex TRUE or FALSE. If TRUE code use will be summarised by sex.
 #' @param ageGroup A list of ageGroup vectors of length two. Code use will be
 #' thus summarised by age groups.
+#' @param sample An integer to sample the tables to only that number of records.
+#' If NULL no sample is done.
 #' @param dateRange A list containing the minimum and the maximum dates
 #' defining the time range within which the analysis is performed.
 #' @return A summarised_result object with results overall and, if specified, by

R/summariseClinicalRecords.R

@@ -22,6 +22,8 @@
 #' @param ageGroup A list of age groups to stratify results by.
 #' @param sex Boolean variable. Whether to stratify by sex (TRUE) or not
 #' (FALSE).
+#' @param sample An integer to sample the tables to only that number of records.
+#' If NULL no sample is done.
 #' @param dateRange A list containing the minimum and the maximum dates
 #' defining the time range within which the analysis is performed.
 #' @return A summarised_result object.

R/summariseConceptSetCounts.R

@@ -10,6 +10,8 @@
 #' @param sex TRUE or FALSE. If TRUE code use will be summarised by sex.
 #' @param ageGroup A list of ageGroup vectors of length two. Code use will be
 #' thus summarised by age groups.
+#' @param sample An integer to sample the tables in the cdm object to only that number of records.
+#' If NULL no sample is done.
 #' @param dateRange A list containing the minimum and the maximum dates
 #' defining the time range within which the analysis is performed.
 #' @return A summarised_result object with results overall and, if specified, by

R/summariseRecordCount.R

@@ -9,6 +9,8 @@
 #' @param sex Whether to stratify by sex (TRUE) or not (FALSE).
 #' @param dateRange A list containing the minimum and the maximum dates
 #' defining the time range within which the analysis is performed.
+#' @param sample An integer to sample the tables to only that number of records.
+#' If NULL no sample is done.
 #' @return A summarised_result object.
 #' @export
 #' @examples

tests/testthat/test-summariseAllConceptCounts.R

@@ -76,6 +76,20 @@ test_that("dateRange argument works", {
   expect_equal(colnames(settings(y)), colnames(settings(x)))
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
+test_that("sample argument works", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  expect_no_error(x<-summariseAllConceptCounts(cdm,"drug_exposure", sample = 50))
+  expect_no_error(y<-summariseAllConceptCounts(cdm,"drug_exposure"))
+  n <- cdm$drug_exposure |>
+    dplyr::tally()|>
+    dplyr::pull(n)
+  expect_no_error(z<-summariseAllConceptCounts(cdm,"drug_exposure",sample = n))
+  expect_equal(y,z)
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
 
 test_that("tableAllConceptCounts() works", {
   skip_on_cran()

tests/testthat/test-summariseClinicalRecords.R

@@ -247,6 +247,21 @@ test_that("dateRange argument works", {
 
 })
 
+test_that("sample argument works", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  expect_no_error(x<-summariseClinicalRecords(cdm,"drug_exposure", sample = 50))
+  expect_no_error(y<-summariseClinicalRecords(cdm,"drug_exposure"))
+  n <- cdm$drug_exposure |>
+    dplyr::tally()|>
+    dplyr::pull(n)
+  expect_no_error(z<-summariseClinicalRecords(cdm,"drug_exposure",sample = n))
+  expect_equal(y,z)
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
+
 test_that("tableClinicalRecords() works", {
   skip_on_cran()
   # Load mock database ----

tests/testthat/test-summariseConceptSetCounts.R

@@ -558,3 +558,19 @@ test_that("dateRange argument works", {
   expect_equal(colnames(settings(z)), colnames(settings(x)))
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
+
+
+test_that("sample argument works", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  expect_no_error(x<-summariseConceptSetCounts(cdm,conceptSet = list("x" = c(40213260)), sample = 50))
+  expect_no_error(y<-summariseConceptSetCounts(cdm,conceptSet = list("x" = c(40213260))))
+  n <- cdm$drug_exposure |>
+    dplyr::tally()|>
+    dplyr::pull(n)
+  expect_no_error(z<-summariseConceptSetCounts(cdm,conceptSet = list("x" = c(40213260)),sample = n))
+  expect_equal(y,z)
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})

tests/testthat/test-summariseRecordCount.R

@@ -305,3 +305,17 @@ test_that("dateRnge argument works", {
 })
 
 
+test_that("sample argument works", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  expect_no_error(x<-summariseRecordCount(cdm,"drug_exposure", sample = 50))
+  expect_no_error(y<-summariseRecordCount(cdm,"drug_exposure"))
+  n <- cdm$drug_exposure |>
+    dplyr::tally()|>
+    dplyr::pull(n)
+  expect_no_error(z<-summariseRecordCount(cdm,"drug_exposure",sample = n))
+  expect_equal(y,z)
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})