datatable as table type

OHDSI · Feb 7, 2025 · 71fc035 · 71fc035
1 parent 33ca978
commit 71fc035
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Showing 10 changed files with 16 additions and 9 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 0.2.2
+Date: 2025-01-28 15:48:47 UTC
+SHA: 33ca978939eeb706a018033e8cb218563ab3eeed
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -40,6 +40,7 @@ Suggests:
     CodelistGenerator,
     DBI,
     duckdb,
+    DT,
     flextable,
     gt,
     here,

diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,4 @@
+# OmopSketch 0.2.2.900
+
+-   account for int64 in summariseInObservation by @cecicampanile
+-   add "datatable" as possible table type by @cecicampanile
diff --git a/R/tableClinicalRecords.R b/R/tableClinicalRecords.R
@@ -31,7 +31,7 @@ tableClinicalRecords <- function(result,
   # initial checks
   rlang::check_installed("visOmopResults")
   omopgenerics::validateResultArgument(result)
-  omopgenerics::assertChoice(type, choicesTables())
+  omopgenerics::assertChoice(type, visOmopResults::tableType())
 
   # subset to result_type of interest
   result <- result |>

diff --git a/R/tableConceptIdCounts.R b/R/tableConceptIdCounts.R
@@ -10,7 +10,7 @@ tableConceptIdCounts <- function(result,
   # initial checks
   rlang::check_installed("visOmopResults")
   omopgenerics::validateResultArgument(result)
-  omopgenerics::assertChoice(type, choicesTables())
+  omopgenerics::assertChoice(type, visOmopResults::tableType())
 
   # subset to result_type of interest
   result <- result |>

diff --git a/R/tableMissingData.R b/R/tableMissingData.R
@@ -10,7 +10,7 @@ tableMissingData <- function(result,
   # initial checks
   rlang::check_installed("visOmopResults")
   omopgenerics::validateResultArgument(result)
-  omopgenerics::assertChoice(type, choicesTables())
+  omopgenerics::assertChoice(type, visOmopResults::tableType())
 
   # subset to result_type of interest
   result <- result |>

diff --git a/R/tableObservationPeriod.R b/R/tableObservationPeriod.R
@@ -19,7 +19,7 @@ tableObservationPeriod <- function(result,
   # initial checks
   rlang::check_installed("visOmopResults")
   omopgenerics::validateResultArgument(result)
-  omopgenerics::assertChoice(type, choicesTables())
+  omopgenerics::assertChoice(type, visOmopResults::tableType())
 
   # subset to result_type of interest
   result <- result |>

diff --git a/R/tableOmopSnapshot.R b/R/tableOmopSnapshot.R
@@ -20,7 +20,7 @@ tableOmopSnapshot <- function(result,
   # initial checks
   rlang::check_installed("visOmopResults")
   omopgenerics::validateResultArgument(result)
-  omopgenerics::assertChoice(type, choicesTables())
+  omopgenerics::assertChoice(type, visOmopResults::tableType())
 
   # subset to result_type of interest
   result <- result |>
@@ -64,9 +64,7 @@ emptyTable <- function(type) {
     "flextable" = flextable::flextable(x)
   )
 }
-choicesTables <- function() {
-  c("tibble", "flextable", "gt")
-}
+
 formatColumn <- function(result, col) {
   for (x in col) {
     result <- result |>

diff --git a/tests/testthat/test-summariseClinicalRecords.R b/tests/testthat/test-summariseClinicalRecords.R
@@ -282,7 +282,7 @@ test_that("tableClinicalRecords() works", {
   expect_true(inherits(y,"gt_tbl"))
   expect_warning(t <- summariseClinicalRecords(cdm, "death"))
   expect_warning(inherits(tableClinicalRecords(t),"gt_tbl"))
-
+  expect_no_error(x <- tableClinicalRecords(summariseClinicalRecords(cdm, "condition_occurrence"), type = "datatable"))
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
 

diff --git a/tests/testthat/test-summariseObservationPeriod.R b/tests/testthat/test-summariseObservationPeriod.R
@@ -160,6 +160,7 @@ test_that("check summariseObservationPeriod works", {
 
   # table works
   expect_no_error(tableObservationPeriod(resAll))
+  expect_no_error(tableObservationPeriod(resAll, type = "datatable"))
   expect_no_error(tableObservationPeriod(resOne))
   expect_no_error(tableObservationPeriod(resEmpty))
-Original file line number
+Diff line change
@@ Expand Up / @@ -40,6 +40,7 @@ Suggests: @@
         CodelistGenerator,
         DBI,
         duckdb,
+        DT,
         flextable,
         gt,
         here,
@@ Expand Down @@