change to pull the subset argument (#267)

* change to pull the subset argument

* doc updates

* Updated construction of survdiff() call

* unit test for the subset arg

---------

Co-authored-by: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

Author: ShreyaSreeram27

DESCRIPTION

@@ -4,7 +4,7 @@ Version: 1.2.0.9000
 Authors@R: c(
     person("Daniel D.", "Sjoberg", , "danield.sjoberg@gmail.com", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0003-0862-2018")),
-           person("Shreya", "Sreeram", , "shreyasreeram27@gmail.com", role = "aut"),
+    person("Shreya", "Sreeram", , "shreyasreeram27@gmail.com", role = "aut"),
     person("Mark", "Baillie", , "bailliem@gmail.com", role = "aut"),
     person("Charlotta", "Fruechtenicht", , "charlotta.fruechtenicht@roche.com", role = "aut",
            comment = c(ORCID = "0000-0002-6689-6423")),

R/survfit2_p.R

@@ -42,11 +42,25 @@ survfit2_p <- function(x, pvalue_fun = format_p, prepend_p = TRUE, rho = 0) {
     cli_abort("The {.fun survfit2_p} does not support multi-state models.")
   }
 
-  survival::survdiff(
-    formula = .extract_formula_from_survfit(x),
-    data = .extract_data_from_survfit(x),
-    rho = rho
-  ) %>%
+  # call survdiff
+  survdiff_args <-
+    list(
+      formula = .extract_formula_from_survfit(x),
+      data = .extract_data_from_survfit(x),
+      subset = as.list(x$call)[["subset"]],
+      rho = rho
+    ) %>%
+    # remove NULL entries
+    {Filter(Negate(is.null), x = .)} # styler: off
+
+  survdiff_result <-
+    do.call(
+      what = survival::survdiff,
+      args = survdiff_args,
+      envir = x$.Environment
+    )
+
+  survdiff_result %>%
     broom::glance() %>%
     dplyr::pull("p.value") %>%
     pvalue_fun() %>%

man/add_risktable_strata_symbol.Rd

@@ -38,3 +38,39 @@ test_that("survfit2_p() throws error", {
       add_pvalue()
   )
 })
+
+test_that("survfit2_p() works with subset argument", {
+  #create survfit object with subset argument
+  sf_subset <- survfit2(Surv(time, status) ~ sex, data = df_lung, subset = age >= 75)
+
+  #calculate expectes p val directly with survdiff using the same subset
+  expected_p <- survival::survdiff(
+    Surv(time, status) ~ sex,
+    data = df_lung,
+    subset = age >= 75
+  ) %>%
+    broom::glance() %>%
+    dplyr::pull(p.value) %>%
+    format_p()
+
+  #testing that survfit2_p respects the subset argument
+  expect_equal(
+    survfit2_p(sf_subset, prepend_p = FALSE),
+    expected_p
+  )
+
+  #the subset p-value should be different from full data p-value
+  sf_full <- survfit2(Surv(time, status) ~ sex, data = df_lung)
+
+  expect_false(
+    survfit2_p(sf_subset, prepend_p = FALSE) == survfit2_p(sf_full, prepend_p = FALSE)
+  )
+
+  #testing that subset using filter() gives same result as subset argument
+  sf_filtered <- survfit2(Surv(time, status) ~ sex, data = df_lung %>% dplyr::filter(age >= 75))
+
+  expect_equal(
+    survfit2_p(sf_subset, prepend_p = FALSE),
+    survfit2_p(sf_filtered, prepend_p = FALSE)
+  )
+})