Remove deprecations warnings to size

Author: BjarkeHautop

DESCRIPTION

@@ -34,7 +34,6 @@ Imports:
     ggplot2 (>= 3.4.0),
     ggridges (>= 0.5.5),
     glue,
-    lifecycle,
     posterior,
     reshape2,
     rlang (>= 0.3.0),

NAMESPACE

@@ -224,4 +224,3 @@ importFrom(dplyr,top_n)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
 importFrom(ggplot2,"%+replace%")
-importFrom(lifecycle,deprecated)

R/ppc-censoring.R

@@ -15,9 +15,8 @@
 #' @family PPCs
 #'
 #' @template args-y-yrep
-#' @param linewidth,alpha Passed to the appropriate geom to control the appearance of
+#' @param size,alpha Passed to the appropriate geom to control the appearance of
 #'   the `yrep` distributions.
-#' @param size `r lifecycle::badge("deprecated")` Please use `linewidth` instead of `size`.
 #' @param ... Currently only used internally.
 #'
 #' @template return-ggplot
@@ -97,27 +96,16 @@ NULL
 #'   posterior predictive draws may not be shown by default because of the
 #'   controlled extrapolation. To display all posterior predictive draws, set
 #'   `extrapolation_factor = Inf`.
-#' @importFrom lifecycle deprecated
 ppc_km_overlay <- function(
   y,
   yrep,
   ...,
   status_y,
   left_truncation_y = NULL,
   extrapolation_factor = 1.2,
-  linewidth = 0.25,
-  size = deprecated(),
+  size = 0.25,
   alpha = 0.7
 ) {
-  if (lifecycle::is_present(size)) {
-    lifecycle::deprecate_warn(
-      "1.16.0",
-      "ppc_km_overlay(size)",
-      details = "Please use `linewidth` instead of `size`."
-    )
-    linewidth <- size
-  }
-
   check_ignored_arguments(..., ok_args = "add_group")
   add_group <- list(...)$add_group
 
@@ -184,7 +172,7 @@ ppc_km_overlay <- function(
   }
 
   fsf$is_y_color <- as.factor(sub("\\[rep\\] \\(.*$", "rep", sub("^italic\\(y\\)", "y", fsf$strata)))
-  fsf$is_y_linewidth <- ifelse(fsf$is_y_color == "yrep", linewidth, 1)
+  fsf$is_y_linewidth <- ifelse(fsf$is_y_color == "yrep", size, 1)
   fsf$is_y_alpha <- ifelse(fsf$is_y_color == "yrep", alpha, 1)
 
   max_time_y <- max(y, na.rm = TRUE)
@@ -229,7 +217,6 @@ ppc_km_overlay <- function(
 #' @export
 #' @rdname PPC-censoring
 #' @template args-group
-#' @importFrom lifecycle deprecated
 ppc_km_overlay_grouped <- function(
   y,
   yrep,
@@ -238,18 +225,9 @@ ppc_km_overlay_grouped <- function(
   status_y,
   left_truncation_y = NULL,
   extrapolation_factor = 1.2,
-  linewidth = 0.25,
-  size = deprecated(),
+  size = 0.25,
   alpha = 0.7
 ) {
-  if (lifecycle::is_present(size)) {
-    lifecycle::deprecate_warn(
-      "1.16.0",
-      "ppc_km_overlay_grouped(size)",
-      details = "Please use `linewidth` instead of `size`."
-    )
-    linewidth <- size
-  }
   check_ignored_arguments(...)
 
   p_overlay <- ppc_km_overlay(
@@ -259,7 +237,7 @@ ppc_km_overlay_grouped <- function(
     ...,
     status_y = status_y,
     left_truncation_y = left_truncation_y,
-    linewidth = linewidth,
+    size = size,
     alpha = alpha,
     extrapolation_factor = extrapolation_factor
   )

man/PPC-censoring.Rd

@@ -2,8 +2,8 @@ source(test_path("data-for-ppc-tests.R"))
 
 test_that("ppc_km_overlay returns a ggplot object", {
   skip_if_not_installed("ggfortify")
-  expect_gg(ppc_km_overlay(y, yrep, status_y = status_y, left_truncation_y = left_truncation_y, linewidth = 0.5, alpha = 0.2, extrapolation_factor = Inf))
-  expect_gg(ppc_km_overlay(y, yrep, status_y = status_y, left_truncation_y = left_truncation_y, linewidth = 0.5, alpha = 0.2, extrapolation_factor = 1))
+  expect_gg(ppc_km_overlay(y, yrep, status_y = status_y, left_truncation_y = left_truncation_y, size = 0.5, alpha = 0.2, extrapolation_factor = Inf))
+  expect_gg(ppc_km_overlay(y, yrep, status_y = status_y, left_truncation_y = left_truncation_y, size = 0.5, alpha = 0.2, extrapolation_factor = 1))
   expect_gg(ppc_km_overlay(y2, yrep2, status_y = status_y2))
 })
 
@@ -12,15 +12,15 @@ test_that("ppc_km_overlay_grouped returns a ggplot object", {
   expect_gg(ppc_km_overlay_grouped(y, yrep, group,
                                    status_y = status_y,
                                    left_truncation_y = left_truncation_y,
-                                   linewidth = 0.5, alpha = 0.2))
+                                   size = 0.5, alpha = 0.2))
   expect_gg(ppc_km_overlay_grouped(y, yrep, as.numeric(group),
                                    status_y = status_y,
                                    left_truncation_y = left_truncation_y,
-                                   linewidth = 0.5, alpha = 0.2))
+                                   size = 0.5, alpha = 0.2))
   expect_gg(ppc_km_overlay_grouped(y, yrep, as.integer(group),
                                    status_y = status_y,
                                    left_truncation_y = left_truncation_y,
-                                   linewidth = 0.5, alpha = 0.2))
+                                   size = 0.5, alpha = 0.2))
 
   expect_gg(ppc_km_overlay_grouped(y2, yrep2, group2,
                                    status_y = status_y2))
@@ -89,7 +89,7 @@ test_that("ppc_km_overlay renders correctly", {
     vdiff_y2,
     vdiff_yrep2,
     status_y = vdiff_status_y2,
-    linewidth = 2,
+    size = 2,
     alpha = .2)
   vdiffr::expect_doppelganger("ppc_km_overlay (size, alpha)", p_custom)
 
@@ -138,7 +138,7 @@ test_that("ppc_km_overlay_grouped renders correctly", {
     vdiff_yrep2,
     vdiff_group2,
     status_y = vdiff_status_y2,
-    linewidth = 2,
+    size = 2,
     alpha = .2
   )