Adding unit tests for all crit fns (#2)

* Adding unit tests for all crit fns

* Fixing dep bug. Still need to consider the need for stat helper fns

Author: nsjohnsen

DESCRIPTION

@@ -10,7 +10,7 @@ Description: A collection of criterion functions for statistical evidence genera
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3
 Imports: 
     chef,
@@ -21,10 +21,10 @@ Imports:
     dplyr,
     knitr
 Suggests: 
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
     pharmaverseadam
 Remotes:
-    hta-pharma/chefStats
+    hta-pharma/chefStats,
     hta-pharma/chef
 VignetteBuilder: 
     knitr

R/crit_by_strata_by_trt.R

@@ -17,7 +17,7 @@
 crit_bb_nsubev_01 <- function(dat, event_index, subjectid_var, n_subj_event_min, ...){
 
   # Evaluate criterion
-  crit_accept <- dat[J(event_index)] |>
+  crit_accept <- dat[list(event_index)] |>
     unique(by = c(subjectid_var)) |>
     nrow() >= n_subj_event_min
 

R/crit_endpoint.R

@@ -19,9 +19,9 @@ crit_ep_nsubev_01 <- function(dat,
                               event_index,
                               subjectid_var,
                               treatment_var,
-                              n_subj_event_min = 10,
+                              n_subj_event_min,
                               ...) {
-  stat <- dat[J(event_index)] |>
+  stat <- dat[list(event_index)] |>
     unique(by = c(subjectid_var, treatment_var))
 
   return(any(table(stat[[treatment_var]]) >= n_subj_event_min))

man/crit_ep_nsubev_01.Rd

@@ -15,6 +15,7 @@ n_sub <- function(dat,
 
   return(data.table(
     description = "Number of subjects",
+    qualifiers = NA_character_,
     label = "N",
     value = stat
   ))
@@ -35,6 +36,7 @@ n_subev <- function(dat,
 
   return(data.table(
     description = "Number of subjects with events",
+    qualifiers = NA_character_,
     label = "n",
     value = stat
   ))
@@ -58,6 +60,7 @@ p_subev <- function(dat,
 
   out <-
     data.table(description = "Proportion of subjects with events",
+               qualifiers = NA_character_,
                label = "(%)",
                value = n_subev / n_sub * 100)
 
@@ -101,6 +104,7 @@ summary_stats <- function(dat,
 
   return(data.table(
     description = "Summary statistics",
+    qualifiers = NA_character_,
     label = names(stat),
     value = as.list(stat)
   ))
@@ -126,12 +130,10 @@ n_subev_trt_diff <- function(dat,
   # In case stat is invalid, e.g. if obs. only exists in one treatment arm then replace stat with NA
   stat <- ifelse(length(stat) == 0, NA, stat)
 
-  out <-
-
-    data.table(description = "Absolute difference in number of subjects with events between treatment arms",
-               label = "n_trt_diff",
-               value = stat)
-
+  out <-  data.table(description = "Absolute difference in number of subjects with events between treatment arms",
+                      qualifiers = NA_character_,
+                      label = "n_trt_diff",
+                      value = stat)
 
   return(out)
 }
@@ -157,6 +159,7 @@ contingency2x2_ptest <- function(dat,
   # Prepare output
   out = data.table::data.table(
     description = "Fisher's exact test for count data",
+    qualifiers = NA_character_,
     label = c("Pval_independency", "CI_upper", "CI_lower"),
     value = c(res$p.value, res$conf.int[1], res$conf.int[2])
   )
@@ -189,6 +192,7 @@ contingency2x2_strata_test <- function(dat,
   # Prepare output
   out <- data.table::data.table(
     description = "Cochran-mante-haenszel test for odds ratios across strata",
+    qualifiers = NA_character_,
     label = c("Pval_independency", "CI_lower", "CI_upper"),
     value = c(res$p.value, res$conf.int[[1]], res$conf.int[[2]])
 

