Merge branch 'main' into 1130_update_descs@main

insightsengineering · Sep 5, 2024 · a83862a · a83862a
2 parents 4120fbb + f9fb467
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.5.9017
-Date: 2024-09-04
+Version: 0.9.5.9019
+Date: 2024-09-05
 Authors@R: c(
     person("Joe", "Zhu", , "joe.zhu@roche.com", role = c("aut", "cre")),
     person("Daniel", "Sabanés Bové", , "daniel.sabanes_bove@roche.com", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,11 @@
-# tern 0.9.5.9017
+# tern 0.9.5.9019
 ### Enhancements
 * Added `errorbar_width` and `linetype` parameters to `g_lineplot`.
 * Reworking of `summarize_glm_count()` documentation and all its associated functions to better describe the results and the functions' purpose.
 * Added the `.formats` argument to `tabulate_rsp_subgroups` and `tabulate_survival_subgroups` to allow users to specify formats.
 * Added the `riskdiff` argument to `tabulate_rsp_subgroups` and `tabulate_survival_subgroups` to allow users to add a risk difference table column, and function `control_riskdiff` to specify settings for the risk difference column.
+* Added warning to `tabulate_rsp_subgroups` when `pval` statistic is selected but `df` has not been correctly generated to add p-values to the output table.
+* Added `n_rate` statistic as a non-default option to `estimate_incidence_rate` which returns both number of events observed and estimated incidence rate.
 
 ### Bug Fixes
 * Fixed a bug in `a_surv_time` that threw an error when split only has `"is_event"`.

diff --git a/R/argument_convention.R b/R/argument_convention.R
@@ -43,7 +43,7 @@
 #'   for more information.
 #' @param lyt (`PreDataTableLayouts`)\cr layout that analyses will be added to.
 #' @param method (`string` or `NULL`)\cr specifies the test used to calculate the p-value for the difference between
-#'   two proportions. For options, see [s_test_proportion_diff()]. Default is `NULL` so no test is performed.
+#'   two proportions. For options, see [test_proportion_diff()]. Default is `NULL` so no test is performed.
 #' @param na.rm (`flag`)\cr whether `NA` values should be removed from `x` prior to analysis.
 #' @param na_str (`string`)\cr string used to replace all `NA` or empty values in the output.
 #' @param nested (`flag`)\cr whether this layout instruction should be applied within the existing layout structure _if

diff --git a/R/incidence_rate.R b/R/incidence_rate.R
@@ -35,6 +35,7 @@ NULL
 #'   - `n_events`: Total number of events observed.
 #'   - `rate`: Estimated incidence rate.
 #'   - `rate_ci`: Confidence interval for the incidence rate.
+#'   - `n_rate`: Total number of events observed & estimated incidence rate.
 #'
 #' @keywords internal
 s_incidence_rate <- function(df,
@@ -79,7 +80,11 @@ s_incidence_rate <- function(df,
     person_years = formatters::with_label(person_years, "Total patient-years at risk"),
     n_events = formatters::with_label(n_events, "Number of adverse events observed"),
     rate = formatters::with_label(result$rate, paste("AE rate per", num_pt_year, "patient-years")),
-    rate_ci = formatters::with_label(result$rate_ci, f_conf_level(conf_level))
+    rate_ci = formatters::with_label(result$rate_ci, f_conf_level(conf_level)),
+    n_rate = formatters::with_label(
+      c(n_events, result$rate),
+      paste("Number of adverse events observed (AE rate per", num_pt_year, "patient-years)")
+    )
   )
 }
 
@@ -96,7 +101,8 @@ a_incidence_rate <- make_afun(
     "person_years" = "xx.x",
     "n_events" = "xx",
     "rate" = "xx.xx",
-    "rate_ci" = "(xx.xx, xx.xx)"
+    "rate_ci" = "(xx.xx, xx.xx)",
+    "n_rate" = "xx (xx.x)"
   )
 )
 
@@ -144,7 +150,7 @@ estimate_incidence_rate <- function(lyt,
                                     ...,
                                     show_labels = "hidden",
                                     table_names = vars,
-                                    .stats = NULL,
+                                    .stats = c("person_years", "n_events", "rate", "rate_ci"),
                                     .formats = NULL,
                                     .labels = NULL,
                                     .indent_mods = NULL) {

diff --git a/R/response_subgroups.R b/R/response_subgroups.R
@@ -225,6 +225,14 @@ tabulate_rsp_subgroups <- function(lyt,
                                    )) {
   checkmate::assert_list(riskdiff, null.ok = TRUE)
   checkmate::assert_true(all(c("n_tot", "or", "ci") %in% vars))
+  if ("pval" %in% vars && !"pval" %in% names(df$or)) {
+    warning(
+      'The "pval" statistic has been selected but is not present in "df" so it will not be included in the output ',
+      'table. To include the "pval" statistic, please specify a p-value test when generating "df" via ',
+      'the "method" argument to `extract_rsp_subgroups()`. If method = "cmh", strata must also be specified via the ',
+      '"variables" argument to `extract_rsp_subgroups()`.'
+    )
+  }
 
