0.8.0 release

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DrugUtilisation
 Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP 
     Common Data Model 
-Version: 0.7.1
+Version: 0.8.0
 Authors@R: c(
     person(
         "Martí", "Català", email = "[email protected]", 
@@ -67,7 +67,8 @@ Suggests:
     ggtext,
     scales,
     DBI,
-    bit64
+    bit64,
+    visOmopResults (>= 0.5.0)
 Config/testthat/edition: 3
 Imports: 
     CDMConnector (>= 1.4.0),
@@ -81,7 +82,6 @@ Imports:
     PatientProfiles (>= 1.0.0),
     purrr,
     omopgenerics (>= 0.4.0),
-    visOmopResults (>= 0.5.0),
     lifecycle,
     stringr
 Depends: 

NEWS.md

@@ -1,3 +1,33 @@
+# DrugUtilisation 0.8.0
+
+* Account for omopgenerics 0.4.0 by @catalamarti
+* Add argument ... to generateATC/IngredientCohortSet by @catalamarti
+* benchmarkDrugUtilisation to test all functions by @MimiYuchenGuo
+* Add messages about dropped records in cohort creation by @catalamarti
+* Refactor of table functions following visOmopResults 0.5.0 release by @catalamart
+* Add confidence intervals to PPC by @catalamarti
+* Cast settings to characters by @catalamarti
+* checkVersion utility function for tables and plots by @catalamarti
+* Export erafyCohort by @catalamarti
+* Deprecation warnings to errors for deprecated arguments in geenrateDrugUtilisation by @catalamarti
+* Add numberExposures and daysPrescribed to generate functions by @catalamarti
+* Add subsetCohort and subsetCohortId arguments to cohort creation functions by @catalamarti
+* New function: addDrugRestart by @catalamarti
+* Add initialExposureDuration by @catalamarti
+* Add message if too many indications by @catalamarti
+* not treated -> untreated by @catalamarti
+* warn overwrite columns by @catalamarti
+* Use omopgenerics assert function by @catalamarti
+* add documentation helpers for consistent argument documentation by @catalamarti
+* allow integer64 in sampleSize by @catalamarti
+* add cohortId to summarise* functions by @catalamarti
+* Fix cast warning in mock by @catalamarti
+* addDaysPrescribed by @catalamarti
+* exposedTime -> daysExposed by @catalamarti
+* test addDaysPrescribed by @catalamarti
+* plotDrugUtilisation by @catalamarti
+* refactor plots to use visOmopResults plot tools by @catalamarti
+
 # DrugUtilisation 0.7.0
 
 * Deprecate dose specific functions: `addDailyDose`, `addRoute`, 

R/addIntersect.R

@@ -34,8 +34,8 @@
 #' @param mutuallyExclusive Whether to consider mutually exclusive categories
 #' (one column per window) or not (one column per window and indication).
 #' @param nameStyle Name style for the indications. By default:
-#' 'indication_{window_name}' (mutuallyExclusive = TRUE),
-#' 'indication_{window_name}_{cohort_name}' (mutuallyExclusive = FALSE).
+#' 'indication_\{window_name\}' (mutuallyExclusive = TRUE),
+#' 'indication_\{window_name\}_\{cohort_name\}' (mutuallyExclusive = FALSE).
 #' @inheritParams compNameDoc
 #'
 #' @return The original table with a variable added that summarises the
@@ -106,8 +106,8 @@ addIndication <- function(cohort,
 #' @param mutuallyExclusive Whether to consider mutually exclusive categories
 #' (one column per window) or not (one column per window and treatment).
 #' @param nameStyle Name style for the treatment columns. By default:
-#' 'treatment_{window_name}' (mutuallyExclusive = TRUE),
-#' 'treatment_{window_name}_{cohort_name}' (mutuallyExclusive = FALSE).
+#' 'treatment_\{window_name\}' (mutuallyExclusive = TRUE),
+#' 'treatment_\{window_name\}_\{cohort_name\}' (mutuallyExclusive = FALSE).
 #' @inheritParams compNameDoc
 #'
 #' @return The original table with a variable added that summarises the

R/documentationHelpers.R

@@ -99,9 +99,9 @@ NULL
 #' first drug exposure record).
 #' @param cumulativeQuantity Whether to include 'cumulative_quantity' (sum of
 #' the quantity of the different exposures considered in the analysis).
-#' @param initialDailyDose Whether to include 'initial_daily_dose_{unit}'
+#' @param initialDailyDose Whether to include 'initial_daily_dose_\{unit\}'
 #' (daily dose of the first considered prescription).
-#' @param cumulativeDose Whether to include 'cumulative_dose_{unit}' (sum of
+#' @param cumulativeDose Whether to include 'cumulative_dose_\{unit\}' (sum of
 #' the cumulative dose of the analysed drug exposure records).
 #' @param exposedTime deprecated.
 #'

