Change ompTable name

OHDSI · Jul 23, 2024 · b345049 · b345049
1 parent 7a04a27
commit b345049
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Showing 3 changed files with 30 additions and 30 deletions.
diff --git a/R/summariseOmopTable.R → R/summariseClinicalRecords.R b/R/summariseOmopTable.R → R/summariseClinicalRecords.R
@@ -18,7 +18,7 @@
 #'
 #' @export
 #'
-summariseOmopTable <- function(omopTable,
+summariseClinicalTables <- function(omopTable,
                                recordsPerPerson = c("mean", "sd", "median", "q25", "q75", "min", "max"),
                                inObservation = TRUE,
                                standardConcept = TRUE,

diff --git a/R/tableOmopTable.R → R/tableClinicalRecords.R b/R/tableOmopTable.R → R/tableClinicalRecords.R
@@ -1,21 +1,21 @@
 #' Create a gt table from a summarised omop_table.
 #'
-#' @param summarisedOmopTable A summarised_result object with the output from summariseOmopTable().
+#' @param summarisedClinicalRecords A summarised_result object with the output from summariseOmopTable().
 #'
 #' @return A gt object with the summarised data.
 #'
 #' @export
 #'
-tableOmopTable <- function(summarisedOmopTable) {
+tableClinicalRecords <- function(summarisedClinicalRecords) {
 
   # Initial checks ----
-  assertClass(summarisedOmopTable, "summarised_result")
+  assertClass(summarisedClinicalRecords, "summarised_result")
 
-  if(summarisedOmopTable |> dplyr::tally() |> dplyr::pull("n") == 0){
-    cli::cli_warn("summarisedOmopTable is empty.")
+  if(summarisedClinicalRecords |> dplyr::tally() |> dplyr::pull("n") == 0){
+    cli::cli_warn("summarisedClinicalRecords is empty.")
 
     return(
-      summarisedOmopTable |>
+      summarisedClinicalRecords |>
       visOmopResults::splitGroup() |>
       visOmopResults::formatHeader(header = "cdm_name") |>
       dplyr::select(-c("estimate_type", "result_id",
@@ -29,7 +29,7 @@ tableOmopTable <- function(summarisedOmopTable) {
     )
   }
 
-  t <- summarisedOmopTable |>
+  t <- summarisedClinicalRecords |>
     dplyr::mutate(order = dplyr::case_when(
       variable_name == "Number of subjects"  ~ 1,
       variable_name == "Number of records" ~ 2,

diff --git a/tests/testthat/test-summariseOmopTable.R → .../testthat/test-summariseClinicalRecords.R b/tests/testthat/test-summariseOmopTable.R → .../testthat/test-summariseClinicalRecords.R
@@ -1,4 +1,4 @@
-test_that("summariseOmopTable() works", {
+test_that("summariseClinicalRecords() works", {
 
   # Load mock database ----
   con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
@@ -7,50 +7,50 @@ test_that("summariseOmopTable() works", {
   )
 
   # Check all tables work ----
-  expect_true(inherits(summariseOmopTable(cdm$observation_period),"summarised_result"))
-  expect_no_error(summariseOmopTable(cdm$observation_period))
-  expect_no_error(summariseOmopTable(cdm$visit_occurrence))
-  expect_no_error(summariseOmopTable(cdm$condition_occurrence))
-  expect_no_error(summariseOmopTable(cdm$drug_exposure))
-  expect_no_error(summariseOmopTable(cdm$procedure_occurrence))
-  expect_warning(summariseOmopTable(cdm$device_exposure))
-  expect_no_error(summariseOmopTable(cdm$measurement))
-  expect_no_error(summariseOmopTable(cdm$observation))
-  expect_warning(summariseOmopTable(cdm$death))
+  expect_true(inherits(summariseClinicalRecords(cdm$observation_period),"summarised_result"))
+  expect_no_error(summariseClinicalRecords(cdm$observation_period))
+  expect_no_error(summariseClinicalRecords(cdm$visit_occurrence))
+  expect_no_error(summariseClinicalRecords(cdm$condition_occurrence))
+  expect_no_error(summariseClinicalRecords(cdm$drug_exposure))
+  expect_no_error(summariseClinicalRecords(cdm$procedure_occurrence))
+  expect_warning(summariseClinicalRecords(cdm$device_exposure))
+  expect_no_error(summariseClinicalRecords(cdm$measurement))
+  expect_no_error(summariseClinicalRecords(cdm$observation))
+  expect_warning(summariseClinicalRecords(cdm$death))
 
