From 349d440857d369501209acec8e4093fe123169b8 Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Thu, 18 Apr 2024 20:08:33 -0300
Subject: [PATCH 1/9] chore: Update deprecation warnings in ggally_cor function

---
 NEWS.md           |  2 ++
 R/gg-plots.R      | 23 ++++++++++++++++-------
 man/ggally_cor.Rd |  6 +++---
 3 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 12445271a..5b5b511b4 100644
--- a/NEWS.md
+++ b/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)
diff --git a/R/gg-plots.R b/R/gg-plots.R
index 588722f29..1cbbcab95 100644
--- a/R/gg-plots.R
+++ b/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
   }
 
diff --git a/man/ggally_cor.Rd b/man/ggally_cor.Rd
index 13a33a789..cc361f863 100644
--- a/man/ggally_cor.Rd
+++ b/man/ggally_cor.Rd
@@ -18,8 +18,8 @@ ggally_cor(
   justify_labels = "right",
   align_percent = 0.5,
   title = "Corr",
-  alignPercent = warning("deprecated. Use `align_percent`"),
-  displayGrid = warning("deprecated. Use `display_grid`")
+  alignPercent = deprecated(),
+  displayGrid = deprecated()
 )
 }
 \arguments{
@@ -55,7 +55,7 @@ ggally_cor(
 
 \item{title}{title text to be displayed}
 
-\item{alignPercent, displayGrid}{deprecated. Please use their snake-case counterparts.}
+\item{alignPercent, displayGrid}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}. Please use their snake-case counterparts.}
 }
 \description{
 Estimate correlation from the given data. If a color variable is supplied, the correlation will also be calculated per group.

From abe82d8bff96aa35512126b5d9f6b5edd7cceb9e Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Mon, 22 Apr 2024 19:38:05 -0300
Subject: [PATCH 2/9] Update v1_ggmatrix_theme deprecation warning

---
 R/deprecated.R                      | 36 +++++++++++++++++++++++++++--
 man/v1_ggmatrix_theme.Rd            | 29 +++++++++++++++++++++--
 tests/testthat/_snaps/deprecated.md | 22 ++++++++++++++++++
 tests/testthat/test-deprecated.R    |  6 +++++
 4 files changed, 89 insertions(+), 4 deletions(-)
 create mode 100644 tests/testthat/_snaps/deprecated.md

diff --git a/R/deprecated.R b/R/deprecated.R
index c81a507bf..c79d69b57 100644
--- a/R/deprecated.R
+++ b/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"
diff --git a/man/v1_ggmatrix_theme.Rd b/man/v1_ggmatrix_theme.Rd
index 87e8ed474..c65ebe6eb 100644
--- a/man/v1_ggmatrix_theme.Rd
+++ b/man/v1_ggmatrix_theme.Rd
@@ -7,13 +7,38 @@
 v1_ggmatrix_theme()
 }
 \description{
-Modify a \code{\link{ggmatrix}} object by adding an \pkg{ggplot2} object to all
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[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).
 }
 \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"
+  )
+)
 }
diff --git a/tests/testthat/_snaps/deprecated.md b/tests/testthat/_snaps/deprecated.md
new file mode 100644
index 000000000..76ba7ca1b
--- /dev/null
+++ b/tests/testthat/_snaps/deprecated.md
@@ -0,0 +1,22 @@
+# v1_ggmatrix_theme is deprecated
+
+    Code
+      v1_ggmatrix_theme()
+    Condition
+      Warning:
+      `v1_ggmatrix_theme()` was deprecated in GGally 2.2.2.
+      i This function will be removed in future releases.
+    Output
+      List of 2
+       $ strip.background:List of 5
+        ..$ fill         : chr "white"
+        ..$ colour       : NULL
+        ..$ linewidth    : NULL
+        ..$ linetype     : NULL
+        ..$ inherit.blank: logi FALSE
+        ..- attr(*, "class")= chr [1:2] "element_rect" "element"
+       $ strip.placement : chr "outside"
+       - attr(*, "class")= chr [1:2] "theme" "gg"
+       - attr(*, "complete")= logi FALSE
+       - attr(*, "validate")= logi TRUE
+
diff --git a/tests/testthat/test-deprecated.R b/tests/testthat/test-deprecated.R
index d573db1c1..eaaa9c1c0 100644
--- a/tests/testthat/test-deprecated.R
+++ b/tests/testthat/test-deprecated.R
@@ -6,3 +6,9 @@ test_that("ggally-cor", {
     p <- ggally_cor_v1_5(tips, ggplot2::aes(!!as.name("total_bill"), !!as.name("tip")))
   )
 })
+
+test_that("v1_ggmatrix_theme is deprecated", {
+  expect_snapshot(
+    v1_ggmatrix_theme()
+  )
+})

