use clock package

OHDSI · Jul 25, 2024 · b3b7d5a · b3b7d5a
1 parent a0fd274
commit b3b7d5a
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Showing 5 changed files with 22 additions and 18 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -39,7 +39,8 @@ Imports:
     stringr,
     tibble,
     tidyr,
-    visOmopResults
+    visOmopResults,
+    clock
 Depends: 
     R (>= 2.10)
 URL: https://oxford-pharmacoepi.github.io/OmopSketch/

diff --git a/R/summariseInObservation.R b/R/summariseInObservation.R
@@ -112,8 +112,8 @@ countRecords <- function(observationPeriod, cdm, start_date_name, end_date_name,
   tablePrefix <- omopgenerics::tmpPrefix()
 
   x <- observationPeriod %>%
-    dplyr::mutate("start" = lubridate::floor_date(.data[[start_date_name]], unit = "month")) |>
-    dplyr::mutate("end"   = lubridate::floor_date(.data[[end_date_name]], unit = "month")) |>
+    dplyr::mutate("start" = as.Date(paste0(clock::get_year(.data[[start_date_name]]),"/",clock::get_month(.data[[start_date_name]]),"/01"))) |>
+    dplyr::mutate("end"   = as.Date(paste0(clock::get_year(.data[[start_end_name]]),"/",clock::get_month(.data[[start_end_name]]),"/01"))) |>
     dplyr::group_by(.data$start, .data$end, .data$sex) |>
     dplyr::summarise(n = dplyr::n()) |>
     dplyr::compute(

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -1,6 +1,7 @@
 on_cran <- function() {
   !interactive() && !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
 }
+
 if (!on_cran()) {
   withr::local_envvar(
     R_USER_CACHE_DIR = tempfile(),
@@ -9,3 +10,5 @@ if (!on_cran()) {
   )
   CDMConnector::downloadEunomiaData(overwrite = TRUE)
 }
+
+
diff --git a/tests/testthat/test-summariseInObservation.R b/tests/testthat/test-summariseInObservation.R
@@ -131,12 +131,12 @@ test_that("check sex argument works", {
 
 })
 # Load mock database ----
-# con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
-# cdm <- CDMConnector::cdmFromCon(
-#   con = con, cdmSchema = "main", writeSchema = "main"
-# )
-#
-# observationPeriod <- cdm$observation_period
-# unit <- "year"
-# unitInterval <- 2
-# sex <- FALSE
+con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
+cdm <- CDMConnector::cdmFromCon(
+  con = con, cdmSchema = "main", writeSchema = "main"
+)
+
+observationPeriod <- cdm$observation_period
+unit <- "year"
+unitInterval <- 2
+sex <- FALSE
diff --git a/tests/testthat/test-summariseRecordCount.R b/tests/testthat/test-summariseRecordCount.R
@@ -83,7 +83,7 @@ test_that("plotRecordCount() works", {
     con = con, cdmSchema = "main", writeSchema = "main"
   )
   expect_warning(inherits(plotRecordCount(summariseRecordCount(cdm$drug_exposure, unitInterval = 8)),"ggplot"))
-  # expect_warning(inherits(plotRecordCount(summariseRecordCount(cdm$death, unitInterval = 8)),"ggplot"))
+  expect_warning(inherits(plotRecordCount(summariseRecordCount(cdm$death, unitInterval = 8)),"ggplot"))
 })
 
 test_that("summariseRecordCount() ageGroup argument works", {
@@ -201,8 +201,8 @@ test_that("summariseRecordCount() sex argument works", {
 
 
 
-# omopTable <- cdm$observation_period
-# ageGroup  <- NULL #list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60), ">60" = c(61, Inf))
-# unit <- "year"
-# unitInterval <- 10
-# sex <- TRUE
+omopTable <- cdm$observation_period
+ageGroup  <- NULL #list("<=20" = c(0,20), "21 to 40" = c(21,40), "41 to 60" = c(41,60), ">60" = c(61, Inf))
+unit <- "month"
+unitInterval <- 5
+sex <- TRUE