Merge 7678607 into 605de00

NAMESPACE

@@ -9,6 +9,7 @@ S3method(a_summary,factor)
 S3method(a_summary,logical)
 S3method(a_summary,numeric)
 S3method(as.rtable,data.frame)
+S3method(h_coxreg_inter_effect,character)
 S3method(h_coxreg_inter_effect,factor)
 S3method(h_coxreg_inter_effect,numeric)
 S3method(s_compare,character)

NEWS.md

@@ -1,7 +1,10 @@
 # tern 0.8.3.9001
 
+### Enhancements
+* Added method for `character` class to `h_coxreg_inter_effect` enabling `character` covariates in `summarize_coxreg`.
+
 ### Miscellaneous
-* Began deprecation of `time_unit_input` and `time_unit_output` arguments and replaced them with the `input_time_unit` and `n_pt_years_rate`, respectively, in `control_incidence_rate`.
+* Began deprecation of `time_unit_input` and `time_unit_output` arguments and replaced them with the `input_time_unit` and `num_pt_year`, respectively, in `control_incidence_rate`.
 
 # tern 0.8.3
 

R/control_incidence_rate.R

@@ -10,7 +10,7 @@
 #'   for confidence interval type.
 #' @param input_time_unit (`string`)\cr `day`, `week`, `month`, or `year` (default)
 #'   indicating time unit for data input.
-#' @param num_pt_year (`numeric`)\cr number of patient-years to use when calculating AE rate.
+#' @param num_pt_year (`numeric`)\cr number of patient-years to use when calculating adverse event rates.
 #' @param time_unit_input `r lifecycle::badge("deprecated")` Please use the `input_time_unit` argument instead.
 #' @param time_unit_output `r lifecycle::badge("deprecated")` Please use the `num_pt_year` argument instead.
 #'

R/cox_regression_inter.R

@@ -7,7 +7,7 @@
 #' of the covariate, in comparison to the treatment control.
 #'
 #' @inheritParams argument_convention
-#' @param x (`numeric` or `factor`)\cr the values of the effect to be tested.
+#' @param x (`numeric` or `factor`)\cr the values of the covariate to be tested.
 #' @param effect (`string`)\cr the name of the effect to be tested and estimated.
 #' @param covar (`string`)\cr the name of the covariate in the model.
 #' @param mod (`coxph`)\cr the Cox regression model.
@@ -66,7 +66,9 @@ h_coxreg_inter_effect <- function(x,
   UseMethod("h_coxreg_inter_effect", x)
 }
 
-#' @describeIn cox_regression_inter Estimate the interaction with a `numeric` covariate.
+#' @describeIn cox_regression_inter Method for `numeric` class. Estimates the interaction with a `numeric` covariate.
+#'
+#' @method h_coxreg_inter_effect numeric
 #'
 #' @param at (`list`)\cr a list with items named after the covariate, every
 #'   item is a vector of levels at which the interaction should be estimated.
@@ -118,7 +120,9 @@ h_coxreg_inter_effect.numeric <- function(x,
   )
 }
 
-#' @describeIn cox_regression_inter Estimate the interaction with a `factor` covariate.
+#' @describeIn cox_regression_inter Method for `factor` class. Estimate the interaction with a `factor` covariate.
+#'
+#' @method h_coxreg_inter_effect factor
 #'
 #' @param data (`data.frame`)\cr the data frame on which the model was fit.
 #'
@@ -131,19 +135,20 @@ h_coxreg_inter_effect.factor <- function(x,
                                          control,
                                          data,
                                          ...) {
+  lvl_given <- levels(x)
   y <- h_coxreg_inter_estimations(
     variable = effect, given = covar,
     lvl_var = levels(data[[effect]]),
-    lvl_given = levels(data[[covar]]),
+    lvl_given = lvl_given,
     mod = mod,
     conf_level = 0.95
   )[[1]]
 
   data.frame(
     effect = "Covariate:",
     term = rep(covar, nrow(y)),
-    term_label = as.character(paste0("  ", levels(data[[covar]]))),
-    level = as.character(levels(data[[covar]])),
+    term_label = paste0("  ", lvl_given),
+    level = lvl_given,
     n = NA,
     hr = y[, "hr"],
     lcl = y[, "lcl"],
@@ -154,6 +159,39 @@ h_coxreg_inter_effect.factor <- function(x,
   )
 }
 