From 7ec5651ed6e2f6204e3f9ae8a6d2a17669be3049 Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Mon, 22 Apr 2024 20:13:20 -0300
Subject: [PATCH 3/9] Update ggally_cor_v1_5() deprecation warning

---
 DESCRIPTION                         |  3 ++-
 R/deprecated.R                      | 16 ++++++++++++----
 man/ggally_cor_v1_5.Rd              | 10 +++++++---
 man/v1_ggmatrix_theme.Rd            |  1 +
 tests/testthat/_snaps/deprecated.md | 12 +++++++++++-
 tests/testthat/test-deprecated.R    | 12 +++++++++---
 6 files changed, 42 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5b259721b..8a84f972e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -69,7 +69,8 @@ Suggests:
     knitr,
     spelling,
     emmeans,
-    vdiffr
+    vdiffr,
+    withr (>= 3.0.0)
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 SystemRequirements: openssl
diff --git a/R/deprecated.R b/R/deprecated.R
index c79d69b57..78604781e 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -52,12 +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
@@ -72,7 +75,7 @@ v1_ggmatrix_theme <- function() {
 #' @importFrom stats complete.cases cor
 #' @seealso \code{\link{ggally_cor}}
 #' @export
-#' @keywords hplot
+#' @keywords hplot internal
 #' @examples
 #' # Small function to display plots only if it's interactive
 #' p_ <- GGally::print_if_interactive
@@ -109,6 +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'")
   }
diff --git a/man/ggally_cor_v1_5.Rd b/man/ggally_cor_v1_5.Rd
index 1b3130497..8ab7ca2de 100644
--- a/man/ggally_cor_v1_5.Rd
+++ b/man/ggally_cor_v1_5.Rd
@@ -39,10 +39,13 @@ ggally_cor_v1_5(
 \item{...}{other arguments being supplied to geom_text}
 }
 \description{
-(Deprecated. See \code{\link{ggally_cor}}.)
-}
-\details{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
+
 Estimate correlation from the given data.
+
+This function is deprecated and will be removed in future releases.
+
+See \code{\link{ggally_cor}}.
 }
 \examples{
 # Small function to display plots only if it's interactive
@@ -80,3 +83,4 @@ p_(ggally_cor_v1_5(
 Barret Schloerke
 }
 \keyword{hplot}
+\keyword{internal}
diff --git a/man/v1_ggmatrix_theme.Rd b/man/v1_ggmatrix_theme.Rd
index c65ebe6eb..a2e2d2e09 100644
--- a/man/v1_ggmatrix_theme.Rd
+++ b/man/v1_ggmatrix_theme.Rd
@@ -42,3 +42,4 @@ p_(
   )
 )
 }
+\keyword{internal}
diff --git a/tests/testthat/_snaps/deprecated.md b/tests/testthat/_snaps/deprecated.md
index 76ba7ca1b..d0090d001 100644
--- a/tests/testthat/_snaps/deprecated.md
+++ b/tests/testthat/_snaps/deprecated.md
@@ -1,4 +1,4 @@
-# v1_ggmatrix_theme is deprecated
+# v1_ggmatrix_theme() is deprecated
 
     Code
       v1_ggmatrix_theme()
@@ -20,3 +20,13 @@
        - attr(*, "complete")= logi FALSE
        - attr(*, "validate")= logi TRUE
 
+# ggally_cor_v1_5() is deprecated
+
+    Code
+      p <- ggally_cor_v1_5(tips, ggplot2::aes(!!as.name("total_bill"), !!as.name(
+        "tip")))
+    Condition
+      Warning:
+      `ggally_cor_v1_5()` was deprecated in GGally 2.2.2.
+      i Please use `ggally_cor()` instead.
+
diff --git a/tests/testthat/test-deprecated.R b/tests/testthat/test-deprecated.R
index eaaa9c1c0..0a6d0adf9 100644
--- a/tests/testthat/test-deprecated.R
+++ b/tests/testthat/test-deprecated.R
@@ -1,14 +1,20 @@
-
 data(tips)
 
