Merge pull request #272 from OHDSI/issue_208

test for interval argument in summariseConceptCount

DESCRIPTION

@@ -44,6 +44,7 @@ Suggests:
     gt,
     here,
     knitr,
+    lubridate,
     odbc,
     remotes,
     rmarkdown,

R/checks.R

@@ -17,7 +17,7 @@ validateIntervals <- function(interval, call = parent.frame()){
 
   unitInterval <- dplyr::case_when(
     interval == "overall" ~ NA,
-    interval == "quarters" ~ 4,
+    interval == "quarters" ~ 3,
     interval == "months" ~ 1,
     interval == "years" ~ 1
   )

R/summariseRecordCount.R

@@ -204,15 +204,15 @@ getOmopTableEndDate   <- function(omopTable, date){
 }
 
 getIntervalTibble <- function(omopTable, start_date_name, end_date_name, interval, unitInterval){
-  startDate <- getOmopTableStartDate(omopTable, start_date_name)
-  endDate   <- getOmopTableEndDate(omopTable, end_date_name)
+    startDate <- getOmopTableStartDate(omopTable, start_date_name)
+    endDate <- getOmopTableEndDate(omopTable, end_date_name)
 
   tibble::tibble(
     "group" = seq.Date(as.Date(startDate), as.Date(endDate), "month")
   ) |>
     dplyr::rowwise() |>
     dplyr::mutate("interval" = max(which(
-      .data$group >= seq.Date(from = startDate, to = endDate, by = paste(.env$unitInterval, .env$interval))
+      .data$group >= seq.Date(from = startDate, to = endDate, by = paste(.env$interval))
     ),
     na.rm = TRUE)) |>
     dplyr::ungroup() |>
@@ -227,9 +227,9 @@ getIntervalTibble <- function(omopTable, start_date_name, end_date_name, interva
       "interval_start_date" = as.Date(.data$interval_start_date),
       "interval_end_date" = as.Date(.data$interval_end_date)
     ) |>
-    dplyr::mutate(
+      dplyr::mutate(
       "interval_group" = paste(.data$interval_start_date,"to",.data$interval_end_date)
-    ) |>
+      ) |>
     dplyr::ungroup() |>
     dplyr::mutate("my" = paste0(clock::get_month(.data$group),"-",clock::get_year(.data$group))) |>
     dplyr::select("interval_group", "my", "interval_start_date","interval_end_date") |>

tests/testthat/test-summariseConceptSetCounts.R

@@ -558,3 +558,104 @@ test_that("dateRange argument works", {
   expect_equal(colnames(settings(z)), colnames(settings(x)))
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
+test_that("interval argument works", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- mockOmopSketch()
+  expect_no_error(y<-summariseConceptCounts(list(ANTIHISTAMINES= c(21603444)),
+                         cdm = cdm,
+                         interval = "years"))
+
+  expect_no_error(o<-summariseConceptCounts(list(ANTIHISTAMINES= c(21603444)),
+                                            cdm = cdm,
+                                            interval = "overall"))
+  expect_no_error(q<-summariseConceptCounts(list(ANTIHISTAMINES= c(21603444)),
+                                            cdm = cdm,
+                                            interval = "quarters"))
+  expect_no_error(m<-summariseConceptCounts(list(ANTIHISTAMINES= c(21603444)),
+                                            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::mutate(
+      start_date = as.Date(sub(" to .*", "", time_interval)),
+      quarter_start = lubridate::quarter(start_date, type = "date_first"),
+      quarter_end = lubridate::quarter(start_date, type = "date_last"),
+      quarter = paste(quarter_start, "to", quarter_end)
+    ) |>
+    dplyr::select(!c("time_interval", "start_date", "quarter_start", "quarter_end")) |>
+    dplyr::group_by(quarter,)|>
+    dplyr::summarise(count = sum(count), .groups = "drop") |>
+    dplyr::rename("time_interval" = quarter) |>
+    dplyr::arrange(time_interval)
+
+  q_quarters <- q|>omopgenerics::splitAdditional()|>
+   omopgenerics::pivotEstimates()|>
+   dplyr::filter(time_interval != "overall" & variable_name == "Number records"& standard_concept_id == 21603444)|>
+   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::mutate(
+     # Extract the start date
+     start_date = clock::date_parse(stringr::str_extract(time_interval, "^\\d{4}-\\d{2}-\\d{2}")),
+     # Convert start_date to a year-month-day object and extract the year
+     year = clock::get_year(clock::as_year_month_day(start_date))
+   )|>
+   omopgenerics::pivotEstimates()|>
+   dplyr::group_by(year) %>%
+   dplyr::summarise(
+     count = sum(count),
+     .groups = "drop"
+   )|>
+   dplyr::arrange(year)
+  y_year <- y|>
+   omopgenerics::splitAdditional()|>
+   dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 21603444)|>
+   dplyr::mutate(
+     # Extract the start date
+     start_date = clock::date_parse(stringr::str_extract(time_interval, "^\\d{4}-\\d{2}-\\d{2}")),
+     # Convert start_date to a year-month-day object and extract the year
+     year = clock::get_year(clock::as_year_month_day(start_date))
+   )|>
+   omopgenerics::pivotEstimates()|>
+   dplyr::select(year, count)|>
+   dplyr::arrange(year)
+
+  expect_equal(m_year, y_year)
+  o <- o |> omopgenerics::splitAdditional()|>
+   dplyr::filter(variable_name == "Number records" & standard_concept_id == 21603444)|>
+   omopgenerics::pivotEstimates()|>
+   dplyr::select(count)
+
+  expect_equal(y_year|>dplyr::summarise(count = sum(count)), o)
+
+
+  q_year <- q|>
+   omopgenerics::splitAdditional()|>
+   dplyr::filter(time_interval != "overall" & variable_name == "Number records" & standard_concept_id == 21603444)|>
+   dplyr::mutate(
+     # Extract the start date
+     start_date = clock::date_parse(stringr::str_extract(time_interval, "^\\d{4}-\\d{2}-\\d{2}")),
+     # Convert start_date to a year-month-day object and extract the year
+     year = clock::get_year(clock::as_year_month_day(start_date))
+   )|>
+   omopgenerics::pivotEstimates()|>
+   dplyr::group_by(year) %>%
+   dplyr::summarise(
+     count = sum(count),
+     .groups = "drop"
+   )|>
+   dplyr::arrange(year)
+
+  expect_equal(q_year, y_year)
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})