Merge pull request #243 from OHDSI/issue_242

Issue 242

R/summariseClinicalRecords.R

@@ -576,10 +576,11 @@ summaryData <- function(x, denominator, strata, cdm) {
 }
 
 formatResults <- function(x, variableName, variableLevel, denominator, strata) {
-
+  attr(denominator, "settings")$strata <- paste(unique(unlist(strata)), collapse = " &&& ")
   denominator <- denominator |>
     dplyr::select("strata_name", "strata_level", "denominator" = "estimate_value") |>
-    visOmopResults::splitStrata()
+    dplyr::filter(.data$strata_name != "overall") |>
+    omopgenerics::splitStrata()
 
   strataCols <- unique(unlist(strata))
 

R/summariseObservationPeriod.R

@@ -134,7 +134,7 @@ addOrdinalLevels <- function(x) {
   xx <- suppressWarnings(as.integer(x$id))
   desena <- (floor(xx/10)) %% 10
   unitat <- xx %% 10
-  val <- rep("overall", length(xx))
+  val <- rep("overall_", length(xx))
   id0 <- !is.na(xx)
   val[id0] <- paste0(xx[id0], "th")
   id <- id0 & desena != 1L & unitat == 1L
@@ -162,7 +162,7 @@ arrangeSr <- function(x, estimates) {
 
   order <- dplyr::tibble(
     "variable_name" = c("number records"),
-    "group_level"   = "overall",
+    "group_level"   = "overall_",
     "strata_level"  = "overall",
     "estimate_name" = "count"
   ) |>

tests/testthat/test-summariseConceptCounts.R

@@ -33,7 +33,7 @@ test_that("summarise code use - eunomia", {
           time_interval == "1909-01-01 to 1909-12-31",
           group_level == "acetiminophen") |>
         dplyr::pull("estimate_value"),
-      as.character(NA)
+     "-"
   )
 
   # check is a summarised result

tests/testthat/test-summariseObservationPeriod.R

@@ -68,7 +68,7 @@ test_that("check summariseObservationPeriod works", {
   # counts
   expect_identical(resAll$estimate_value[resAll$variable_name == "number records"], "8")
   x <- dplyr::tibble(
-    group_level = c("overall", "1st", "2nd", "3rd"),
+    group_level = c("overall_", "1st", "2nd", "3rd"),
     variable_name = "number subjects",
     estimate_value = c("4", "4", "3", "1"))
   expect_identical(nrow(x), resAll |> dplyr::inner_join(x, by = colnames(x)) |> nrow())
@@ -88,21 +88,39 @@ test_that("check summariseObservationPeriod works", {
       dplyr::filter(variable_name == "duration in days", estimate_name == "mean") |>
       dplyr::pull("estimate_value"),
     as.character(c(
-      mean(c(20, 6, 113, 144, 18, 9, 29, 276)), mean(c(20, 18, 9, 276)),
-      mean(c(6, 29, 144)), 113
+      mean(c(20, 18, 9, 276)),
+      mean(c(6, 29, 144)), 113,  mean(c(20, 6, 113, 144, 18, 9, 29, 276))
     ))
   )
+  # when it will be group_level = "overall"
+  # expect_identical(
+  #   resAll |>
+  #     dplyr::filter(variable_name == "duration in days", estimate_name == "mean") |>
+  #     dplyr::pull("estimate_value"),
+  #   as.character(c(
+  #     mean(c(20, 6, 113, 144, 18, 9, 29, 276)), mean(c(20, 18, 9, 276)),
+  #     mean(c(6, 29, 144)), 113
+  #   ))
+  # )
 
   # days to next observation period
   expect_identical(
     resAll |>
       dplyr::filter(variable_name == "days to next observation period", estimate_name == "mean") |>
       dplyr::pull("estimate_value"),
     as.character(c(
-      mean(c(5, 32, 136, 26)), mean(c(5, 32, 136)), 26, NA
+      mean(c(5, 32, 136)), 26, NA,  mean(c(5, 32, 136, 26))
     ))
   )
-
+  # when it will be group_level="overall"
+  # expect_identical(
+  #   resAll |>
+  #     dplyr::filter(variable_name == "days to next observation period", estimate_name == "mean") |>
+  #     dplyr::pull("estimate_value"),
+  #   as.character(c(
+  #     mean(c(5, 32, 136, 26)), mean(c(5, 32, 136)), 26, NA
+  #   ))
+  # )
   # duration - density
   xx <- resAllD |>
     dplyr::filter(variable_name == "duration in days", !is.na(variable_level)) |>
@@ -144,7 +162,7 @@ test_that("check summariseObservationPeriod works", {
   # counts
   expect_identical(resOne$estimate_value[resOne$variable_name == "number records"], "4")
   x <- dplyr::tibble(
-    group_level = c("overall", "1st"),
+    group_level = c("overall_", "1st"),
     variable_name = "number subjects",
     estimate_value = c("4", "4"))
   expect_identical(nrow(x), resOne |> dplyr::inner_join(x, by = colnames(x)) |> nrow())