Merge pull request #385 from OHDSI/og_0.4

Og 0.4
OHDSI · Nov 24, 2024 · a2a0952 · a2a0952
2 parents ea30962 + d5f2048
commit a2a0952
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Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: CohortConstructor
 Title: Build and Manipulate Study Cohorts Using a Common Data Model
-Version: 0.3.2
+Version: 0.3.2.900
 Authors@R: c(
     person("Edward", "Burn", , "[email protected]", 
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9286-1128")),
@@ -35,7 +35,7 @@ Imports:
     dplyr,
     glue,
     magrittr,
-    omopgenerics (>= 0.2.1),
+    omopgenerics (>= 0.4.0),
     PatientProfiles (>= 1.2.0),
     purrr,
     rlang,

diff --git a/data/benchmarkData.rda b/data/benchmarkData.rda
diff --git a/tests/testthat/test-requireDemographics.R b/tests/testthat/test-requireDemographics.R
@@ -439,7 +439,7 @@ test_that("codelist kept with >1 requirement", {
   cdm$cohort1 <- conceptCohort(cdm = cdm, conceptSet = list(a = 1, b = 2), name = "cohort1")
 
   cdm$cohort2 <- cdm$cohort1 |> requireDemographics(name = "cohort2", minPriorObservation = c(0,3), cohortId = 1)
-  expect_identical(attr(cdm$cohort2, "cohort_codelist") |> dplyr::collect() |> dplyr::arrange(.data$cohort_definition_id), dplyr::tibble(
+  expect_equal(attr(cdm$cohort2, "cohort_codelist") |> dplyr::collect() |> dplyr::arrange(.data$cohort_definition_id), dplyr::tibble(
       cohort_definition_id = as.integer(1:3),
       codelist_name = c("a", "b", "a"),
       concept_id = as.integer(c(1, 2, 1)),

diff --git a/vignettes/a11_benchmark.Rmd b/vignettes/a11_benchmark.Rmd
@@ -30,6 +30,7 @@ library(tidyr)
 library(gt)
 library(scales)
 library(CohortConstructor)
+library(gt)
 
 niceOverlapLabels <- function(labels) {
   new_labels <- gsub("_", " ", gsub(" and.*|cc_", "", labels))
@@ -213,7 +214,7 @@ The table below depicts the total time it took to create the nine cohorts when u
 ```{r}
 header_prefix <- "[header]Time by tool (minutes)\n[header_level]"
 benchmarkData$time_domain |>
-  gtTable(colsToMergeRows = "all_columns") |>
+  formatTable() |> 
   tab_style(style = list(cell_fill(color = "#e1e1e1"), cell_text(weight = "bold")), 
             locations = cells_column_labels()) |>
   tab_style(style = list(cell_text(weight = "bold")), 
@@ -226,7 +227,7 @@ Cohorts are often stratified in studies. With Atlas cohort definitions, each str
 
 ```{r}
 benchmarkData$time_strata |>
-  gtTable(colsToMergeRows = "all_columns") |>
+  formatTable() |>
   tab_style(style = list(cell_fill(color = "#e1e1e1"), cell_text(weight = "bold")), 
             locations = cells_column_labels()) |>
   tab_style(style = list(cell_text(weight = "bold")),