   # Create "ci" column from "lcl" and "ucl"
   df$or$ci <- combine_vectors(df$or$lcl, df$or$ucl)

diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R
@@ -382,7 +382,7 @@ tern_default_stats <- list(
   count_patients_with_flags = c("n", "count", "count_fraction", "count_fraction_fixed_dp", "n_blq"),
   count_values = c("n", "count", "count_fraction", "count_fraction_fixed_dp", "n_blq"),
   coxph_pairwise = c("pvalue", "hr", "hr_ci", "n_tot", "n_tot_events"),
-  estimate_incidence_rate = c("person_years", "n_events", "rate", "rate_ci"),
+  estimate_incidence_rate = c("person_years", "n_events", "rate", "rate_ci", "n_rate"),
   estimate_multinomial_response = c("n_prop", "prop_ci"),
   estimate_odds_ratio = c("or_ci", "n_tot"),
   estimate_proportion = c("n_prop", "prop_ci"),

diff --git a/man/argument_convention.Rd b/man/argument_convention.Rd
diff --git a/man/d_rsp_subgroups_colvars.Rd b/man/d_rsp_subgroups_colvars.Rd
diff --git a/man/extract_rsp_subgroups.Rd b/man/extract_rsp_subgroups.Rd
diff --git a/man/h_response_subgroups.Rd b/man/h_response_subgroups.Rd
diff --git a/man/incidence_rate.Rd b/man/incidence_rate.Rd
diff --git a/tests/testthat/_snaps/estimate_incidence_rate.md b/tests/testthat/_snaps/estimate_incidence_rate.md
@@ -101,6 +101,11 @@
       attr(,"label")
       [1] "90% CI"
       
+      $n_rate
+      [1]  4.00000 44.15823
+      attr(,"label")
+      [1] "Number of adverse events observed (AE rate per 100 patient-years)"
+      
 
 # estimate_incidence_rate works as expected with healthy input
 
@@ -115,3 +120,15 @@
       AE rate per 100 patient-years           26.20             57.23     
       90% CI                              (5.06, 135.73)   (22.14, 147.94)
 
+# estimate_incidence_rate `n_rate` statistic works as expected
+
+    Code
+      res
+    Output
+                                                                             A         B   
+                                                                           (N=3)     (N=3) 
+      —————————————————————————————————————————————————————————————————————————————————————
+      Number of adverse events observed                                      1         3   
+      AE rate per 100 patient-years                                        2.18      4.77  
+      Number of adverse events observed (AE rate per 100 patient-years)   1 (2.2)   3 (4.8)
+
diff --git a/tests/testthat/test-estimate_incidence_rate.R b/tests/testthat/test-estimate_incidence_rate.R
@@ -109,3 +109,27 @@ testthat::test_that("estimate_incidence_rate works as expected with healthy inpu
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
 })
+
+testthat::test_that("estimate_incidence_rate `n_rate` statistic works as expected", {
+  df <- data.frame(
+    USUBJID = as.character(seq(6)),
+    CNSR = c(0, 1, 1, 0, 0, 0),
+    AVAL = c(10.1, 20.4, 15.3, 20.8, 18.7, 23.4),
+    ARM = factor(c("A", "A", "A", "B", "B", "B"))
+  ) %>%
+    dplyr::mutate(is_event = CNSR == 0) %>%
+    dplyr::mutate(n_events = as.integer(is_event))
+
+  result <- basic_table() %>%
+    split_cols_by("ARM") %>%
+    add_colcounts() %>%
+    estimate_incidence_rate(
+      vars = "AVAL",
+      n_events = "n_events",
+      .stats = c("n_events", "rate", "n_rate")
+    ) %>%
+    build_table(df)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+})
diff --git a/tests/testthat/test-response_subgroups.R b/tests/testthat/test-response_subgroups.R
@@ -307,3 +307,24 @@ testthat::test_that("tabulate_rsp_subgroups riskdiff argument works as expected"
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
 })
+
+testthat::test_that("tabulate_rsp_subgroups pval statistic warning works as expected", {
+  adrs <- adrs_200
+
+  df <- extract_rsp_subgroups(
+    variables = list(rsp = "rsp", arm = "ARM", subgroups = c("SEX", "STRATA2")),
+    data = adrs,
+    method = NULL,
+    conf_level = 0.95
+  )
+
+  # warning when no pval in df
+  expect_warning(
+    basic_table() %>%
+      tabulate_rsp_subgroups(
+        df = df,
+        vars = c("n", "prop", "n_tot", "or", "ci", "pval")
+      ),
+    "please specify a p-value test"
+  )
+})