Merge pull request #307 from OHDSI/documentation-helpers

updates documentation of dateRange
OHDSI · Jan 28, 2025 · ec80c69 · ec80c69
2 parents 03f1979 + 06701b8
commit ec80c69
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -73,7 +73,7 @@ Imports:
     tibble,
     tidyr
 Depends: 
-    R (>= 4.1.0)
+    R (>= 4.1)
 URL: https://OHDSI.github.io/OmopSketch/
 BugReports: https://github.com/OHDSI/OmopSketch/issues
 VignetteBuilder: knitr

diff --git a/R/documentationHelper.R b/R/documentationHelper.R
@@ -0,0 +1,12 @@
+# Argument descriptions repeated > 1:
+
+#' Helper for consistent documentation of `dateRange`.
+#'
+#' @param dateRange A vector of two dates defining the desired study period.
+#' Only the `start_date` column of the OMOP table is checked to ensure it falls within this range.
+#' If `dateRange` is `NULL`, no restriction is applied.
+#'
+#'
+#' @name dateRange-startDate
+#' @keywords internal
+NULL
diff --git a/R/summariseClinicalRecords.R b/R/summariseClinicalRecords.R
@@ -22,8 +22,7 @@
 #' @param ageGroup A list of age groups to stratify results by.
 #' @param sex Boolean variable. Whether to stratify by sex (TRUE) or not
 #' (FALSE).
-#' @param dateRange A list containing the minimum and the maximum dates
-#' defining the time range within which the analysis is performed.
+#' @inheritParams dateRange-startDate
 #' @return A summarised_result object.
 #' @export
 #' @examples

diff --git a/R/summariseConceptCounts.R b/R/summariseConceptCounts.R
@@ -12,8 +12,7 @@
 #' @param sex TRUE or FALSE. If TRUE code use will be summarised by sex.
 #' @param ageGroup A list of ageGroup vectors of length two. Code use will be
 #' thus summarised by age groups.
-#' @param dateRange A list containing the minimum and the maximum dates
-#' defining the time range within which the analysis is performed.
+#' @inheritParams dateRange-startDate
 #'
 #' @return A summarised_result object with results overall and, if specified, by
 #' strata.

diff --git a/R/summariseConceptIdCounts.R b/R/summariseConceptIdCounts.R
@@ -12,8 +12,7 @@
 #' thus summarised by age groups.
 #' @param sample An integer to sample the tables to only that number of records.
 #' If NULL no sample is done.
-#' @param dateRange A list containing the minimum and the maximum dates
-#' defining the time range within which the analysis is performed.
+#' @inheritParams dateRange-startDate
 #'
 #' @return A summarised_result object with results overall and, if specified, by
 #' strata.

diff --git a/R/summariseConceptSetCounts.R b/R/summariseConceptSetCounts.R
@@ -10,8 +10,7 @@
 #' @param sex TRUE or FALSE. If TRUE code use will be summarised by sex.
 #' @param ageGroup A list of ageGroup vectors of length two. Code use will be
 #' thus summarised by age groups.
-#' @param dateRange A list containing the minimum and the maximum dates
-#' defining the time range within which the analysis is performed.
+#' @inheritParams dateRange-startDate
 #' @return A summarised_result object with results overall and, if specified, by
 #' strata.
 #' @export

diff --git a/R/summariseInObservation.R b/R/summariseInObservation.R
@@ -10,8 +10,7 @@
 #' @param ageGroup A list of age groups to stratify results by.
 #' @param sex Boolean variable. Whether to stratify by sex (TRUE) or not
 #' (FALSE).
-#' @param dateRange A list containing the minimum and the maximum dates
-#' defining the time range within which the analysis is performed.
+#' @inheritParams dateRange-startDate
 #' @return A summarised_result object.
 #' @export
 #' @examples

diff --git a/R/summariseMissingData.R b/R/summariseMissingData.R
@@ -11,8 +11,7 @@
 #' thus summarised by age groups.
 #' @param sample An integer to sample the table to only that number of records.
 #' If NULL no sample is done.
-#' @param dateRange A list containing the minimum and the maximum dates
-#' defining the time range within which the analysis is performed.
+#' @inheritParams dateRange-startDate
 #'
 #' @return A summarised_result object with results overall and, if specified, by
 #' strata.

diff --git a/R/summariseObservationPeriod.R b/R/summariseObservationPeriod.R
@@ -8,8 +8,7 @@
 #' @param ageGroup A list of age groups to stratify results by.
 #' @param sex Boolean variable. Whether to stratify by sex (TRUE) or not
 #' (FALSE).
-#' @param dateRange A list containing the minimum and the maximum dates
-#' defining the time range within which the analysis is performed.
+#' @inheritParams dateRange-startDate
 #'
 #' @return A summarised_result object with the summarised data.
 #'

diff --git a/R/summariseRecordCount.R b/R/summariseRecordCount.R
@@ -7,8 +7,7 @@
 #' @param interval Time interval to stratify by. It can either be "years", "quarters", "months" or "overall".
 #' @param ageGroup A list of age groups to stratify results by.
 #' @param sex Whether to stratify by sex (TRUE) or not (FALSE).
-#' @param dateRange A list containing the minimum and the maximum dates
-#' defining the time range within which the analysis is performed.
+#' @inheritParams dateRange-startDate
 #' @param sample An integer to sample the tables to only that number of records.
 #' If NULL no sample is done.
 #' @return A summarised_result object.