tests/testthat/helper-04-stats.R

@@ -0,0 +1,76 @@
+test_that("Check crit_bb_nsubev_01", {
+    # SETUP -------------------------------------------------------------------
+
+    dat <- data.table(
+        INDEX_ = 1:10,
+        USUBJID = 1:10
+    )
+
+    setkey(dat, INDEX_)
+    event_index <- c(1, 3, 5, 7)
+    n_subj_event_min <- 5
+    subjectid_var <- "USUBJID"
+
+    # ACT ---------------------------------------------------------------------
+
+    crit_eval_1 <- crit_bb_nsubev_01(dat, event_index, subjectid_var, n_subj_event_min = 3)
+    crit_eval_2 <- crit_bb_nsubev_01(dat, event_index, subjectid_var, n_subj_event_min = 5)
+
+    # EXPECT ------------------------------------------------------------------
+
+    expect_true(crit_eval_1)
+    expect_false(crit_eval_2)
+    expect_error(crit_bb_nsubev_01(dat, event_index, subjectid_var))
+})
+
+test_that("Check crit_bb_pval_01", {
+    # SETUP -------------------------------------------------------------------
+
+    dat <- mk_adae()
+    dat[["INDEX_"]] <- 1:nrow(dat)
+    event_index <- c(1:10, 50:100, 600:700)
+    cell_index <- 500:700
+    treatment_var <- "TRT01A"
+    treatment_refval <- "Xanomeline High Dose"
+    subjectid_var <- "USUBJID"
+
+    pval_max_1 <- 0.87
+    pval_max_2 <- 0.88
+
+    # ACT ---------------------------------------------------------------------
+
+   crit_eval_1 <- crit_bb_pval_01(
+        dat = dat,
+        event_index = event_index,
+        cell_index = cell_index,
+        treatment_var = treatment_var,
+        treatment_refval = treatment_refval,
+        subjectid_var = subjectid_var,
+        pval_max = pval_max_1
+    )
+
+    crit_eval_2 <- crit_bb_pval_01(
+        dat = dat,
+        event_index = event_index,
+        cell_index = cell_index,
+        treatment_var = treatment_var,
+        treatment_refval = treatment_refval,
+        subjectid_var = subjectid_var,
+        pval_max = pval_max_2
+    )
+
+    # EXPECT ------------------------------------------------------------------
+
+    p_value <- chefStats::p_val(
+      dat = dat,
+      event_index = event_index,
+      cell_index = dat[["INDEX_"]],
+      treatment_var = treatment_var,
+      treatment_refval = treatment_refval,
+      subjectid_var = subjectid_var
+    )[["value"]]
+
+    expect_equal(crit_eval_1, p_value < pval_max_1)
+    expect_equal(crit_eval_2, p_value < pval_max_2)
+
+})

tests/testthat/test-crit_by_strata_by_trt.R

@@ -0,0 +1,34 @@
+test_that("Check crit_ep_nsubev_01", {
+    # SETUP -------------------------------------------------------------------
+
+    dat <- mk_adae()
+    dat[["INDEX_"]] <- 1:nrow(dat)
+    setkey(dat, INDEX_)
+    event_index <- c(1:10, 50:100)
+    treatment_var <- "TRT01A"
+    treatment_refval <- "Xanomeline High Dose"
+    subjectid_var <- "USUBJID"
+
+    # ACT ---------------------------------------------------------------------
+
+    crit_eval_1 <- crit_ep_nsubev_01(
+        dat = dat,
+        event_index = event_index,
+        subjectid_var = subjectid_var,
+        treatment_var = treatment_var,
+        n_subj_event_min = 5
+    )
+    crit_eval_2 <- crit_ep_nsubev_01(
+        dat = dat,
+        event_index = event_index,
+        subjectid_var = subjectid_var,
+        treatment_var = treatment_var,
+        n_subj_event_min = 10
+    )
+
+     # EXPECT ------------------------------------------------------------------
+
+    expect_true(crit_eval_1)
+    expect_false(crit_eval_2)
+
+})