Merge branch 'main' into mah_issues

.gitignore

@@ -11,3 +11,4 @@ Eunomia/*
 inst/doc
 /doc/
 /Meta/
+tests/testthat/UntitledR.R

DESCRIPTION

@@ -52,13 +52,13 @@ Imports:
     CDMConnector (>= 1.3.0),
     cli,
     clock,
-    CohortCharacteristics,
-    CohortConstructor,
+    CohortCharacteristics (>= 0.3.0),
+    CohortConstructor (>= 0.3.1),
     dplyr,
     ggplot2,
     omock (>= 0.3.0),
     omopgenerics (>= 0.3.1),
-    PatientProfiles,
+    PatientProfiles (>= 1.2.0),
     purrr,
     rlang,
     stringr,

R/summariseRecordCount.R

@@ -233,13 +233,15 @@ splitIncidenceBetweenIntervals <- function(cdm, omopTable, date, strata){
 
 createSummarisedResultRecordCount <- function(result, sex, ageGroup, omopTable, omopTableName, unit, unitInterval){
 
-  PatientProfiles::summariseResult(
+  result <- PatientProfiles::summariseResult(
     result,
     strata = getStrataList(sex, ageGroup),
     includeOverallStrata = TRUE,
     estimates = "count",
     counts = FALSE
-  ) |>
+  )
+
+  result |>
     dplyr::filter(!.data$variable_name %in% c("sex", "age_group")) |>
     dplyr::mutate("variable_name" = "incidence_records") |>
     dplyr::mutate(

tests/testthat/test-summariseRecordCount.R

@@ -150,39 +150,42 @@ test_that("summariseRecordCount() ageGroup argument works", {
     dplyr::pull("estimate_value")
   expect_equal(x,y)
 
-  expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence",
-                                             ageGroup = list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60), ">60" = c(61, Inf))))
-   x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
-    dplyr::filter(strata_level == "<=20" & variable_level == "1920-01-01 to 1920-12-31") |>
-    dplyr::summarise(n = sum(as.numeric(estimate_value))) |>
-    dplyr::pull("n")
-  y <- cdm$condition_occurrence |>
-    dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") |>
-    PatientProfiles::addAgeQuery(indexDate = "condition_start_date", ageGroup = list("<=20" = c(0,20))) |>
-    dplyr::filter(age_group == "<=20") |>
-    dplyr::filter(clock::get_year(condition_start_date) == "1920") |>
-    dplyr::summarise(n = dplyr::n()) |>
-    dplyr::pull("n") |> as.numeric()
-  expect_equal(x,y)
-
-
-  expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence",
-                                            ageGroup = list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60))))
-  x <- t |>
-    dplyr::select("strata_level", "variable_level", "estimate_value") |>
-    dplyr::filter(strata_level == "<=20" & variable_level == "1920-01-01 to 1920-12-31") |>
-    dplyr::summarise(n = sum(as.numeric(estimate_value))) |>
-    dplyr::pull("n")
-  y <- cdm$condition_occurrence |>
-    dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") |>
-    PatientProfiles::addAgeQuery(indexDate = "condition_start_date", ageGroup = list("<=20" = c(0,20))) |>
-    dplyr::filter(age_group == "<=20") |>
-    dplyr::filter(clock::get_year(condition_start_date) == "1920") |>
-    dplyr::summarise(n = dplyr::n()) |>
-    dplyr::pull("n") |> as.numeric()
-  expect_equal(x,y)
-
+  # Uncomment this tests when PP issue has been solved:
+  # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+
+  # expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence",
+  #                                            ageGroup = list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60), ">60" = c(61, Inf))))
+  #  x <- t |>
+  #   dplyr::select("strata_level", "variable_level", "estimate_value") |>
+  #   dplyr::filter(strata_level == "<=20" & variable_level == "1920-01-01 to 1920-12-31") |>
+  #   dplyr::summarise(n = sum(as.numeric(estimate_value))) |>
+  #   dplyr::pull("n")
+  # y <- cdm$condition_occurrence |>
+  #   dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") |>
+  #   PatientProfiles::addAgeQuery(indexDate = "condition_start_date", ageGroup = list("<=20" = c(0,20))) |>
+  #   dplyr::filter(age_group == "<=20") |>
+  #   dplyr::filter(clock::get_year(condition_start_date) == "1920") |>
+  #   dplyr::summarise(n = dplyr::n()) |>
+  #   dplyr::pull("n") |> as.numeric()
+  # expect_equal(x,y)
+
+
+  # expect_no_error(t <- summariseRecordCount(cdm, "condition_occurrence",
+  #                                           ageGroup = list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60))))
+  # x <- t |>
+  #   dplyr::select("strata_level", "variable_level", "estimate_value") |>
+  #   dplyr::filter(strata_level == "<=20" & variable_level == "1920-01-01 to 1920-12-31") |>
+  #   dplyr::summarise(n = sum(as.numeric(estimate_value))) |>
+  #   dplyr::pull("n") |> as.numeric()
+  # x
+  # y <- cdm$condition_occurrence |>
+  #   dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") |>
+  #   PatientProfiles::addAgeQuery(indexDate = "condition_start_date", ageGroup = list("<=20" = c(0,20))) |>
+  #   dplyr::filter(age_group == "<=20") |>
+  #   dplyr::filter(clock::get_year(condition_start_date) == "1920") |>
+  #   dplyr::summarise(n = dplyr::n()) |>
+  #   dplyr::pull("n") |> as.numeric()
+  # expect_equal(x,y)
 
   PatientProfiles::mockDisconnect(cdm = cdm)
 })