Fix all size warnings calls to ggplot2 (deprecated at 3.4.0). Deprecated arg size and added linewidth as new preferred arg where it made sense.

Author: BjarkeHautop

DESCRIPTION

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

NAMESPACE

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

R/mcmc-traces.R

@@ -337,7 +337,7 @@ mcmc_rank_overlay <- function(x,
     geom_hline(
       yintercept = (right_edge / n_bins) / n_chains,
       color = get_color("dark_highlight"),
-      size = 1,
+      linewidth = 1,
       linetype = "dashed"
     )
   } else {
@@ -417,7 +417,7 @@ mcmc_rank_hist <- function(x,
     geom_hline(
       yintercept = (right_edge / n_bins) / n_chains,
       color = get_color("dark_highlight"),
-      size = .5,
+      linewidth = .5,
       linetype = "dashed"
     )
   } else {

R/ppc-censoring.R

@@ -15,8 +15,9 @@
 #' @family PPCs
 #'
 #' @template args-y-yrep
-#' @param size,alpha Passed to the appropriate geom to control the appearance of
+#' @param linewidth,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
@@ -96,17 +97,27 @@ 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,
-  size = 0.25,
+  linewidth = 0.25,
+  size = deprecated(),
   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
 
@@ -173,7 +184,7 @@ ppc_km_overlay <- function(
   }
 
   fsf$is_y_color <- as.factor(sub("\\[rep\\] \\(.*$", "rep", sub("^italic\\(y\\)", "y", fsf$strata)))
-  fsf$is_y_size <- ifelse(fsf$is_y_color == "yrep", size, 1)
+  fsf$is_y_linewidth <- ifelse(fsf$is_y_color == "yrep", linewidth, 1)
   fsf$is_y_alpha <- ifelse(fsf$is_y_color == "yrep", alpha, 1)
 
   max_time_y <- max(y, na.rm = TRUE)
@@ -189,7 +200,7 @@ ppc_km_overlay <- function(
                        y = .data$surv,
                        color = .data$is_y_color,
                        group = .data$strata,
-                       size = .data$is_y_size,
+                       linewidth = .data$is_y_linewidth,
                        alpha = .data$is_y_alpha)) +
     geom_step() +
     hline_at(
@@ -204,7 +215,7 @@ ppc_km_overlay <- function(
       linetype = 2,
       color = get_color("dh")
     ) +
-    scale_size_identity() +
+    scale_linewidth_identity() +
     scale_alpha_identity() +
     scale_color_ppc() +
     scale_y_continuous(breaks = c(0, 0.5, 1)) +
@@ -218,6 +229,7 @@ ppc_km_overlay <- function(
 #' @export
 #' @rdname PPC-censoring
 #' @template args-group
+#' @importFrom lifecycle deprecated
 ppc_km_overlay_grouped <- function(
   y,
   yrep,
@@ -226,9 +238,18 @@ ppc_km_overlay_grouped <- function(
   status_y,
   left_truncation_y = NULL,
   extrapolation_factor = 1.2,
-  size = 0.25,
+  linewidth = 0.25,
+  size = deprecated(),
   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(
@@ -238,7 +259,7 @@ ppc_km_overlay_grouped <- function(
     ...,
     status_y = status_y,
     left_truncation_y = left_truncation_y,
-    size = size,
+    linewidth = linewidth,
     alpha = alpha,
     extrapolation_factor = extrapolation_factor
   )

R/ppc-discrete.R

@@ -359,7 +359,7 @@ ppc_rootogram <- function(y,
     if (style == "standing") {
       graph <- graph + dont_expand_y_axis()
     } else {
-      graph <- graph + hline_0(size = 0.4)
+      graph <- graph + hline_0(linewidth = 0.4)
     }
   }
 

R/ppd-intervals.R

@@ -162,7 +162,7 @@ ppd_ribbon <-
         linewidth = 0.2 * size,
         alpha = 1
       ) +
-      geom_ribbon(size = 0.5 * size) +
+      geom_ribbon(linewidth = 0.5 * size) +
       geom_line(
         mapping = aes(y = .data$m),
         color = get_color("d"),

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, 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(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(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,
-                                   size = 0.5, alpha = 0.2))
+                                   linewidth = 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,
-                                   size = 0.5, alpha = 0.2))
+                                   linewidth = 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,
-                                   size = 0.5, alpha = 0.2))
+                                   linewidth = 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,
-    size = 2,
+    linewidth = 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,
-    size = 2,
+    linewidth = 2,
     alpha = .2
   )