+#' @describeIn cox_regression_inter Method for `character` class. Estimate the interaction with a `character` covariate.
+#'   This makes an automatic conversion to `factor` and then forwards to the method for factors.
+#'
+#' @method h_coxreg_inter_effect character
+#'
+#' @note
+#' * Automatic conversion of character to factor does not guarantee results can be generated correctly. It is
+#'   therefore better to always pre-process the dataset such that factors are manually created from character
+#'   variables before passing the dataset to [rtables::build_table()].
+#'
+#' @export
+h_coxreg_inter_effect.character <- function(x,
+                                            effect,
+                                            covar,
+                                            mod,
+                                            label,
+                                            control,
+                                            data,
+                                            ...) {
+  y <- as.factor(x)
+
+  h_coxreg_inter_effect(
+    x = y,
+    effect = effect,
+    covar = covar,
+    mod = mod,
+    label = label,
+    control = control,
+    data = data,
+    ...
+  )
+}
+
 #' @describeIn cox_regression_inter A higher level function to get
 #'   the results of the interaction test and the estimated values.
 #'

tests/testthat/test-coxreg.R

@@ -455,6 +455,34 @@ testthat::test_that("h_coxreg_inter_effect.numerics works with _:_ in effect lev
   testthat::expect_equal(result[, -1], expected[, -1], ignore_attr = TRUE)
 })
 
+testthat::test_that("h_coxreg_inter_effect works with character covariate", {
+  dta_bladder_raw$covar2 <- as.character(dta_bladder_raw$covar2)
+
+  mod1 <- survival::coxph(survival::Surv(time, status) ~ armcd * covar2, data = dta_bladder_raw)
+  testthat::expect_silent(
+    h_coxreg_extract_interaction(
+      effect = "armcd", covar = "covar2", mod = mod1, control = control_coxreg(),
+      at = list(), data = dta_bladder_raw
+    )
+  )
+  testthat::expect_silent(
+    h_coxreg_inter_effect(
+      x = dta_bladder_raw[["covar2"]],
+      effect = "armcd", covar = "covar2", mod = mod1, control = control_coxreg(),
+      at = list(), data = dta_bladder_raw
+    )
+  )
+
+  mod2 <- survival::coxph(survival::Surv(time, status) ~ armcd * covar2 + strata(covar1), data = dta_bladder_raw)
+  testthat::expect_silent(
+    h_coxreg_inter_effect(
+      x = dta_bladder_raw[["covar2"]],
+      effect = "armcd", covar = "covar2", mod = mod2, data = dta_bladder_raw,
+      at = list(), control = control_coxreg()
+    )
+  )
+})
+
 # h_coxreg_inter_estimations ----
 
 testthat::test_that("h_coxreg_inter_estimations' results identical to soon deprecated estimate_coef", {

tests/testthat/test-summarize_coxreg.R

@@ -7,7 +7,7 @@ dta_bladder <- local({
     tibble::tibble(
       TIME = stop,
       STATUS = event,
-      ARM = paste("ARM:", as.factor(rx)),
+      ARM = as.factor(paste("ARM:", as.factor(rx))),
       ARMCD = formatters::with_label(as.factor(rx), "ARM"),
       COVAR1 = formatters::with_label(as.factor(enum), "A Covariate Label"),
       COVAR2 = formatters::with_label(
@@ -48,6 +48,18 @@ testthat::test_that("s_coxreg works with which_vars and var_nms arguments", {
   testthat::expect_snapshot(res)
 })
 
+testthat::test_that("s_coxreg works with character covariates in the univariate case when interaction = TRUE", {
+  univar_model <- fit_coxreg_univar(
+    variables = variables,
+    data = dta_bladder,
+    control = control_coxreg(interaction = TRUE)
+  ) %>% broom::tidy()
+  result <- s_coxreg(model_df = univar_model, .stat = "hr")
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+})
+
 # a_coxreg ----
 
 testthat::test_that("a_coxreg works as expected", {
@@ -184,6 +196,36 @@ testthat::test_that("summarize_coxreg works with numeric covariate without treat
   testthat::expect_snapshot(res)
 })
 
+testthat::test_that("summarize_coxreg works with character covariate in univariate case when interaction = TRUE", {
+  # one character covariate
+  variables <- list(time = "TIME", event = "STATUS", arm = "ARM", covariates = "COVAR2")
+  dta_bladder$COVAR2 <- as.character(dta_bladder$COVAR2)
+
+  result <- basic_table() %>%
+    summarize_coxreg(
+      variables = variables,
+      control = control_coxreg(interaction = TRUE)
+    ) %>%
+    build_table(df = dta_bladder)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+
+  # one factor covariate, one character covariate
+  variables <- list(time = "TIME", event = "STATUS", arm = "ARM", covariates = c("COVAR1", "COVAR2"))
+
+  result <- basic_table() %>%
+    summarize_coxreg(
+      variables = variables,
+      control = control_coxreg(interaction = TRUE)
+    ) %>%
+    build_table(df = dta_bladder)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+})
+
+
 testthat::test_that("summarize_coxreg adds the multivariate Cox regression layer to rtables", {
   variables <- list(time = "TIME", event = "STATUS", arm = "ARMCD", covariates = c("AGE", "COVAR1", "COVAR2"))