Merge pull request #174 from OHDSI/mah_mockPhenotypeR

Create mockPhenotypeR() and use it in function examples

DESCRIPTION

@@ -47,7 +47,6 @@ Suggests:
     shinyWidgets,
     plotly,
     tidyr,
-    ggpol,
     scales
 Config/testthat/edition: 3
 RoxygenNote: 7.3.2

NAMESPACE

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

R/addCodelistAttribute.R

@@ -18,23 +18,11 @@
 #'
 #' @examples
 #' \donttest{
-#' library(omock)
-#' library(CDMConnector)
-#' library(DBI)
 #' library(PhenotypeR)
 #'
-#' cdm_local <- mockCdmReference() |>
-#'  mockPerson(nPerson = 100) |>
-#'  mockObservationPeriod() |>
-#'  mockCohort()
+#' cdm <- mockPhenotypeR()
 #'
-#' con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
-#' cdm <- CDMConnector::copy_cdm_to(con = con,
-#'                                 cdm = cdm_local,
-#'                                  schema = "main")
-#' attr(cdm, "write_schema") <- "main"
-#'
-#' cohort <- addCodelistAttribute(cohort = cdm$cohort, codelist = list("cohort_1" = 1L))
+#' cohort <- addCodelistAttribute(cohort = cdm$my_cohort, codelist = list("cohort_1" = 1L))
 #' attr(cohort, "cohort_codelist")
 #'
 #' CDMConnector::cdm_disconnect(cdm)

R/codelistDiagnostics.R

@@ -18,29 +18,16 @@
 #'
 #' @examples
 #' \donttest{
-#' library(omock)
-#' library(CDMConnector)
-#' library(DBI)
 #' library(CohortConstructor)
 #' library(PhenotypeR)
 #'
-#' cdm_local <- mockCdmReference() |>
-#'   mockPerson(nPerson = 100) |>
-#'   mockObservationPeriod() |>
-#'   mockConditionOccurrence()
-#'
-#' con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
-#' cdm <- CDMConnector::copy_cdm_to(con = con,
-#'                                  cdm = cdm_local,
-#'                                  schema = "main")
-#' attr(cdm, "write_schema") <- "main"
+#' cdm <- mockPhenotypeR()
 #'
 #' cdm$arthropathies <- conceptCohort(cdm,
 #'                                    conceptSet = list("arthropathies" = c(40475132)),
 #'                                    name = "arthropathies")
 #'
-#' result <- cdm$arthropathies |>
-#'  codelistDiagnostics()
+#' result <- codelistDiagnostics(cdm$arthropathies)
 #'
 #' CDMConnector::cdmDisconnect(cdm = cdm)
 #' }

R/cohortDiagnostics.R

@@ -16,25 +16,11 @@
 #'
 #' @examples
 #' \donttest{
-#' library(omock)
-#' library(CDMConnector)
-#' library(DBI)
 #' library(PhenotypeR)
 #'
-#' cdm_local <- mockCdmReference() |>
-#'   mockPerson(nPerson = 100) |>
-#'   mockObservationPeriod() |>
-#'   mockConditionOccurrence() |>
-#'   mockVisitOccurrence() |>
-#'   mockCohort(name = "my_cohort")
+#' cdm <- mockPhenotypeR()
 #'
-#' con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
-#' cdm <- CDMConnector::copy_cdm_to(con = con,
-#'                                  cdm = cdm_local,
-#'                                  schema = "main")
-#' attr(cdm, "write_schema") <- "main"
-#'
-#' cdm$my_cohort |> cohortDiagnostics()
+#' result <- cohortDiagnostics(cdm$my_cohort)
 #'
 #' CDMConnector::cdmDisconnect(cdm = cdm)
 #' }