diff --git a/man/dateRange-startDate.Rd b/man/dateRange-startDate.Rd
diff --git a/man/summariseClinicalRecords.Rd b/man/summariseClinicalRecords.Rd
diff --git a/man/summariseConceptCounts.Rd b/man/summariseConceptCounts.Rd
diff --git a/man/summariseConceptIdCounts.Rd b/man/summariseConceptIdCounts.Rd
diff --git a/man/summariseConceptSetCounts.Rd b/man/summariseConceptSetCounts.Rd
diff --git a/man/summariseInObservation.Rd b/man/summariseInObservation.Rd
diff --git a/man/summariseMissingData.Rd b/man/summariseMissingData.Rd
diff --git a/man/summariseObservationPeriod.Rd b/man/summariseObservationPeriod.Rd
diff --git a/man/summariseRecordCount.Rd b/man/summariseRecordCount.Rd
diff --git a/tests/testthat/test-summariseConceptSetCounts.R b/tests/testthat/test-summariseConceptSetCounts.R
@@ -562,26 +562,26 @@ test_that("dateRange argument works", {
 test_that("interval argument works", {
   skip_on_cran()
   # Load mock database ----
-  cdm <- mockOmopSketch()
-  expect_no_error(y<-summariseConceptSetCounts(list(ANTIHISTAMINES= c(21603444)),
+  cdm <- cdmEunomia()
+  expect_no_error(y<-summariseConceptSetCounts(list("polio" = c(40213160)),
                          cdm = cdm,
                          interval = "years"))
 
-  expect_no_error(o<-summariseConceptSetCounts(list(ANTIHISTAMINES= c(21603444)),
+  expect_no_error(o<-summariseConceptSetCounts(list("polio" = c(40213160)),
                                             cdm = cdm,
                                             interval = "overall"))
-  expect_no_error(q<-summariseConceptSetCounts(list(ANTIHISTAMINES= c(21603444)),
+  expect_no_error(q<-summariseConceptSetCounts(list("polio" = c(40213160)),
                                             cdm = cdm,
                                             interval = "quarters"))
-  expect_no_error(m<-summariseConceptSetCounts(list(ANTIHISTAMINES= c(21603444)),
+  expect_no_error(m<-summariseConceptSetCounts(list("polio" = c(40213160)),
                                             cdm = cdm,
                                             interval = "months"))
 
 
 
   m_quarters <- m|>omopgenerics::splitAdditional()|>
     omopgenerics::pivotEstimates() |>
-    dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 21603444) |>
+    dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 40213160) |>
     dplyr::mutate(
       start_date = as.Date(sub(" to .*", "", time_interval)),
       quarter_start = lubridate::quarter(start_date, type = "date_first"),
@@ -596,15 +596,15 @@ test_that("interval argument works", {
 
   q_quarters <- q|>omopgenerics::splitAdditional()|>
    omopgenerics::pivotEstimates()|>
-   dplyr::filter(time_interval != "overall" & variable_name == "Number records"& standard_concept_id == 21603444)|>
+   dplyr::filter(time_interval != "overall" & variable_name == "Number records"& standard_concept_id == 40213160)|>
    dplyr::select(time_interval, count)|>
    dplyr::arrange(time_interval)
 
   expect_equal(m_quarters, q_quarters)
 
   m_year <- m|>
    omopgenerics::splitAdditional()|>
-   dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 21603444)|>
+   dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 40213160)|>
    dplyr::mutate(
      # Extract the start date
      start_date = clock::date_parse(stringr::str_extract(time_interval, "^\\d{4}-\\d{2}-\\d{2}")),
@@ -620,7 +620,7 @@ test_that("interval argument works", {
    dplyr::arrange(year)
   y_year <- y|>
    omopgenerics::splitAdditional()|>
-   dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 21603444)|>
+   dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 40213160)|>
    dplyr::mutate(
      # Extract the start date
      start_date = clock::date_parse(stringr::str_extract(time_interval, "^\\d{4}-\\d{2}-\\d{2}")),
@@ -633,7 +633,7 @@ test_that("interval argument works", {
 
   expect_equal(m_year, y_year)
   o <- o |> omopgenerics::splitAdditional()|>
-   dplyr::filter(variable_name == "Number records" & standard_concept_id == 21603444)|>
+   dplyr::filter(variable_name == "Number records" & standard_concept_id == 40213160)|>
    omopgenerics::pivotEstimates()|>
    dplyr::select(count)
 
@@ -642,7 +642,7 @@ test_that("interval argument works", {
 
   q_year <- q|>
    omopgenerics::splitAdditional()|>
-   dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 21603444)|>
+   dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 40213160)|>
    dplyr::mutate(
      # Extract the start date
      start_date = clock::date_parse(stringr::str_extract(time_interval, "^\\d{4}-\\d{2}-\\d{2}")),