R/erafyCohort.R

@@ -5,7 +5,7 @@
 #' @inheritParams gapEraDoc
 #' @inheritParams cohortIdDoc
 #' @param nameStyle String to create the new names of cohorts. Must contain
-#' '{cohort_name}' if more than one cohort is present and '{gap_era}' if more
+#' '\{cohort_name\}' if more than one cohort is present and '\{gap_era\}' if more
 #' than one gapEra is provided.
 #' @inheritParams newNameDoc
 #'

R/plots.R

@@ -200,6 +200,9 @@ plotDrugUtilisation <- function(result,
                                 plotType = "barplot",
                                 facet = strataColumns(result),
                                 colour = "cohort_name") {
+  rlang::check_installed("visOmopResults")
+  rlang::check_installed("ggplot2")
+
   # initial checks
   result <- omopgenerics::validateResultArgument(result)
   result <- result |>

R/summariseDrugUtilisation.R

@@ -193,7 +193,7 @@ summariseDrugUtilisation <- function(cohort,
       by = "ingredient_id"
     ) |>
     dplyr::select(-c(dplyr::starts_with("additional"))) |>
-    visOmopResults::uniteAdditional(cols = c("concept_set", "ingredient")) |>
+    omopgenerics::uniteAdditional(cols = c("concept_set", "ingredient")) |>
     dplyr::select(dplyr::all_of(omopgenerics::resultColumns())) |>
     dplyr::arrange(.data$result_id, .data$group_name, .data$group_level, .data$strata_name, .data$strata_level) |>
     omopgenerics::newSummarisedResult(settings = dplyr::tibble(

R/tables.R

@@ -319,6 +319,8 @@ dusTable <- function(result,
                      estimateName,
                      type,
                      call = parent.frame()) {
+  rlang::check_installed("visOmopResults")
+
   # check inputs
   result <- omopgenerics::validateResultArgument(result, call = call)
   omopgenerics::assertCharacter(header, null = TRUE, call = call)
@@ -332,7 +334,7 @@ dusTable <- function(result,
 
   # subset to result_type
   result <- result |>
-    visOmopResults::filterSettings(.data$result_type == .env$resultType)
+    omopgenerics::filterSettings(.data$result_type == .env$resultType)
   if (nrow(result) == 0) {
     cli::cli_warn("There are no results with `result_type = {resultType}`")
     return(emptyTable(type))

tests/testthat/test-summariseDrugRestart.R

@@ -94,7 +94,7 @@ test_that("summarise drug restart", {
       switchCohortId = 1:2,
       followUpDays = c(10)
     )
-  expect_true(all(visOmopResults::strataColumns(resultsStra) == c("age_group", "sex")))
+  expect_true(all(omopgenerics::strataColumns(resultsStra) == c("age_group", "sex")))
 
   # restrict
   restrict <- cdm$dus_cohort |>

tests/testthat/test-summariseDrugUtilisation.R

@@ -57,7 +57,7 @@ test_that("summariseDrugUtilisation works", {
   expect_true(all(sort(unique(x0$variable_name)) == sort(variables)))
   expect_true(all(unique(x0$variable_level) %in% c(NA, "milligram")))
   expect_true(settings(x0)$result_type == "summarise_drug_utilisation")
-  expect_true(all(visOmopResults::additionalColumns(x0) == c("concept_set", "ingredient")))
+  expect_true(all(omopgenerics::additionalColumns(x0) == c("concept_set", "ingredient")))
   expect_true(
     x0 |> dplyr:::filter(grepl("dose", variable_name)) |> dplyr::pull("additional_level") |> unique() == "ingredient_1125315_descendants &&& acetaminophen"
   )
@@ -80,7 +80,7 @@ test_that("summariseDrugUtilisation works", {
     )
   ))
   expect_true(settings(x1)$result_type == "summarise_drug_utilisation")
-  expect_true(all(x1 |> visOmopResults::strataColumns() == c("sex")))
+  expect_true(all(x1 |> omopgenerics::strataColumns() == c("sex")))
 
   # concept
   codelist <- CodelistGenerator::getDrugIngredientCodes(cdm, name = "acetaminophen")