Merge pull request #247 from oxford-pharmacoepi/final_chanes_010

tableSequenceRatio() vignette
OHDSI · May 29, 2024 · bf525a9 · bf525a9
2 parents d192b71 + 4d510ab
commit bf525a9
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diff --git a/R/displayTables.R b/R/displayTables.R
@@ -145,12 +145,12 @@ tableSequenceRatios <- function(result,
       Index = stringr::str_to_sentence(gsub("_", " ", .data$Index)),
       Marker = stringr::str_to_sentence(gsub("_", " ", .data$Marker))
     ) %>%
-    {if (!indexName) {
-      dplyr::select(., -"Index")
-    } else .} %>%
-    {if (!markerName) {
-      dplyr::select(., -"Marker")
-    } else .} %>%
+    # {if (!indexName) {
+    #   dplyr::select(., -"Index")
+    # } else .} %>%
+    # {if (!markerName) {
+    #   dplyr::select(., -"Marker")
+    # } else .} %>%
     tidyr::pivot_wider(names_from = "estimate_name", values_from = "estimate_value") %>%
     dplyr::select(dplyr::all_of(order_columns))
 

diff --git a/tests/testthat/test-displayTable.R b/tests/testthat/test-displayTable.R
@@ -52,11 +52,11 @@ test_that("tableSequenceRatios - tibble output", {
 test_that("tableSequenceRatios - flextable output", {
   cdm <- mockCohortSymmetry()
   cdm <- generateSequenceCohortSet(cdm = cdm,
-                                                   indexTable = "cohort_1",
-                                                   indexId = 1,
-                                                   markerTable = "cohort_2",
-                                                   markerId = 3,
-                                                   name = "joined_cohort")
+                                   indexTable = "cohort_1",
+                                   indexId = 1,
+                                   markerTable = "cohort_2",
+                                   markerId = 3,
+                                   name = "joined_cohort")
 
   res <- summariseSequenceRatios(cohort = cdm$joined_cohort, minCellCount = 0)
 
@@ -73,3 +73,90 @@ test_that("tableSequenceRatios - flextable output", {
                                                        cdmName = FALSE))
   CDMConnector::cdmDisconnect(cdm)
 })
+
+test_that("tableSequenceRatio options", {
+  cdm <- mockCohortSymmetry()
+  cdm <- generateSequenceCohortSet(cdm = cdm,
+                                   indexTable = "cohort_1",
+                                   markerTable = "cohort_2",
+                                   name = "joined_cohort")
+
+  expect_warning(
+    result <- summariseSequenceRatios(cohort = cdm$joined_cohort, minCellCount = 0)
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = NULL)
+  )
+
+  expect_error(
+    tableSequenceRatios(result = result,
+                        .options = list(titless = "Title"))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(
+                          groupColumn = c("cdm_name")
+                          )))
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(bigMark = " < "))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(decimalMark = " < "))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(keepNotFormatted = F))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(useFormatOrder = F))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(includeHeaderName = T))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(includeHeaderKey = F))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(title = "Title"))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(
+                          title = "Title",
+                          subtitle = "Subtitle"))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(caption = "caption"))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(na = "NA"))
+  )
+
+  expect_no_error(
+    tableSequenceRatios(result = result,
+                        .options = list(groupAsColumn = T))
+  )
+
+  CDMConnector::cdm_disconnect(cdm = cdm)
+})
diff --git a/tests/testthat/test-summariseSequenceRatios.R b/tests/testthat/test-summariseSequenceRatios.R
@@ -893,6 +893,20 @@ test_that("min cell count",{
   )
   )
 
+  expect_error(
+    result_error <- summariseSequenceRatios(
+      cohort = cdm$joined_cohort,
+      minCellCount = Inf
+    )
+  )
+
+  expect_error(
+    result_error2 <- summariseSequenceRatios(
+      cohort = cdm$joined_cohort,
+      minCellCount = -1
+    )
+  )
+
   expect_no_error(
     expect_warning(
     result2 <- summariseSequenceRatios(

diff --git a/vignettes/a04_Visualise_sequence_ratios.Rmd b/vignettes/a04_Visualise_sequence_ratios.Rmd
@@ -83,18 +83,34 @@ The function `tableSequenceRatios` inputs the result from `summariseSequenceRati
 tableSequenceRatios(result = result)
 ```
 
-By default, it has many columns such as Index (name), Marker (name), Study population, CSR and ASR, each of these columns could be suppressed with relevant parameters. For example if one wants to not display study population, one could do the following: 
-
 ## Arguments used to suppress columns
 
+By default, it has many columns such as Index (name), Marker (name), Study population, CSR and ASR, some of these columns could be suppressed with relevant parameters. For example if one wants to not display study population, one could do the following: 
+
 ```{r message= FALSE, warning=FALSE}
 tableSequenceRatios(result = result,
                     studyPopulation = FALSE)
 ```
 
+Or suppress `cdmName` like so 
+
+```{r message= FALSE, warning=FALSE}
+tableSequenceRatios(result = result,
+                    cdmName = FALSE)
+```
+
+There are also `.options` argument that one may wish to specify. For example, the user can specify a title:
+
+```{r message= FALSE, warning=FALSE}
+tableSequenceRatios(result = result,
+                    .options = list(title = "Title"))
+```
+
+Similarly, `subtitle` and `caption` can also be defined this way.
+
 ## Modify `type`
 
-Instead of a gt table, the user may also want to put the sequence ratio results in a flex table format:
+Instead of a gt table, the user may also want to put the sequence ratio results in a flex table format (the rest of the arguments that we saw for a gt table also applies here):
 
 ```{r message= FALSE, warning=FALSE}
 tableSequenceRatios(result = result,