-test_that("ggally-cor", {
+test_that("ggally_cor_v1_5() works", {
+  withr::local_options(lifecycle_verbosity = "quiet")
   expect_silent(
     p <- ggally_cor_v1_5(tips, ggplot2::aes(!!as.name("total_bill"), !!as.name("tip")))
   )
 })
 
-test_that("v1_ggmatrix_theme is deprecated", {
+test_that("v1_ggmatrix_theme() is deprecated", {
   expect_snapshot(
     v1_ggmatrix_theme()
   )
 })
+
+test_that("ggally_cor_v1_5() is deprecated", {
+  expect_snapshot(
+    p <- ggally_cor_v1_5(tips, ggplot2::aes(!!as.name("total_bill"), !!as.name("tip")))
+  )
+})

From 99cb24e8141e9da0ed9bc606158552150e2791f6 Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Mon, 22 Apr 2024 21:10:08 -0300
Subject: [PATCH 4/9] Expect warning when testing v1_ggmatrix_theme in
 test-ggmatrix_add.R

---
 tests/testthat/_snaps/ggmatrix_add.md | 13 +++++++++++++
 tests/testthat/test-ggmatrix_add.R    | 12 ++++++++----
 2 files changed, 21 insertions(+), 4 deletions(-)
 create mode 100644 tests/testthat/_snaps/ggmatrix_add.md

diff --git a/tests/testthat/_snaps/ggmatrix_add.md b/tests/testthat/_snaps/ggmatrix_add.md
new file mode 100644
index 000000000..de8f22a23
--- /dev/null
+++ b/tests/testthat/_snaps/ggmatrix_add.md
@@ -0,0 +1,13 @@
+# v1_ggmatrix_theme
+
+    Code
+      pm <- ggpairs(tips, 1:2)
+      pm1 <- pm + v1_ggmatrix_theme()
+    Condition
+      Warning:
+      `v1_ggmatrix_theme()` was deprecated in GGally 2.2.2.
+      i This function will be removed in future releases.
+    Code
+      expect_true(is.null(pm$gg))
+      expect_true(!is.null(pm1$gg))
+
diff --git a/tests/testthat/test-ggmatrix_add.R b/tests/testthat/test-ggmatrix_add.R
index c085e972e..7c2411af3 100644
--- a/tests/testthat/test-ggmatrix_add.R
+++ b/tests/testthat/test-ggmatrix_add.R
@@ -50,10 +50,14 @@ test_that("add_list", {
 })
 
 test_that("v1_ggmatrix_theme", {
-  pm <- ggpairs(tips, 1:2)
+  expect_snapshot(
+    {
+      pm <- ggpairs(tips, 1:2)
 
-  pm1 <- pm + v1_ggmatrix_theme()
+      pm1 <- pm + v1_ggmatrix_theme()
 
-  expect_true(is.null(pm$gg))
-  expect_true(!is.null(pm1$gg))
+      expect_true(is.null(pm$gg))
+      expect_true(!is.null(pm1$gg))
+    }
+  )
 })

From fee9c6099793e23107bf252edc70d8a00b4770d2 Mon Sep 17 00:00:00 2001
From: Andrei <92amartins@gmail.com>
Date: Wed, 24 Apr 2024 18:33:17 -0300
Subject: [PATCH 5/9] Update R/deprecated.R

Co-authored-by: Barret Schloerke <barret@posit.co>
---
 R/deprecated.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/deprecated.R b/R/deprecated.R
index 78604781e..85a3163ce 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -75,7 +75,7 @@ v1_ggmatrix_theme <- function() {
 #' @importFrom stats complete.cases cor
 #' @seealso \code{\link{ggally_cor}}
 #' @export
-#' @keywords hplot internal
+#' @keywords internal
 #' @examples
 #' # Small function to display plots only if it's interactive
 #' p_ <- GGally::print_if_interactive

From 17bbdc411b3b3ebaf13bc5fdd00cc3bb1a97c6e7 Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Wed, 24 Apr 2024 19:40:40 -0300
Subject: [PATCH 6/9] Deprecate params in ggnet function