 
   # Check inputs ----
-  expect_true(summariseOmopTable(cdm$condition_occurrence,
+  expect_true(summariseClinicalRecords(cdm$condition_occurrence,
                                  recordsPerPerson = NULL) |>
                 dplyr::filter(variable_name %in% "records_per_person") |>
                 dplyr::tally() |>
                 dplyr::pull() == 0)
-  expect_true(summariseOmopTable(cdm$condition_occurrence,
+  expect_true(summariseClinicalRecords(cdm$condition_occurrence,
                                  inObservation = FALSE) |>
                 dplyr::filter(variable_name %in% "In observation") |>
                 dplyr::tally() |>
                 dplyr::pull() == 0)
-  expect_true(summariseOmopTable(cdm$condition_occurrence,
+  expect_true(summariseClinicalRecords(cdm$condition_occurrence,
                                  standardConcept = FALSE) |>
                 dplyr::filter(variable_name %in% "Standard concept") |>
                 dplyr::tally() |>
                 dplyr::pull() == 0)
-  expect_true(summariseOmopTable(cdm$condition_occurrence,
+  expect_true(summariseClinicalRecords(cdm$condition_occurrence,
                                  sourceVocabulary = FALSE) |>
                 dplyr::filter(variable_name %in% "Source vocabulary") |>
                 dplyr::tally() |>
                 dplyr::pull() == 0)
-  expect_true(summariseOmopTable(cdm$condition_occurrence,
+  expect_true(summariseClinicalRecords(cdm$condition_occurrence,
                                  domainId = FALSE) |>
                 dplyr::filter(variable_name %in% "Domain") |>
                 dplyr::tally() |>
                 dplyr::pull() == 0)
-  expect_true(summariseOmopTable(cdm$condition_occurrence,
+  expect_true(summariseClinicalRecords(cdm$condition_occurrence,
                                  typeConcept = FALSE) |>
                 dplyr::filter(variable_name %in% "Type concept id") |>
                 dplyr::tally() |>
                 dplyr::pull() == 0)
-  expect_true(summariseOmopTable(cdm$condition_occurrence,
+  expect_true(summariseClinicalRecords(cdm$condition_occurrence,
                                  recordsPerPerson = NULL,
                                  inObservation = FALSE,
                                  standardConcept = FALSE,
@@ -61,18 +61,18 @@ test_that("summariseOmopTable() works", {
 })
 
 
-test_that("tableOmopTable() works", {
+test_that("tableClinicalRecords() works", {
   # Load mock database ----
   con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
   cdm <- CDMConnector::cdmFromCon(
     con = con, cdmSchema = "main", writeSchema = "main"
   )
 
   # Check that works ----
-  expect_no_error(x <- tableOmopTable(summariseOmopTable(cdm$condition_occurrence)))
+  expect_no_error(x <- tableClinicalRecords(summariseClinicalRecords(cdm$condition_occurrence)))
   expect_true(inherits(x,"gt_tbl"))
-  expect_warning(tableOmopTable(summariseOmopTable(cdm$death)))
-  expect_true(inherits(tableOmopTable(summariseOmopTable(cdm$death)),"gt_tbl"))
+  expect_warning(tableClinicalRecords(summariseClinicalRecords(cdm$death)))
+  expect_true(inherits(tableClinicalRecords(summariseClinicalRecords(cdm$death)),"gt_tbl"))
 
 })