Merge pull request #454 from tidymodels/soft-deprecate-surv_reg

Soft-deprecate `surv_reg()`

Author: hfrick

NEWS.md

@@ -6,7 +6,7 @@
 
 * A new linear SVM model `svm_linear()` is now available with the `LiblineaR` engine (#424) and the `kernlab` engine (#438), and the `LiblineaR` engine is available for `logistic_reg()` as well (#429). These models can use sparse matrices via `fit_xy()` (#447).
 
-* New model specification `survival_reg()` for the new mode `"censored regression"`. (#444)
+* New model specification `survival_reg()` for the new mode `"censored regression"` (#444). `surv_reg()` is now soft-deprecated (#448).
 
 * New model specification `proportional_hazards()` for the `"censored regression"` mode (#451).
 

R/surv_reg.R

@@ -1,5 +1,11 @@
 #' General Interface for Parametric Survival Models
 #'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' This function is soft-deprecated in favor of `survival_reg()` which uses the
+#' `"censored regression"` mode.
+#'
 #' `surv_reg()` is a way to generate a _specification_ of a model
 #'  before fitting and allows the model to be created using
 #'  R. The main argument for the
@@ -51,9 +57,19 @@
 #' # Parameters can be represented by a placeholder:
 #' surv_reg(dist = varying())
 #'
+#' # ->
+#' show_engines("survival_reg")
+#'
+#' survival_reg()
+#' # Parameters can be represented by a placeholder:
+#' survival_reg(dist = varying())
+#'
+#' @keywords internal
 #' @export
 surv_reg <- function(mode = "regression", dist = NULL) {
 
+  lifecycle::deprecate_soft("0.1.6", "surv_reg()", "survival_reg()")
+
     args <- list(
       dist = enquo(dist)
     )

man/figures/lifecycle-archived.svg

@@ -11,6 +11,8 @@ source("helpers.R")
 # ------------------------------------------------------------------------------
 
 test_that('primary arguments', {
+  rlang::local_options(lifecycle_verbosity = "quiet")
+
   basic <- surv_reg()
   basic_flexsurv <- translate(basic %>% set_engine("flexsurv"))
 
@@ -46,6 +48,8 @@ test_that('primary arguments', {
 })
 
 test_that('engine arguments', {
+  rlang::local_options(lifecycle_verbosity = "quiet")
+
   fs_cl <- surv_reg()
   expect_equal(translate(fs_cl %>% set_engine("flexsurv", cl = .99))$method$fit$args,
                list(
@@ -60,6 +64,8 @@ test_that('engine arguments', {
 
 
 test_that('updating', {
+  rlang::local_options(lifecycle_verbosity = "quiet")
+
   expr1     <- surv_reg() %>% set_engine("flexsurv", cl = varying())
   expr1_exp <- surv_reg(dist = "lnorm") %>% set_engine("flexsurv", cl = .99)
   expect_equal(update(expr1, dist = "lnorm", cl = 0.99), expr1_exp)
@@ -75,7 +81,14 @@ test_that('updating', {
 })
 
 test_that('bad input', {
+  rlang::local_options(lifecycle_verbosity = "quiet")
+
   expect_error(surv_reg(mode = ", classification"))
   expect_error(translate(surv_reg() %>% set_engine("wat")))
   expect_error(translate(surv_reg() %>% set_engine(NULL)))
 })
+
+test_that("deprecation warning", {
+  rlang::local_options(lifecycle_verbosity = "warning")
+  expect_warning(surv_reg())
+})

man/figures/lifecycle-defunct.svg

@@ -8,17 +8,17 @@ library(tibble)
 
 source(test_path("helper-objects.R"))
 
-
 basic_form <- Surv(time, status) ~ age
 complete_form <- Surv(time) ~ age
 
-surv_basic <- surv_reg() %>% set_engine("flexsurv")
-
 # ------------------------------------------------------------------------------
 
 test_that('flexsurv execution', {
   skip_if_not_installed("flexsurv")
 
+  rlang::local_options(lifecycle_verbosity = "quiet")
+  surv_basic <- surv_reg() %>% set_engine("flexsurv")
+
   expect_error(
     res <- fit(
       surv_basic,
@@ -53,6 +53,9 @@ test_that('flexsurv execution', {
 test_that('flexsurv prediction', {
   skip_if_not_installed("flexsurv")
 
+  rlang::local_options(lifecycle_verbosity = "quiet")
+  surv_basic <- surv_reg() %>% set_engine("flexsurv")
+
   res <- fit(
     surv_basic,
     Surv(time, status) ~ age,

man/figures/lifecycle-deprecated.svg

@@ -10,15 +10,15 @@ source(test_path("helper-objects.R"))
 basic_form <- Surv(time, status) ~ group
 complete_form <- Surv(time) ~ group
 
-surv_basic <- surv_reg() %>% set_engine("survival")
-surv_lnorm <- surv_reg(dist = "lognormal") %>% set_engine("survival")
-
 # ------------------------------------------------------------------------------
 
 test_that('survival execution', {
-
   skip_on_travis()
 
+  rlang::local_options(lifecycle_verbosity = "quiet")
+  surv_basic <- surv_reg() %>% set_engine("survival")
+  surv_lnorm <- surv_reg(dist = "lognormal") %>% set_engine("survival")
+
   expect_error(
     res <- fit(
       surv_basic,
@@ -51,6 +51,10 @@ test_that('survival execution', {
 test_that('survival prediction', {
   skip_on_travis()
 
+  rlang::local_options(lifecycle_verbosity = "quiet")
+  surv_basic <- surv_reg() %>% set_engine("survival")
+  surv_lnorm <- surv_reg(dist = "lognormal") %>% set_engine("survival")
+
   res <- fit(
     surv_basic,
     Surv(time, status) ~ age + sex,