From 1b8169ac784153b7bf9c745e6f6e41f27643b3ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Fri, 8 Dec 2023 08:42:28 -0500
Subject: [PATCH 1/6] move filter function to standalone

---
 R/standalone-survival.R        | 24 ++++++++++++++++++++++++
 R/survival-censoring-weights.R | 25 -------------------------
 2 files changed, 24 insertions(+), 25 deletions(-)

diff --git a/R/standalone-survival.R b/R/standalone-survival.R
index df4808081..57e6c1bcd 100644
--- a/R/standalone-survival.R
+++ b/R/standalone-survival.R
@@ -96,4 +96,28 @@
   }
   unname(res)
 }
+
+.filter_eval_time <- function(eval_time, fail = TRUE) {
+  if (!is.null(eval_time)) {
+    eval_time <- as.numeric(eval_time)
+  }
+  eval_time_0 <- eval_time
+  # will still propagate nulls:
+  eval_time <- eval_time[!is.na(eval_time)]
+  eval_time <- eval_time[eval_time >= 0 & is.finite(eval_time)]
+  eval_time <- unique(eval_time)
+  if (fail && identical(eval_time, numeric(0))) {
+    cli::cli_abort(
+      "There were no usable evaluation times (finite, non-missing, and >= 0).",
+      call = NULL
+    )
+  }
+  if (!identical(eval_time, eval_time_0)) {
+    diffs <- setdiff(eval_time_0, eval_time)
+    cli::cli_warn("There {?was/were} {length(diffs)} inappropriate evaluation
+                  time point{?s} that {?was/were} removed.", call = NULL)
+
+  }
+  eval_time
+}
 # nocov end
diff --git a/R/survival-censoring-weights.R b/R/survival-censoring-weights.R
index 28b935c0c..39ab2626d 100644
--- a/R/survival-censoring-weights.R
+++ b/R/survival-censoring-weights.R
@@ -18,31 +18,6 @@ trunc_probs <- function(probs, trunc = 0.01) {
   probs
 }
 
-.filter_eval_time <- function(eval_time, fail = TRUE) {
-  if (!is.null(eval_time)) {
-    eval_time <- as.numeric(eval_time)
-  }
-  eval_time_0 <- eval_time
-  # will still propagate nulls:
-  eval_time <- eval_time[!is.na(eval_time)]
-  eval_time <- eval_time[eval_time >= 0 & is.finite(eval_time)]
-  eval_time <- unique(eval_time)
-  if (fail && identical(eval_time, numeric(0))) {
-    rlang::abort(
-      "There were no usable evaluation times (finite, non-missing, and >= 0).",
-      call = NULL
-    )
-  }
-  if (!identical(eval_time, eval_time_0)) {
-    diffs <- setdiff(eval_time_0, eval_time)
-    msg <-
-      cli::pluralize(
-        "There {?was/were} {length(diffs)} inappropriate evaluation time point{?s} that {?was/were} removed.")
-    rlang::warn(msg)
-  }
-  eval_time
-}
-
 # nocov start
 # these are tested in extratests
 

From 65fa3350c8f1a7a064fb2df0642b7a3302a85901 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Fri, 8 Dec 2023 08:46:03 -0500
Subject: [PATCH 2/6] reverse changelog order

---
 R/standalone-survival.R | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/R/standalone-survival.R b/R/standalone-survival.R
index 57e6c1bcd..55997f13f 100644
--- a/R/standalone-survival.R
+++ b/R/standalone-survival.R
@@ -5,22 +5,25 @@
 # license: https://unlicense.org
 # ---
 
-# This file provides a portable set of helper functions for Surv objects
+# This file provides a portable set of helper functions for survival analysis.
+#
 
 # ## Changelog
-
-# 2023-02-28:
-# * Initial version
+# 2023-12-08
+# * move .filter_eval_time to this file
 #
-# 2023-05-18
-# * added time to factor conversion
+# 2023-11-09
+# * make sure survival vectors are unnamed.
 #
 # 2023-06-14
 # * removed time to factor conversion
 #
-# 2023-11-09
-# * make sure survival vectors are unnamed.
-
+# 2023-05-18
+# * added time to factor conversion
+#
+# 2023-02-28:
+# * Initial version
+#
 # @param surv A [survival::Surv()] object
 # @details
 # `.is_censored_right()` always returns a logical while

From ad410d614529ddc96772378a77efeaac4552c034 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Fri, 8 Dec 2023 08:47:08 -0500
Subject: [PATCH 3/6] versioning and docs

