pass checks

NAMESPACE

@@ -25,6 +25,7 @@ export(tableMissingData)
 export(tableObservationPeriod)
 export(tableOmopSnapshot)
 importFrom(dplyr,"%>%")
+importFrom(lifecycle,deprecated)
 importFrom(omopgenerics,bind)
 importFrom(omopgenerics,exportSummarisedResult)
 importFrom(omopgenerics,importSummarisedResult)

R/OmopSketch-package.R

@@ -2,10 +2,11 @@
 "_PACKAGE"
 
 ## usethis namespace: start
+#' @importFrom dplyr %>%
+#' @importFrom lifecycle deprecated
+#' @importFrom rlang :=
 #' @importFrom rlang .data
 #' @importFrom rlang .env
-#' @importFrom rlang :=
 #' @importFrom rlang %||%
-#' @importFrom dplyr %>%
 ## usethis namespace: end
 NULL

R/summariseAllConceptCounts.R

@@ -1,22 +1,4 @@
 
-my_getStrataList <- function(sex = FALSE, ageGroup = NULL, year = FALSE){
-  c(names(ageGroup), "sex"[sex], "year"[year])
-}
-checkFeasibility <- function(omopTable, tableName, conceptId) {
-
-  if (omopgenerics::isTableEmpty(omopTable)){
-    cli::cli_warn(paste0(tableName, " omop table is empty."))
-    return(NULL)
-  }
-
-  if (is.na(conceptId)){
-    cli::cli_warn(paste0(tableName, " omop table doesn't contain standard concepts."))
-    return(NULL)
-  }
-
-  return(TRUE)
-}
-
 #' Summarise concept use in patient-level data
 #'
 #' @param cdm A cdm object
@@ -67,35 +49,39 @@ summariseAllConceptCounts <- function(cdm,
   omopgenerics::assertChoice(omopTableName, choices = omopgenerics::omopTables(), unique = TRUE)
   ageGroup <- omopgenerics::validateAgeGroupArgument(ageGroup)
   dateRange <- validateStudyPeriod(cdm, dateRange)
+  omopgenerics::assertNumeric(sample, integerish = TRUE, min = 1, null = TRUE, length = 1)
 
   # settings for the created results
   set <- createSettings(result_type = "summarise_all_concept_counts", study_period = dateRange)
 
   # get strata
-  strata <- my_getStrataList(sex = sex, year = year, ageGroup = ageGroup) |>
-    omopgenerics::combineStrata()
+  strata <- omopgenerics::combineStrata(c(strataCols(sex = sex, ageGroup = ageGroup), "year"[year]))
+  concepts <- c("concept_id", "concept_name")
+  stratax <- c(list(concepts), purrr::map(strata, \(x) c(concepts, x)))
 
   # how to count
   counts <- c("records", "person_id")[c("record", "person") %in% countBy]
 
   # summarise counts
-  resultTables <- purrr::map(omopTableName, function(table) {
-    # check that table is not empty
+  resultTables <- purrr::map(omopTableName, \(table) {
+    # initial table
     omopTable <- dplyr::ungroup(cdm[[table]])
-    conceptId <- standardConcept(table)
-    if (is.null(checkFeasibility(omopTable, table, conceptId))) {
+    conceptId <- omopgenerics::omopColumns(table = table, field = "standard_concept")
+    if (is.na(conceptId)) {
+      cli::cli_warn(c("!" = "No standard concept identified for {table}."))
       return(NULL)
     }
-    prefix <- omopgenerics::tmpPrefix()
 
-    # add concept id to stratification
-    concepts <- c("concept_id", "concept_name")
-    stratax <- c(list(concepts), purrr::map(strata, \(x) c(concepts, x)))
+    prefix <- omopgenerics::tmpPrefix()
 
     # restrict study period
     omopTable <- restrictStudyPeriod(omopTable, dateRange)
     if (is.null(omopTable)) return(NULL)
 
+    # sample table
+    omopTable <- omopTable |>
+      sampleOmopTable(sample = sample, name = omopgenerics::uniqueTableName(prefix))
+
     result <- omopTable |>
       # add concept names
       dplyr::rename(concept_id = dplyr::all_of(conceptId)) |>
@@ -106,7 +92,7 @@ summariseAllConceptCounts <- function(cdm,
       ) |>
       # add demographics and year
       addStratifications(
-        indexDate = startDate(omopgenerics::tableName(omopTable)),
+        indexDate = omopgenerics::omopColumns(table = table, field = "start_date"),
         sex = sex,
         ageGroup = ageGroup,
         interval = dplyr::if_else(year, "years", "overall"),

R/summariseClinicalRecords.R

@@ -57,7 +57,7 @@ summariseClinicalRecords <- function(cdm,
                                      typeConcept = TRUE,
                                      sex = FALSE,
                                      ageGroup = NULL,
-                                     sample = 1000000,
+                                     sample = NULL,
                                      dateRange = NULL) {
   # Initial checks ----
   omopgenerics::validateCdmArgument(cdm)
@@ -78,6 +78,7 @@ summariseClinicalRecords <- function(cdm,
   omopgenerics::assertLogical(typeConcept, length = 1)
   omopgenerics::assertLogical(sex, length = 1)
   ageGroup <- omopgenerics::validateAgeGroupArgument(ageGroup, multipleAgeGroup = FALSE)
+  omopgenerics::assertNumeric(sample, integerish = TRUE, min = 1, null = TRUE, length = 1)
 
   # warnings for observation_period
   warnStandardConcept <- standardConcept & !missing(standardConcept)
@@ -90,7 +91,7 @@ summariseClinicalRecords <- function(cdm,
   # get strata
   strata <- c(
     list(character()),
-    omopgenerics::combineStrata(c(names(ageGroup), "sex"[sex]))
+    omopgenerics::combineStrata(strataCols(sex = sex, ageGroup = ageGroup))
   )
 
   # create denominator for record count
@@ -278,9 +279,6 @@ summariseClinicalRecords <- function(cdm,
   return(result)
 }
 
-getStrataList <- function(sex, ageGroup){
-  omopgenerics::combineStrata(c("age_group"[!is.null(ageGroup)], "sex"[sex]))
-}
 summariseRecordsPerPerson <- function(x, den, strata, estimates) {
   # strata
   strataCols <- unique(unlist(strata))
@@ -394,12 +392,12 @@ addVariables <- function(x, inObservation, standardConcept, sourceVocabulary, do
   newNames <- c(
     # here to support death table
     person_id = "person_id",
-    id = tableId(name),
-    start_date = startDate(name),
-    end_date = endDate(name),
-    standard = standardConcept(name),
-    source = sourceConcept(name),
-    type_concept = typeConcept(name)
+    id = omopgenerics::omopColumns(table = name, field = "unique_id"),
+    start_date = omopgenerics::omopColumns(table = name, field = "start_date"),
+    end_date = omopgenerics::omopColumns(table = name, field = "end_date"),
+    standard = omopgenerics::omopColumns(table = name, field = "standard_concept"),
+    source = omopgenerics::omopColumns(table = name, field = "source_concept"),
+    type_concept = omopgenerics::omopColumns(table = name, field = "type_concept")
   )
 
   newNames <- newNames[!is.na(newNames)]