Update deprecation warnings with lifecycle

NEWS.md

@@ -1,5 +1,7 @@
 # GGally (development version)
 
+* Use lifecycle for deprecation warnings (#494, #496)
+
 # GGally 2.2.1
 
 * Fix compatibility with ggplot2 3.5.0 (@teunbrand, #481)

R/deprecated.R

@@ -1,16 +1,48 @@
 #' Modify a \code{\link{ggmatrix}} object by adding an \pkg{ggplot2} object to all
+#' @description
+#' `r lifecycle::badge("deprecated")`
 #'
-# \lifecycle{deprecated}
+#' This function allows cleaner axis labels for your plots, but is deprecated.
+#' You can achieve the same effect by specifying strip's background and placement
+#' properties (see Examples).
+#'
+#' @keywords internal
 #'
 #' @export
 #' @examples
 #' # Small function to display plots only if it's interactive
 #' p_ <- GGally::print_if_interactive
 #'
+#' # Cleaner axis labels with v1_ggmatrix_theme
 #' p_(ggpairs(iris, 1:2) + v1_ggmatrix_theme())
-#' # move the column names to the left and bottom
+#'
+#' # Move the column names to the left and bottom
 #' p_(ggpairs(iris, 1:2, switch = "both") + v1_ggmatrix_theme())
+#'
+#' # Manually specifying axis labels properties
+#' p_(
+#'   ggpairs(iris, 1:2) +
+#'   theme(
+#'     strip.background = element_rect(fill = "white"),
+#'     strip.placement = "outside"
+#'   )
+#')
+#'
+#' # This way you have even more control over how the final plot looks.
+#' # For example, if you want to set the background color to yellow:
+#' p_(
+#'   ggpairs(iris, 1:2) +
+#'   theme(
+#'     strip.background = element_rect(fill = "yellow"),
+#'     strip.placement = "outside"
+#'   )
+#')
 v1_ggmatrix_theme <- function() {
+  lifecycle::deprecate_soft(
+    when = "2.2.2",
+    what = "v1_ggmatrix_theme()",
+    details = "This function will be removed in future releases."
+  )
   theme(
     strip.background = element_rect(fill = "white"),
     strip.placement = "outside"
@@ -20,12 +52,15 @@ v1_ggmatrix_theme <- function() {
 
 #' Correlation value plot
 #'
-# \lifecycle{deprecated}
-#'
-#' (Deprecated. See \code{\link{ggally_cor}}.)
+#' @description
+#' `r lifecycle::badge("deprecated")`
 #'
 #' Estimate correlation from the given data.
 #'
+#' This function is deprecated and will be removed in future releases.
+#'
+#' See \code{\link{ggally_cor}}.
+#'
 #' @param data data set using
 #' @param mapping aesthetics being used
 #' @param alignPercent right align position of numbers. Default is 60 percent across the horizontal
@@ -40,7 +75,7 @@ v1_ggmatrix_theme <- function() {
 #' @importFrom stats complete.cases cor
 #' @seealso \code{\link{ggally_cor}}
 #' @export
-#' @keywords hplot
+#' @keywords internal
 #' @examples
 #' # Small function to display plots only if it's interactive
 #' p_ <- GGally::print_if_interactive
@@ -77,6 +112,11 @@ ggally_cor_v1_5 <- function(
     corAlignPercent = NULL, corMethod = NULL, corUse = NULL,
     displayGrid = TRUE,
     ...) {
+  lifecycle::deprecate_soft(
+    when = "2.2.2",
+    what = "ggally_cor_v1_5()",
+    with = "ggally_cor()"
+  )
   if (!is.null(corAlignPercent)) {
     stop("'corAlignPercent' is deprecated.  Please use argument 'alignPercent'")
   }

