From f5616ea18d9a6fad1e7d5ab8fe46a031b5f85f7d Mon Sep 17 00:00:00 2001
From: Joe Zhu <joe.zhu@roche.com>
Date: Tue, 8 Oct 2024 20:34:30 +0800
Subject: [PATCH] Update DESCRIPTION (#1321)

use survival 3.6-4

# Pull Request

<!--- Replace `#nnn` with your issue link for reference. -->

Fixes #nnn

Signed-off-by: Joe Zhu <joe.zhu@roche.com>
---
 DESCRIPTION                      |  2 +-
 tests/testthat/test-odds_ratio.R | 90 +++++++++++++++++++++-----------
 2 files changed, 60 insertions(+), 32 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5ea0bd0216..3817fc1c69 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -48,7 +48,7 @@ Imports:
     rlang (>= 1.1.0),
     scales (>= 1.2.0),
     stats,
-    survival (>= 3.7-0),
+    survival (>= 3.6-4),
     tibble (>= 2.0.0),
     tidyr (>= 0.8.3),
     utils
diff --git a/tests/testthat/test-odds_ratio.R b/tests/testthat/test-odds_ratio.R
index 0a00b93866..6ab89bbe5c 100644
--- a/tests/testthat/test-odds_ratio.R
+++ b/tests/testthat/test-odds_ratio.R
@@ -30,7 +30,11 @@ testthat::test_that("or_clogit estimates right OR and CI", {
     stringsAsFactors = TRUE
   )
 
-  result <- or_clogit(data, conf_level = 0.95)
+  # https://github.com/therneau/survival/issues/240
+  withr::with_options(
+    opts_partial_match_old,
+    result <- or_clogit(data, conf_level = 0.95)
+  )
 
   # from SAS
   res <- testthat::expect_silent(result)
@@ -62,13 +66,17 @@ testthat::test_that("s_odds_ratio estimates right OR and CI (stratified analysis
     strata = factor(sample(c("C", "D"), 100, TRUE))
   )
 
-  result <- s_odds_ratio(
-    df = subset(dta, grp == "A"),
-    .var = "rsp",
-    .ref_group = subset(dta, grp == "B"),
-    .in_ref_col = FALSE,
-    .df_row = dta,
-    variables = list(arm = "grp", strata = "strata")
+  # https://github.com/therneau/survival/issues/240
+  withr::with_options(
+    opts_partial_match_old,
+    result <- s_odds_ratio(
+      df = subset(dta, grp == "A"),
+      .var = "rsp",
+      .ref_group = subset(dta, grp == "B"),
+      .in_ref_col = FALSE,
+      .df_row = dta,
+      variables = list(arm = "grp", strata = "strata")
+    )
   )
 
   res <- testthat::expect_silent(result)
@@ -86,15 +94,19 @@ testthat::test_that("s_odds_ratio returns error for incorrect groups", {
     "Arms A+B" = c("A", "B")
   )
 
-  testthat::expect_error(result <- s_odds_ratio(
-    df = subset(data, grp == "A"),
-    .var = "rsp",
-    .ref_group = subset(data, grp == "B"),
-    .in_ref_col = FALSE,
-    .df_row = data,
-    variables = list(arm = "grp", strata = "strata"),
-    groups_list = groups
-  ))
+  # https://github.com/therneau/survival/issues/240
+  withr::with_options(
+    opts_partial_match_old,
+    result <- testthat::expect_error(s_odds_ratio(
+      df = subset(data, grp == "A"),
+      .var = "rsp",
+      .ref_group = subset(data, grp == "B"),
+      .in_ref_col = FALSE,
+      .df_row = data,
+      variables = list(arm = "grp", strata = "strata"),
+      groups_list = groups
+    ))
+  )
 })
 
 testthat::test_that("estimate_odds_ratio estimates right OR and CI (unstratified analysis)", {
@@ -120,10 +132,14 @@ testthat::test_that("estimate_odds_ratio estimates right OR and CI (stratified a
     strata = factor(sample(c("C", "D"), 100, TRUE))
   )
 
-  result <- basic_table() %>%
-    split_cols_by(var = "grp", ref_group = "A", split_fun = ref_group_position("first")) %>%
-    estimate_odds_ratio(vars = "rsp", variables = list(arm = "grp", strata = "strata")) %>%
-    build_table(df = data)
+  # https://github.com/therneau/survival/issues/240
+  withr::with_options(
+    opts_partial_match_old,
+    result <- basic_table() %>%
+      split_cols_by(var = "grp", ref_group = "A", split_fun = ref_group_position("first")) %>%
+      estimate_odds_ratio(vars = "rsp", variables = list(arm = "grp", strata = "strata")) %>%
+      build_table(df = data)
+  )
 
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
@@ -154,7 +170,11 @@ testthat::test_that("estimate_odds_ratio works with strata and combined groups",
       groups_list = groups
     )
 
-  result <- build_table(lyt = lyt, df = anl)
+  # https://github.com/therneau/survival/issues/240
+  withr::with_options(
+    opts_partial_match_old,
+    result <- build_table(lyt = lyt, df = anl)
+  )
 
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
@@ -172,14 +192,18 @@ testthat::test_that("s_odds_ratio method argument works", {
     stringsAsFactors = TRUE
   )
 
-  res <- s_odds_ratio(
-    df = subset(dta, grp == "A"),
-    .var = "rsp",
-    .ref_group = subset(dta, grp == "B"),
-    .in_ref_col = FALSE,
-    .df_row = dta,
-    variables = list(arm = "grp", strata = "strata"),
-    method = "approximate"
+  # https://github.com/therneau/survival/issues/240
+  withr::with_options(
+    opts_partial_match_old,
+    res <- s_odds_ratio(
+      df = subset(dta, grp == "A"),
+      .var = "rsp",
+      .ref_group = subset(dta, grp == "B"),
+      .in_ref_col = FALSE,
+      .df_row = dta,
+      variables = list(arm = "grp", strata = "strata"),
+      method = "approximate"
+    )
   )
 
   testthat::expect_false(all(is.na(res$or_ci)))
@@ -213,7 +237,11 @@ testthat::test_that("estimate_odds_ratio method argument works", {
     split_cols_by(var = "grp", ref_group = "B") %>%
     estimate_odds_ratio(vars = "rsp", variables = list(arm = "grp", strata = "strata"), method = "approximate")
 
-  result <- build_table(lyt, df = dta)
+  # https://github.com/therneau/survival/issues/240
+  withr::with_options(
+    opts_partial_match_old,
+    result <- build_table(lyt, df = dta)
+  )
 
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)