update summariseTemporalSymmetry validation fun

R/inputValidation.R

@@ -92,37 +92,6 @@ checkInputSummariseSequenceRatios <- function(cohort,
   checkmate::reportAssertions(collection = errorMessage)
 }
 
-checkInputSummariseTemporalSymmetry <- function(cohort,
-                                                cohortId,
-                                                timescale,
-                                                minCellCount) {
-
-  # Check cdm objects, writing schema and index/marker tables
-  cdm <- omopgenerics::cdmReference(cohort)
-  checkCdm(cdm)
-
-  cohort_row <- cohort |> dplyr::tally() |> dplyr::pull()
-  if (cohort_row <=0){
-    cli::cli_abort("Aborted! The cohort has no rows, please revisit the cohort")
-  }
-
-  checkCohortIds(cohort = cohort,
-                 cohortId = cohortId,
-                 errorMessage = errorMessage)
-
-  # Check the rest of inputs
-  errorMessage <- checkmate::makeAssertCollection()
-
-  # Check minCellCount
-  checkMinCellCount(minCellCount, errorMessage)
-
-  # Check timescale
-  checkTimeScale(timescale, errorMessage)
-
-  # Report errors
-  checkmate::reportAssertions(collection = errorMessage)
-}
-
 checkSequenceSymmetry <- function(result) {
   omopgenerics::newSummarisedResult(result)
 }

R/summariseTemporalSymmetry.R

@@ -32,11 +32,18 @@ summariseTemporalSymmetry <- function(cohort,
                                       timescale = "month",
                                       minCellCount = 5) {
   # checks
-  checkInputSummariseTemporalSymmetry(cohort = cohort,
-                                      cohortId = cohortId,
-                                      timescale = timescale,
-                                      minCellCount = minCellCount)
+  cdm <- omopgenerics::cdmReference(cohort)
+  cdm <- omopgenerics::validateCdmArgument(cdm = cdm)
+  cohortId <- omopgenerics::validateCohortIdArgument({{cohortId}}, cohort)
+  omopgenerics::assertChoice(timescale,
+                             choices = c("day", "week","month", "year"),
+                             length = 1)
+  omopgenerics::assertNumeric(minCellCount,
+                              min = 0,
+                              max = 99999999,
+                              length = 1)
 
+  # pulling out data
   index_names <- attr(cohort, "cohort_set") |>
     dplyr::select("cohort_definition_id", "index_name", "index_id", "marker_id")
   marker_names <- attr(cohort, "cohort_set") |>
@@ -47,6 +54,7 @@ summariseTemporalSymmetry <- function(cohort,
   settings <- c("cohort_date_range", "days_prior_observation", "washout_window", "index_marker_gap",
                 "combination_window", "moving_average_restriction", "timescale")
 
+  # computing the output
   output <- cohort %>%
     dplyr::mutate(time = as.numeric(!!CDMConnector::datediff(
       "index_date", "marker_date", interval = timescale))) |>
@@ -107,6 +115,7 @@ summariseTemporalSymmetry <- function(cohort,
                   package_version = as.character(utils::packageVersion("CohortSymmetry")),
                   timescale = .env$timescale)
 
+  # new summarise result
   output_sum <- output_sum |>
     dplyr::left_join(setting, by = c("cdm_name", "days_prior_observation", "washout_window",
                                      "index_marker_gap", "combination_window", "timescale")) |>

tests/testthat/test-summariseTemporalSymmetry.R

@@ -149,20 +149,3 @@ test_that("input validation",{
   CDMConnector::cdmDisconnect(cdm = cdm)
 
 })
-
-test_that("edge case",{
-  skip_on_cran()
-  cdm <- mockCohortSymmetry()
-  cdm <- generateSequenceCohortSet(
-    cdm = cdm,
-    name = "joined_cohorts",
-    indexTable = "cohort_1",
-    markerTable = "cohort_2",
-    combinationWindow = c(10, 11)
-  )
-
-  expect_error(
-    result <- summariseTemporalSymmetry(cohort = cdm$joined_cohorts)
-  )
-
-})