R/gg-plots.R

@@ -261,10 +261,11 @@ ggally_density <- function(data, mapping, ...) {
 #' @param group_args arguments being supplied to the split-by-color group's \code{\link[ggplot2]{geom_text}()}
 #' @param justify_labels \code{justify} argument supplied when \code{\link[base]{format}}ting the labels
 #' @param align_percent relative align position of the text. When \code{justify_labels = 0.5}, this should not be needed to be set.
-#' @param alignPercent,displayGrid deprecated. Please use their snake-case counterparts.
+#' @param alignPercent,displayGrid `r lifecycle::badge("deprecated")`. Please use their snake-case counterparts.
 #' @param title title text to be displayed
 #' @author Barret Schloerke
 #' @importFrom stats complete.cases cor
+#' @importFrom lifecycle deprecated
 #' @seealso \code{\link{ggally_statistic}}, \code{\link{ggally_cor_v1_5}}
 #' @export
 #' @keywords hplot
@@ -308,14 +309,22 @@ ggally_cor <- function(
     justify_labels = "right",
     align_percent = 0.5,
     title = "Corr",
-    alignPercent = warning("deprecated. Use `align_percent`"),
-    displayGrid = warning("deprecated. Use `display_grid`")) {
-  if (!missing(alignPercent)) {
-    warning("`alignPercent` is deprecated. Please use `align_percent` if alignment still needs to be adjusted")
+    alignPercent = deprecated(),
+    displayGrid = deprecated()) {
+  if (lifecycle::is_present(alignPercent)) {
+    lifecycle::deprecate_soft(
+      when = "2.2.2",
+      what = "ggally_cor(alignPercent)",
+      details = "Please use `align_percent` if alignment still needs to be adjusted."
+    )
     align_percent <- alignPercent
   }
-  if (!missing(displayGrid)) {
-    warning("`displayGrid` is deprecated. Please use `display_grid`")
+  if (lifecycle::is_present(displayGrid)) {
+    lifecycle::deprecate_soft(
+      when = "2.2.2",
+      what = "ggally_cor(displayGrid)",
+      details = "Please use `display_grid`"
+    )
     display_grid <- displayGrid
   }
 

R/ggmatrix_gtable.R

@@ -4,7 +4,7 @@
 #'
 #' @param pm \code{\link{ggmatrix}} object to be plotted
 #' @param ... ignored
-#' @param progress,progress_format Please use the 'progress' parameter in your \code{\link{ggmatrix}}-like function.  See \code{\link{ggmatrix_progress}} for a few examples.  These parameters will soon be deprecated.
+#' @param progress,progress_format `r lifecycle::badge("deprecated")` Please use the 'progress' parameter in your \code{\link{ggmatrix}}-like function.  See \code{\link{ggmatrix_progress}} for a few examples.
 #' @author Barret Schloerke
 #' @importFrom grid gpar grid.layout grid.newpage grid.text grid.rect popViewport pushViewport viewport grid.draw
 #' @export
@@ -25,7 +25,11 @@ ggmatrix_gtable <- function(
     hasProgressBar <- !isFALSE(pm$progress)
     progress_fn <- pm$progress
   } else {
-    warning("Please use the 'progress' parameter in your ggmatrix-like function call.  See ?ggmatrix_progress for a few examples.  ggmatrix_gtable 'progress' and 'progress_format' will soon be deprecated.", immediate = TRUE)
+    lifecycle::deprecate_soft(
+      when = "2.2.2",
+      what = I("`progress` and `progress_format`"),
+      details = "Please use the 'progress' parameter in your ggmatrix-like function call.  See ?ggmatrix_progress for a few examples."
+    )
 
