Merge pull request #69 from OHDSI/populationDiagnostics_paceholder

placeholder for pop diagnostics

NAMESPACE

@@ -9,6 +9,7 @@ export(exportSummarisedResult)
 export(importSummarisedResult)
 export(matchedDiagnostics)
 export(phenotypeDiagnostics)
+export(populationDiagnostics)
 export(settings)
 export(shinyDiagnostics)
 export(summariseAchillesCodeUse)

R/phenotypeDiagnostics.R

@@ -5,6 +5,9 @@
 #' @param databaseDiagnostics If TRUE, database diagnostics will be run.
 #' @param codelistDiagnostics If TRUE, codelist diagnostics will be run.
 #' @param cohortDiagnostics If TRUE, cohort diagnostics will be run.
+#' @param populationDiagnostics If TRUE, population diagnostics will be run.
+#' @param populationSample N of people from the cdm to sample. If NULL no
+#' sampling will be performed
 #' @param matchedDiagnostics If TRUE, cohort to population
 #' diagnostics will be run.
 #' @param nSample The number of people to take a random sample for matching to
@@ -19,8 +22,11 @@ phenotypeDiagnostics <- function(cohort,
                                  databaseDiagnostics = TRUE,
                                  codelistDiagnostics = TRUE,
                                  cohortDiagnostics = TRUE,
+                                 populationDiagnostics = TRUE,
+                                 populationSample = 1000000,
                                  matchedDiagnostics = TRUE,
                                  nSample = 1000) {
+
   cdm <- omopgenerics::cdmReference(cohort)
 
   results <- list()
@@ -36,9 +42,14 @@ phenotypeDiagnostics <- function(cohort,
     cli::cli("Running cohort diagnostics")
     results[["cohort_diag"]] <- cohortDiagnostics(cohort)
   }
+  if (isTRUE(populationDiagnostics)) {
+    cli::cli("Running population diagnostics")
+    results[["pop_diag"]] <- populationDiagnostics(cohort,
+                                                   populationSample = populationSample)
+  }
   if (isTRUE(matchedDiagnostics)) {
     cli::cli("Running matched diagnostics")
-    results[["cohort_to_pop_diag"]] <- matchedDiagnostics(cohort,
+    results[["matched_diag"]] <- matchedDiagnostics(cohort,
       nSample = nSample
     )
   }

R/populationDiagnostics.R

@@ -0,0 +1,19 @@
+
+
+#' Population-level diagnostics
+#'
+#' @param cohort Cohort
+#' @param populationSample N of people from the cdm to sample. If NULL no
+#' sampling will be performed
+#'
+#' @return
+#' @export
+#'
+#' @examples
+populationDiagnostics <- function(cohort,
+                                  populationSample = 1000000) {
+
+cli::cli_inform("populationDiagnostics not yet implemented")
+omopgenerics::emptySummarisedResult()
+
+}

_pkgdown.yml

@@ -12,7 +12,7 @@ reference:
   - matches("phenotypeDiagnostics")
 - subtitle: Run individual diagnostics
 - contents:
-  - matches("databaseDiagnostics|codelistDiagnostics|cohortDiagnostics|matchedDiagnostics")
+  - matches("databaseDiagnostics|codelistDiagnostics|cohortDiagnostics|populationDiagnostics|matchedDiagnostics")
 - subtitle: Visualise results
 - contents:
   - matches("shinyDiagnostics")

tests/testthat/test-populationDiagnostics.R

@@ -0,0 +1,3 @@
+test_that("multiplication works", {
+  expect_equal(2 * 2, 4)
+})