---
 R/ggnet.R                   | 67 +++++++++++++++++++++++++------------
 man/ggally_cor_v1_5.Rd      |  1 -
 man/ggnet.Rd                | 20 +++++------
 tests/testthat/test-ggnet.R | 10 +++---
 4 files changed, 60 insertions(+), 38 deletions(-)

diff --git a/R/ggnet.R b/R/ggnet.R
index a453a1b74..8fa72decd 100644
--- a/R/ggnet.R
+++ b/R/ggnet.R
@@ -114,12 +114,12 @@ 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,
@@ -199,11 +199,11 @@ 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(),
   ...
 ) {
 
@@ -213,32 +213,55 @@ ggnet <- function(
   # -- 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)
   }
 
diff --git a/man/ggally_cor_v1_5.Rd b/man/ggally_cor_v1_5.Rd
index 8ab7ca2de..1159e3626 100644
--- a/man/ggally_cor_v1_5.Rd
+++ b/man/ggally_cor_v1_5.Rd
@@ -82,5 +82,4 @@ p_(ggally_cor_v1_5(
 \author{
 Barret Schloerke
 }
-\keyword{hplot}
 \keyword{internal}
diff --git a/man/ggnet.Rd b/man/ggnet.Rd
index e371d9061..d10847d0b 100644
--- a/man/ggnet.Rd
+++ b/man/ggnet.Rd
@@ -35,11 +35,11 @@ ggnet(
   label.trim = FALSE,
   legend.size = 9,
   legend.position = "right",
-  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(),
   ...
 )
 }
@@ -177,16 +177,16 @@ Defaults to \code{9}.}
 \code{legend.position} values supported by \code{\link[ggplot2]{theme}}.
 Defaults to \code{"right"}.}
 
-\item{names}{deprecated: see \code{group.legend} and \code{size.legend}}
+\item{names}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} see \code{group.legend} and \code{size.legend}}
 
-\item{quantize.weights}{deprecated: see \code{weight.cut}}
+\item{quantize.weights}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} see \code{weight.cut}}
 
-\item{subset.threshold}{deprecated: see \code{weight.min}}
+\item{subset.threshold}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} see \code{weight.min}}
 
-\item{top8.nodes}{deprecated: this functionality was experimental and has
+\item{top8.nodes}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} this functionality was experimental and has
 been removed entirely from \code{ggnet}}
 
-\item{trim.labels}{deprecated: see \code{label.trim}}
+\item{trim.labels}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} see \code{label.trim}}
 
 \item{...}{other arguments passed to the \code{geom_text} object that sets
 the node labels: see \code{\link[ggplot2]{geom_text}} for details.}
diff --git a/tests/testthat/test-ggnet.R b/tests/testthat/test-ggnet.R
index 23f37fab8..589749e58 100644
--- a/tests/testthat/test-ggnet.R
+++ b/tests/testthat/test-ggnet.R
@@ -49,10 +49,10 @@ test_that("examples", {
   xy <- gplot.layout.circle(n) # nolint
   n %v% "lon" <- xy[, 1]
   n %v% "lat" <- xy[, 2]
-  expect_warning(ggnet(n, mode = "geo"), "deprecated")
+  lifecycle::expect_deprecated(ggnet(n, mode = "geo"))
 
   # test names = c(x, y)
-  expect_warning(ggnet(n, names = c("a", "b")), "deprecated")
+  lifecycle::expect_deprecated(ggnet(n, names = c("a", "b")))
 
   # test quantize.weights
   with_options(list(warn = 2), {
@@ -62,14 +62,14 @@ test_that("examples", {
 
   # test subset.threshold
   suppressMessages({
-    expect_warning(ggnet(n, subset.threshold = 2))
+    lifecycle::expect_deprecated(ggnet(n, subset.threshold = 2))
   })
 
   # test top8.nodes
-  expect_warning(ggnet(n, top8.nodes = TRUE))
+  lifecycle::expect_deprecated(ggnet(n, top8.nodes = TRUE))
 
   # test trim.labels
-  expect_warning(ggnet(n, trim.labels = TRUE))
+  lifecycle::expect_deprecated(ggnet(n, trim.labels = TRUE))
 
   #   # test subset.threshold by removing all nodes
   #   expect_warning(

From 75224360000e232b5ae0c3e887f5e388c495e684 Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Wed, 24 Apr 2024 19:49:00 -0300
Subject: [PATCH 7/9] Deprecate ggnet function in favor of ggnet2