     # has progress variable defined
     # overrides pm$progress

R/ggnet.R

@@ -4,6 +4,9 @@ if (getRversion() >= "2.15.1") {
 
 #' Network plot
 #'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
 #' Function for plotting network objects using \pkg{ggplot2}, now replaced by the
 #' \code{\link{ggnet2}} function, which provides additional control over
 #' plotting parameters. Please visit \url{https://github.com/briatte/ggnet} for
@@ -114,12 +117,12 @@ if (getRversion() >= "2.15.1") {
 #' @param legend.position the location of the plot legend(s). Accepts all
 #' \code{legend.position} values supported by \code{\link[ggplot2]{theme}}.
 #' Defaults to \code{"right"}.
-#' @param names deprecated: see \code{group.legend} and \code{size.legend}
-#' @param quantize.weights deprecated: see \code{weight.cut}
-#' @param subset.threshold deprecated: see \code{weight.min}
-#' @param top8.nodes deprecated: this functionality was experimental and has
+#' @param names `r lifecycle::badge("deprecated")` see \code{group.legend} and \code{size.legend}
+#' @param quantize.weights `r lifecycle::badge("deprecated")` see \code{weight.cut}
+#' @param subset.threshold `r lifecycle::badge("deprecated")` see \code{weight.min}
+#' @param top8.nodes `r lifecycle::badge("deprecated")` this functionality was experimental and has
 #' been removed entirely from \code{ggnet}
-#' @param trim.labels deprecated: see \code{label.trim}
+#' @param trim.labels `r lifecycle::badge("deprecated")` see \code{label.trim}
 #' @param ... other arguments passed to the \code{geom_text} object that sets
 #' the node labels: see \code{\link[ggplot2]{geom_text}} for details.
 #' @seealso \code{\link{ggnet2}} in this package,
@@ -135,6 +138,7 @@ if (getRversion() >= "2.15.1") {
 #' @importFrom stats quantile na.omit
 #' @importFrom utils head installed.packages
 #' @importFrom grDevices gray.colors
+#' @keywords internal
 #' @examples
 #' # Small function to display plots only if it's interactive
 #' p_ <- GGally::print_if_interactive
@@ -199,46 +203,70 @@ ggnet <- function(
   legend.size      = 9,
   legend.position  = "right",
   # -- deprecated arguments ----------------------------------------------------
-  names            = c("", ""),
-  quantize.weights = FALSE,
-  subset.threshold = 0,
-  top8.nodes       = FALSE,
-  trim.labels      = FALSE,
+  names            = deprecated(),
+  quantize.weights = deprecated(),
+  subset.threshold = deprecated(),
+  top8.nodes       = deprecated(),
+  trim.labels      = deprecated(),
   ...
 ) {
+  lifecycle::deprecate_soft("2.2.2", "ggnet()", "ggnet2()")
 
   # -- packages ----------------------------------------------------------------
 
   require_namespaces(c("network", "sna", "scales"))
   # -- deprecations ------------------------------------------------------------
 
   if (length(mode) == 1 && mode == "geo") {
-    warning("mode = 'geo' is deprecated; please use mode = c('lon', 'lat') instead")
+    lifecycle::deprecate_warn(
+      when = "2.2.2",
+      what = "ggnet(mode='cannot be `geo`')",
+      details = "Please use mode = c('lon', 'lat') instead"
+    )
     mode = c("lon", "lat")
   }
 
-  if (!identical(names, c("", ""))) {
-    warning("names is deprecated; please use group.legend and size.legend instead")
+  if (lifecycle::is_present(names)) {
+    lifecycle::deprecate_warn(
+      when = "2.2.2",
+      what = "ggnet(names)",
+      details = "Please use group.legend and size.legend instead"
+    )
     group.legend = names[1]
     size.legend  = names[2]
   }
 
-  if (isTRUE(quantize.weights)) {
-    warning("quantize.weights is deprecated; please use weight.cut instead")
-    weight.cut = TRUE
+  if (lifecycle::is_present(quantize.weights)) {
+    lifecycle::deprecate_warn(
+      when = "2.2.2",
+      what = "ggnet(quantize.weights)",
+      details = "Please use weight.cut instead"
+    )
+    weight.cut = quantize.weights
   }
 
-  if (subset.threshold > 0) {
-    warning("subset.threshold is deprecated; please use weight.min instead")
+  if (lifecycle::is_present(subset.threshold)) {
+    lifecycle::deprecate_warn(
+      when = "2.2.2",
+      what = "ggnet(subset.threshold)",
+      details = "Please use weight.min instead"
+    )
     weight.min = subset.threshold
   }
 
-  if (isTRUE(top8.nodes)) {
-    warning("top8.nodes is deprecated")
+  if (lifecycle::is_present(top8.nodes)) {
+    lifecycle::deprecate_warn(
+      when = "2.2.2",
+      what = "ggnet(top8.nodes)"
+    )
   }
 
-  if (isTRUE(trim.labels)) {
-    warning("trim.labels is deprecated; please use label.trim instead")
+  if (lifecycle::is_present(trim.labels)) {
+    lifecycle::deprecate_warn(
+      when = "2.2.2",
+      what = "ggnet(trim.labels)",
+      details = "Please use label.trim instead"
+    )
     label.trim = function(x) gsub("^@|^http://(www\\.)?|/$", "", x)
   }