R/databaseDiagnostics.R

@@ -14,27 +14,12 @@
 #'
 #' @examples
 #' \donttest{
-#' library(omock)
-#' library(CDMConnector)
-#' library(DBI)
 #' library(PhenotypeR)
 #'
-#' cdm_local <- mockCdmReference() |>
-#'   mockPerson(nPerson = 100) |>
-#'   mockObservationPeriod() |>
-#'   mockConditionOccurrence() |>
-#'   mockDrugExposure() |>
-#'   mockObservation() |>
-#'   mockMeasurement() |>
-#'   mockCohort(name = "my_cohort", numberCohorts = 2)
-#'
-#' con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
-#' cdm <- CDMConnector::copy_cdm_to(con = con,
-#'                                  cdm = cdm_local,
-#'                                  schema = "main")
-#' attr(cdm, "write_schema") <- "main"
-#'
-#' db_diag <- databaseDiagnostics(cdm)
+#' cdm <- mockPhenotypeR()
+#'
+#' result <- databaseDiagnostics(cdm)
+#'
 #' CDMConnector::cdmDisconnect(cdm = cdm)
 #' }
 databaseDiagnostics <- function(cdm){

R/matchedDiagnostics.R

@@ -21,29 +21,12 @@
 #'
 #' @examples
 #' \donttest{
-#' library(omock)
-#' library(CDMConnector)
-#' library(DBI)
 #' library(PhenotypeR)
 #'
-#' cdm_local <- mockCdmReference() |>
-#'   mockPerson(nPerson = 100) |>
-#'  mockObservationPeriod() |>
-#'   mockConditionOccurrence() |>
-#'   mockDrugExposure() |>
-#'   mockObservation() |>
-#'   mockMeasurement() |>
-#'   mockVisitOccurrence() |>
-#'   mockProcedureOccurrence() |>
-#'   mockCohort(name = "my_cohort")
+#' cdm <- mockPhenotypeR()
 #'
-#' con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
-#' cdm <- CDMConnector::copy_cdm_to(con = con,
-#'                                 cdm = cdm_local,
-#'                                  schema = "main")
-#' attr(cdm, "write_schema") <- "main"
+#' result <- matchedDiagnostics(cdm$my_cohort)
 #'
-#' result <- cdm$my_cohort |> matchedDiagnostics()
 #' CDMConnector::cdmDisconnect(cdm = cdm)
 #' }
 matchedDiagnostics <- function(cohort,

R/mockPhenotypeR.R

@@ -0,0 +1,55 @@
+#' Function to create a mock cdm reference for mockPhenotypeR
+#'
+#' @description
+#' `mockPhenotypeR()` creates an example dataset that can be used to show how
+#' the package works
+#'
+#' @param nPerson number of people in the cdm.
+#' @param con  A DBI connection to create the cdm mock object.
+#' @param writeSchema Name of an schema on the same connection with writing
+#' permissions.
+#' @param seed seed to use when creating the mock data.
+#'
+#' @return cdm object
+#' @export
+#'
+#' @examples
+#' \donttest{
+#' library(PhenotypeR)
+#'
+#' cdm <- mockPhenotypeR()
+#'
+#' cdm
+#' }
+mockPhenotypeR <- function(nPerson = 100,
+                           con = DBI::dbConnect(duckdb::duckdb()),
+                           writeSchema = "main",
+                           seed = 111){
+
+  omopgenerics::assertNumeric(nPerson, length = 1, na = FALSE, null = FALSE)
+  omopgenerics::assertNumeric(seed, length = 1, na = FALSE, null = FALSE)
+  omopgenerics::assertCharacter(writeSchema, length = 1, na = FALSE, null = FALSE)
+
+  cdm_local <- omock::mockCdmReference() |>
+    omock::mockPerson(nPerson = 100, seed = seed) |>
+    omock::mockObservationPeriod(seed = seed) |>
+    omock::mockConditionOccurrence(seed = seed) |>
+    omock::mockVisitOccurrence(seed = seed) |>
+    omock::mockDrugExposure(seed = seed) |>
+    omock::mockObservation(seed = seed) |>
+    omock::mockMeasurement(seed = seed) |>
+    omock::mockProcedureOccurrence(seed = seed) |>
+    omock::mockCohort(name = "my_cohort", numberCohorts = 2)
+
+  cdm <- CDMConnector::copy_cdm_to(con = con,
+                                   cdm = cdm_local,
+                                   schema = writeSchema,
+                                   overwrite = TRUE)
+  attr(cdm, "write_schema") <- writeSchema
+
+  return(cdm)
+}
+
+
+
+

