Adds junit as reporter

hta-pharma · Mar 15, 2024 · 62e189b · 62e189b
1 parent ee747a5
commit 62e189b
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Showing 4 changed files with 33 additions and 33 deletions.
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -9,4 +9,4 @@
 library(testthat)
 library(ramnog)
 
-test_check("ramnog")
+test_check("ramnog", reporter = JunitReporter$new(file = "junit_result.xml"))
diff --git a/tests/testthat/binary_type_2.R b/tests/testthat/binary_type_2.R
@@ -2,19 +2,21 @@ test_that("Binary outcomes of type 2 work", {
  # SETUP -------------------------------------------------------------------
  testr::create_local_project()
 
- mk_ep_def <- function(){
- chef::mk_endpoint_str(
- data_prepare = mk_adae,
- pop_var = "SAFFL",
- pop_value = "Y",
- treatment_var = "TRT01A",
- treatment_refval = "Xanomeline High Dose",
- group_by = list(list(AESOC = c())),
- stratify_by = list(c("AEDECOD")),
- stat_by_strata_by_trt = list(chefStats::n_subj_event,
- chefStats::n_event)
- )
-}
+ mk_ep_def <- function() {
+ chef::mk_endpoint_str(
+ data_prepare = mk_adae,
+ pop_var = "SAFFL",
+ pop_value = "Y",
+ treatment_var = "TRT01A",
+ treatment_refval = "Xanomeline High Dose",
+ group_by = list(list(AESOC = c())),
+ stratify_by = list(c("AEDECOD")),
+ stat_by_strata_by_trt = list(
+ chefStats::n_subj_event,
+ chefStats::n_event
+ )
+ )
+ }
  chef::use_chef(
  pipeline_dir = "pipeline",
  r_functions_dir = "R/",
@@ -23,32 +25,34 @@ test_that("Binary outcomes of type 2 work", {
  mk_adam_fn = list(mk_adae),
  )
  # ACT ---------------------------------------------------------------------
- browser()
  targets::tar_make()
  targets::tar_load(ep_stat)
 
  # EXPECT ------------------------------------------------------------------
  actual <-
- tidyr::unnest(ep_stat[grepl("GASTRO", endpoint_group_filter) |
- grepl("CARDIAC", endpoint_group_filter),
- .(endpoint_group_filter,
- stat_filter,
- stat_empty,
- fn_name,
- stat_result)], cols = stat_result) |>
+ tidyr::unnest(ep_stat[
+ grepl("GASTRO", endpoint_group_filter) |
+ grepl("CARDIAC", endpoint_group_filter),
+ .(
+ endpoint_group_filter,
+ stat_filter,
+ stat_empty,
+ fn_name,
+ stat_result
+ )
+ ], cols = stat_result) |>
  setDT() |>
  setorder(-value)
 
  x <- mk_adae()
  n <- x[AESOC == "CARDIAC DISORDERS" &
-  AEDECOD == "SINUS BRADYCARDIA" & TRT01A == "Xanomeline High Dose"] |> uniqueN(by="USUBJID")
+ AEDECOD == "SINUS BRADYCARDIA" & TRT01A == "Xanomeline High Dose"] |> uniqueN(by = "USUBJID")
  E <- x[AESOC == "CARDIAC DISORDERS" &
-  AEDECOD == "SINUS BRADYCARDIA" & TRT01A == "Xanomeline High Dose"] |> nrow()
+ AEDECOD == "SINUS BRADYCARDIA" & TRT01A == "Xanomeline High Dose"] |> nrow()
 
  actual_values <- actual[grepl("CARDIAC", endpoint_group_filter) &
- grepl("SINUS BRADYCARDIA", stat_filter) &
- grepl("Xan", stat_filter)&(label == "n" |
- label == "E")][order(label)][,value]
-expect_equal(actual_values, c(E, n))
-
+ grepl("SINUS BRADYCARDIA", stat_filter) &
+ grepl("Xan", stat_filter) & (label == "n" |
+ label == "E")][order(label)][, value]
+ expect_equal(actual_values, c(E, n))
 })
diff --git a/tests/testthat/test-binary_type_2.R b/tests/testthat/test-binary_type_2.R
@@ -13,7 +13,6 @@ test_that("multiplication works", {
  stratify_by = list(c("AEDECOD")),
  stat_by_strata_by_trt = list(chefStats::p_subj_event)
  )
-
  }
 
 
@@ -27,6 +26,4 @@ test_that("multiplication works", {
  # ACT ---------------------------------------------------------------------
  targets::tar_make()
  targets::tar_load(ep_stat)
- browser()
-
 })
diff --git a/vignettes/validation.Rmd b/vignettes/validation.Rmd
@@ -87,7 +87,6 @@ test_that("Valide stats when one strata level is not found",
  targets::tar_make()
  targets::tar_load(ep_stat)
  # EXPECT ------------------------------------------------------------------
- browser()
  x <- mk_adae_demo()
  # Relative Risk
  actual <-