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 944167379..e6477f6ed 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: parsnip
 Title: A Common API to Modeling and Analysis Functions
-Version: 1.1.1.9004
+Version: 1.1.1.9005
 Authors@R: c(
     person("Max", "Kuhn", , "max@posit.co", role = c("aut", "cre")),
     person("Davis", "Vaughan", , "davis@posit.co", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index f409d97eb..55d83f157 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
 # parsnip (development version)
 
+* `.filter_eval_time()` was moved to the survival standalone file. 
+
 * Improved errors and documentation related to special terms in formulas. See `?model_formula` to learn more. (#770, #1014)
 
 * Improved errors in cases where the outcome column is mis-specified. (#1003)

From 07ae1621136c4811250da6d17ae9a7f71521ae70 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Fri, 8 Dec 2023 08:57:10 -0500
Subject: [PATCH 4/6] comments and updated date

---
 R/standalone-survival.R | 40 ++++++++++++++++++++++++++++------------
 1 file changed, 28 insertions(+), 12 deletions(-)

diff --git a/R/standalone-survival.R b/R/standalone-survival.R
index 55997f13f..208577ed1 100644
--- a/R/standalone-survival.R
+++ b/R/standalone-survival.R
@@ -1,7 +1,7 @@
 # ---
 # repo: tidymodels/parsnip
 # file: standalone-survival.R
-# last-updated: 2023-06-14
+# last-updated: 2023-12-08
 # license: https://unlicense.org
 # ---
 
@@ -24,6 +24,8 @@
 # 2023-02-28:
 # * Initial version
 #
+# ------------------------------------------------------------------------------
+#
 # @param surv A [survival::Surv()] object
 # @details
 # `.is_censored_right()` always returns a logical while
@@ -54,17 +56,23 @@
   attr(surv, "type")
 }
 
-.check_cens_type <- function(surv, type = "right", fail = TRUE, call = rlang::caller_env()) {
-  .is_surv(surv, call = call)
-  obj_type <- .extract_surv_type(surv)
-  good_type <- all(obj_type %in% type)
-  if (!good_type && fail) {
-    c_list <- paste0("'", type, "'")
-    msg <- cli::format_inline("For this usage, the allowed censoring type{?s} {?is/are}: {c_list}")
-    rlang::abort(msg, call = call)
+.check_cens_type <-
+  function(surv,
+           type = "right",
+           fail = TRUE,
+           call = rlang::caller_env()) {
+    .is_surv(surv, call = call)
+    obj_type <- .extract_surv_type(surv)
+    good_type <- all(obj_type %in% type)
+    if (!good_type && fail) {
+      c_list <- paste0("'", type, "'")
+      msg <-
+        cli::format_inline("For this usage, the allowed censoring type{?s}
+                            {?is/are}: {c_list}")
+      rlang::abort(msg, call = call)
+    }
+    good_type
   }
-  good_type
-}
 
 .is_censored_right <- function(surv) {
   .check_cens_type(surv, type = "right", fail = FALSE)
@@ -91,7 +99,8 @@
   .is_surv(surv)
   res <-   surv[, "status"]
   un_vals <- sort(unique(res))
-  event_type_to_01 <- !(.extract_surv_type(surv) %in% c("interval", "interval2", "mstate"))
+  event_type_to_01 <-
+    !(.extract_surv_type(surv) %in% c("interval", "interval2", "mstate"))
   if (
     event_type_to_01 &&
     (identical(un_vals, 1:2) | identical(un_vals, c(1.0, 2.0))) ) {
@@ -100,6 +109,13 @@
   unname(res)
 }
 
+# ------------------------------------------------------------------------------
+
+# @param eval_time A vector of numeric time points
+# @details
+# `.filter_eval_time` checks the validity of the time points.
+#
+# @return A potentially modified vector of time points.
 .filter_eval_time <- function(eval_time, fail = TRUE) {
   if (!is.null(eval_time)) {
     eval_time <- as.numeric(eval_time)

From ee10a3bdad55b172812755a2321b4ea200fed920 Mon Sep 17 00:00:00 2001
From: Hannah Frick <hannah@posit.co>
Date: Mon, 11 Dec 2023 11:08:47 +0000
Subject: [PATCH 5/6] move corresponding test

---
 R/standalone-survival.R                       |  3 +-
 ...ring-weights.md => standalone-survival.md} |  0
 tests/testthat/test-standalone-survival.R     | 28 ++++++++++++++++++
 .../test-survival-censoring-weights.R         | 29 -------------------
 4 files changed, 30 insertions(+), 30 deletions(-)
 rename tests/testthat/_snaps/{survival-censoring-weights.md => standalone-survival.md} (100%)
 create mode 100644 tests/testthat/test-standalone-survival.R

diff --git a/R/standalone-survival.R b/R/standalone-survival.R
index 208577ed1..501bfb5fe 100644
--- a/R/standalone-survival.R
+++ b/R/standalone-survival.R
@@ -109,6 +109,8 @@
   unname(res)
 }
 