R/phenotypeDiagnostics.R

@@ -25,29 +25,12 @@
 #'
 #' @examples
 #' \donttest{
-#' library(omock)
-#' library(CDMConnector)
-#' library(DBI)
 #' library(PhenotypeR)
 #'
-#' cdm_local <- mockCdmReference() |>
-#'   mockPerson(nPerson = 100) |>
-#'   mockObservationPeriod() |>
-#'   mockConditionOccurrence() |>
-#'   mockDrugExposure() |>
-#'   mockObservation() |>
-#'   mockMeasurement() |>
-#'   mockVisitOccurrence() |>
-#'   mockProcedureOccurrence() |>
-#'   mockCohort(name = "my_cohort")
+#' cdm <- mockPhenotypeR()
 #'
-#' con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
-#' cdm <- CDMConnector::copy_cdm_to(con = con,
-#'                                  cdm = cdm_local,
-#'                                  schema = "main")
-#' attr(cdm, "write_schema") <- "main"
+#' result <- phenotypeDiagnostics(cdm$my_cohort)
 #'
-#' result <- cdm$my_cohort |> phenotypeDiagnostics()
 #' CDMConnector::cdmDisconnect(cdm = cdm)
 #' }
 phenotypeDiagnostics <- function(cohort,

R/populationDiagnostics.R

@@ -15,27 +15,10 @@
 #'
 #' @examples
 #' \donttest{
-#' library(omock)
-#' library(CDMConnector)
-#' library(DBI)
 #' library(PhenotypeR)
 #' library(dplyr)
 #'
-#' cdm_local <- mockCdmReference() |>
-#'   mockPerson(nPerson = 1000) |>
-#'   mockObservationPeriod() |>
-#'   mockConditionOccurrence() |>
-#'   mockDrugExposure() |>
-#'   mockObservation() |>
-#'   mockMeasurement() |>
-#'   mockVisitOccurrence() |>
-#'   mockCohort(name = "my_cohort")
-#'
-#' con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
-#' cdm <- CDMConnector::copy_cdm_to(con = con,
-#'                                  cdm = cdm_local,
-#'                                  schema = "main")
-#' attr(cdm, "write_schema") <- "main"
+#' cdm <- mockPhenotypeR()
 #'
 #' dateStart <- cdm$my_cohort |>
 #'   summarise(start = min(cohort_start_date, na.rm = TRUE)) |>
@@ -46,6 +29,7 @@
 #'
 #' result <- cdm$my_cohort |>
 #'   populationDiagnostics(populationDateRange = c(dateStart, dateEnd))
+#'
 #' CDMConnector::cdmDisconnect(cdm = cdm)
 #' }
 populationDiagnostics <- function(cohort,

R/shinyDiagnostics.R

@@ -21,30 +21,11 @@
 #'
 #' @examples
 #' \donttest{
-#' library(omock)
-#' library(CDMConnector)
-#' library(DBI)
 #' library(PhenotypeR)
 #'
-#' cdm_local <- mockCdmReference() |>
-#'   mockPerson(nPerson = 1000) |>
-#'   mockObservationPeriod() |>
-#'   mockConditionOccurrence() |>
-#'   mockDrugExposure() |>
-#'   mockObservation() |>
-#'   mockMeasurement() |>
-#'   mockVisitOccurrence() |>
-#'   mockProcedureOccurrence() |>
-#'   mockCohort(name = "my_cohort")
+#' cdm <- mockPhenotypeR()
 #'
-#' con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
-#' cdm <- CDMConnector::copy_cdm_to(con = con,
-#'                                  cdm = cdm_local,
-#'                                  schema = "main")
-#' attr(cdm, "write_schema") <- "main"
-#'
-#' result <- cdm$my_cohort |>
-#'   phenotypeDiagnostics()
+#' result <- phenotypeDiagnostics(cdm$my_cohort)
 #'
 #' shinyDiagnostics(result, tempdir())
 #'

_pkgdown.yml

@@ -19,3 +19,6 @@ reference:
 - subtitle: Codelist diagnostics helper
 - contents:
   - matches("addCodelistAttribute")
+- subtitle: Mock data
+- contents:
+  - matches("mockPhenotypeR")