Merge pull request #246 from oxford-pharmacoepi/min_cell_count

remove problem arguments
OHDSI · May 28, 2024 · b0bd52a · b0bd52a
2 parents 032a4ca + 4ab8713
commit b0bd52a
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Showing 3 changed files with 19 additions and 30 deletions.
diff --git a/R/displayTables.R b/R/displayTables.R
@@ -13,11 +13,7 @@
 #'  gt table or flextable. See visOmopResults package for more information on
 #'  how to define a style. Alternatively, use "default" to get visOmopResults
 #'  style, or NULL for gt/flextable default styling.
-#' @param crude whether to report crude results.
-#' @param adjusted whether to report adjusted results.
 #' @param studyPopulation whether to report the study population.
-#' @param indexName whether to report index names.
-#' @param markerName whether to report marker names
 #' @param cdmName whether to report database names.
 #' @param .options named list with additional formatting options.
 #' tableSequenceRatiosOptions() shows allowed arguments and
@@ -31,9 +27,9 @@
 #' library(CohortSymmetry)
 #' cdm <- mockCohortSymmetry()
 #' cdm <- generateSequenceCohortSet(cdm = cdm,
-#'                                                  indexTable = "cohort_1",
-#'                                                  markerTable = "cohort_2",
-#'                                                  name = "joined_cohort")
+#'                                  indexTable = "cohort_1",
+#'                                  markerTable = "cohort_2",
+#'                                  name = "joined_cohort")
 #' res <- summariseSequenceRatios(cohort = cdm$joined_cohort)
 #' gtResult <- tableSequenceRatios(res)
 #' CDMConnector::cdmDisconnect(cdm = cdm)
@@ -46,14 +42,14 @@ tableSequenceRatios <- function(result,
                                   c("N (%)" = "<count> (<percentage> %)",
                                     "SR (CI)" = "<point_estimate> (<lower_CI> - <upper_CI>)"),
                                 style = "default",
-                                crude = TRUE,
-                                adjusted = TRUE,
                                 studyPopulation = TRUE,
-                                indexName = TRUE,
-                                markerName = TRUE,
                                 cdmName = TRUE,
                                 .options = NULL) {
   # checks
+  crude <- T
+  adjusted <- T
+  indexName <- T
+  markerName <- T
   checkSequenceSymmetry(result)
   checksFormatSequenceSymmetry(type, crude, adjusted, studyPopulation, indexName,
                                markerName, cdmName, .options)

diff --git a/man/tableSequenceRatios.Rd b/man/tableSequenceRatios.Rd
diff --git a/tests/testthat/test-displayTable.R b/tests/testthat/test-displayTable.R
@@ -7,7 +7,7 @@ test_that("tableSequenceRatios - gt output", {
                                                    markerId = 3,
                                                    name = "joined_cohort")
 
-  res <- summariseSequenceRatios(cohort = cdm$joined_cohort)
+  res <- summariseSequenceRatios(cohort = cdm$joined_cohort, minCellCount = 0)
 
   gtResult <- tableSequenceRatios(res)
   expect_true("gt_tbl" %in% (gtResult %>% class()))
@@ -16,8 +16,9 @@ test_that("tableSequenceRatios - gt output", {
                       "Index first, N (%)", "Marker first, N (%)", "CSR (95% CI)",
                       "ASR (95% CI)")))
   expect_no_error(gtResult <- tableSequenceRatios(res, studyPopulation = FALSE))
+  expect_no_error(gtResult <- tableSequenceRatios(res, cdmName = FALSE))
   expect_true(all(colnames(gtResult$`_data`) %in%
-                    c("Database name", "Index", "Marker",
+                    c("Index", "Marker", "Study population",
                       "Index first, N (%)", "Marker first, N (%)", "CSR (95% CI)",
                       "ASR (95% CI)")))
   CDMConnector::cdmDisconnect(cdm)
@@ -32,7 +33,7 @@ test_that("tableSequenceRatios - tibble output", {
                                                    markerId = 3,
                                                    name = "joined_cohort")
 
-  res <- summariseSequenceRatios(cohort = cdm$joined_cohort)
+  res <- summariseSequenceRatios(cohort = cdm$joined_cohort, minCellCount = 0)
 
   tibble_res <- tableSequenceRatios(res, type = "tibble")
 
@@ -43,6 +44,8 @@ test_that("tableSequenceRatios - tibble output", {
                       "ASR (95% CI)")))
   expect_no_error(tibble_res <- tableSequenceRatios(res, type = "tibble",
                                                   studyPopulation = FALSE))
+  expect_no_error(gtResult <- tableSequenceRatios(res, type = "tibble",
+                                                  cdmName = FALSE))
   CDMConnector::cdmDisconnect(cdm)
 })
 
@@ -55,7 +58,7 @@ test_that("tableSequenceRatios - flextable output", {
                                                    markerId = 3,
                                                    name = "joined_cohort")
 
-  res <- summariseSequenceRatios(cohort = cdm$joined_cohort)
+  res <- summariseSequenceRatios(cohort = cdm$joined_cohort, minCellCount = 0)
 
   flextable_res <- tableSequenceRatios(res, type = "flextable")
 
@@ -66,5 +69,7 @@ test_that("tableSequenceRatios - flextable output", {
                       "ASR (95% CI)")))
   expect_no_error(flextable_res <- tableSequenceRatios(res, type = "flextable",
                                                     studyPopulation = FALSE))
+  expect_no_error(flextable_res <- tableSequenceRatios(res, type = "flextable",
+                                                       cdmName = FALSE))
   CDMConnector::cdmDisconnect(cdm)
 })