+# nocov end
+
 # ------------------------------------------------------------------------------
 
 # @param eval_time A vector of numeric time points
@@ -139,4 +141,3 @@
   }
   eval_time
 }
-# nocov end
diff --git a/tests/testthat/_snaps/survival-censoring-weights.md b/tests/testthat/_snaps/standalone-survival.md
similarity index 100%
rename from tests/testthat/_snaps/survival-censoring-weights.md
rename to tests/testthat/_snaps/standalone-survival.md
diff --git a/tests/testthat/test-standalone-survival.R b/tests/testthat/test-standalone-survival.R
new file mode 100644
index 000000000..eac864921
--- /dev/null
+++ b/tests/testthat/test-standalone-survival.R
@@ -0,0 +1,28 @@
+test_that(".filter_eval_time()", {
+  times_basic <- 0:10
+  expect_equal(
+    parsnip:::.filter_eval_time(times_basic),
+    times_basic
+  )
+
+  times_dont_reorder <- c(10, 1:9)
+  expect_equal(
+    parsnip:::.filter_eval_time(times_dont_reorder),
+    times_dont_reorder
+  )
+
+  expect_null(parsnip:::.filter_eval_time(NULL))
+
+  times_duplicated <- c(times_basic, times_basic)
+  expect_snapshot(
+    parsnip:::.filter_eval_time(times_duplicated)
+  )
+
+  expect_snapshot(error = TRUE, parsnip:::.filter_eval_time(-1))
+
+  times_remove_plural <- c(Inf, NA, -3, times_basic)
+  expect_snapshot(parsnip:::.filter_eval_time(times_remove_plural))
+
+  times_remove_singular <- c(-3, times_basic)
+  expect_snapshot(parsnip:::.filter_eval_time(times_remove_singular))
+})
diff --git a/tests/testthat/test-survival-censoring-weights.R b/tests/testthat/test-survival-censoring-weights.R
index 3885c35a4..770b5f6a1 100644
--- a/tests/testthat/test-survival-censoring-weights.R
+++ b/tests/testthat/test-survival-censoring-weights.R
@@ -21,32 +21,3 @@ test_that("probability truncation via trunc_probs()", {
     probs
   )
 })
-
-test_that(".filter_eval_time()", {
-  times_basic <- 0:10
-  expect_equal(
-    parsnip:::.filter_eval_time(times_basic),
-    times_basic
-  )
-
-  times_dont_reorder <- c(10, 1:9)
-  expect_equal(
-    parsnip:::.filter_eval_time(times_dont_reorder),
-    times_dont_reorder
-  )
-
-  expect_null(parsnip:::.filter_eval_time(NULL))
-
-  times_duplicated <- c(times_basic, times_basic)
-  expect_snapshot(
-    parsnip:::.filter_eval_time(times_duplicated)
-  )
-
-  expect_snapshot(error = TRUE, parsnip:::.filter_eval_time(-1))
-
-  times_remove_plural <- c(Inf, NA, -3, times_basic)
-  expect_snapshot(parsnip:::.filter_eval_time(times_remove_plural))
-
-  times_remove_singular <- c(-3, times_basic)
-  expect_snapshot(parsnip:::.filter_eval_time(times_remove_singular))
-})

From 94f457478b371f9b3609bf226fe1221aec8b3801 Mon Sep 17 00:00:00 2001
From: Max Kuhn <mxkuhn@gmail.com>
Date: Mon, 11 Dec 2023 06:52:38 -0500
Subject: [PATCH 6/6] revert msg formatting

---
 R/standalone-survival.R | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/R/standalone-survival.R b/R/standalone-survival.R
index 501bfb5fe..bf46c1346 100644
--- a/R/standalone-survival.R
+++ b/R/standalone-survival.R
@@ -66,9 +66,7 @@
     good_type <- all(obj_type %in% type)
     if (!good_type && fail) {
       c_list <- paste0("'", type, "'")
-      msg <-
-        cli::format_inline("For this usage, the allowed censoring type{?s}
-                            {?is/are}: {c_list}")
+      msg <- cli::format_inline("For this usage, the allowed censoring type{?s} {?is/are}: {c_list}")
       rlang::abort(msg, call = call)
     }
     good_type