---
 R/ggnet.R    | 5 +++++
 man/ggnet.Rd | 3 +++
 2 files changed, 8 insertions(+)

diff --git a/R/ggnet.R b/R/ggnet.R
index 8fa72decd..2136848eb 100644
--- a/R/ggnet.R
+++ b/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
@@ -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
@@ -206,6 +210,7 @@ ggnet <- function(
   trim.labels      = deprecated(),
   ...
 ) {
+  lifecycle::deprecate_soft("2.2.2", "ggnet()", "ggnet2()")
 
   # -- packages ----------------------------------------------------------------
 
diff --git a/man/ggnet.Rd b/man/ggnet.Rd
index d10847d0b..7d5174b61 100644
--- a/man/ggnet.Rd
+++ b/man/ggnet.Rd
@@ -192,6 +192,8 @@ been removed entirely from \code{ggnet}}
 the node labels: see \code{\link[ggplot2]{geom_text}} for details.}
 }
 \description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[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
@@ -247,3 +249,4 @@ package
 Moritz Marbach and Francois Briatte, with help from Heike Hofmann,
 Pedro Jordano and Ming-Yu Liu
 }
+\keyword{internal}

From 7e0adb0bfcb55323bfa444882b4f005ff7274459 Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Wed, 24 Apr 2024 20:12:51 -0300
Subject: [PATCH 8/9] Update ggally_cor_v1_5 test

---
 DESCRIPTION                      | 3 +--
 tests/testthat/test-deprecated.R | 7 ++++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8a84f972e..5b259721b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -69,8 +69,7 @@ Suggests:
     knitr,
     spelling,
     emmeans,
-    vdiffr,
-    withr (>= 3.0.0)
+    vdiffr
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 SystemRequirements: openssl
diff --git a/tests/testthat/test-deprecated.R b/tests/testthat/test-deprecated.R
index 0a6d0adf9..7b48a5ac8 100644
--- a/tests/testthat/test-deprecated.R
+++ b/tests/testthat/test-deprecated.R
@@ -1,9 +1,10 @@
 data(tips)
 
 test_that("ggally_cor_v1_5() works", {
-  withr::local_options(lifecycle_verbosity = "quiet")
-  expect_silent(
-    p <- ggally_cor_v1_5(tips, ggplot2::aes(!!as.name("total_bill"), !!as.name("tip")))
+  lifecycle::expect_deprecated(
+    {
+      p <- ggally_cor_v1_5(tips, ggplot2::aes(!!as.name("total_bill"), !!as.name("tip")))
+    }
   )
 })
 

From e9a7f1b7e7433bbcd3bad9e4888b54e8089a8e9c Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Wed, 24 Apr 2024 20:37:04 -0300
Subject: [PATCH 9/9] Update deprecation warnings in ggmatrix_gtable function

---
 R/ggmatrix_gtable.R            | 8 ++++++--
 man/ggmatrix_gtable.Rd         | 2 +-
 tests/testthat/test-ggmatrix.R | 4 ++--
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/R/ggmatrix_gtable.R b/R/ggmatrix_gtable.R
index c63631a27..372e6591e 100644
--- a/R/ggmatrix_gtable.R
+++ b/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
diff --git a/man/ggmatrix_gtable.Rd b/man/ggmatrix_gtable.Rd
index 5a474d11a..8bed9c566 100644
--- a/man/ggmatrix_gtable.Rd
+++ b/man/ggmatrix_gtable.Rd
@@ -16,7 +16,7 @@ ggmatrix_gtable(
 
 \item{...}{ignored}
 
-\item{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.}
+\item{progress, progress_format}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Please use the 'progress' parameter in your \code{\link{ggmatrix}}-like function.  See \code{\link{ggmatrix_progress}} for a few examples.}
 }
 \description{
 Specialized method to print the \code{\link{ggmatrix}} object.
diff --git a/tests/testthat/test-ggmatrix.R b/tests/testthat/test-ggmatrix.R
index 0dd714c03..198ce670d 100644
--- a/tests/testthat/test-ggmatrix.R
+++ b/tests/testthat/test-ggmatrix.R
@@ -155,10 +155,10 @@ test_that("ggmatrix_gtable progress", {
   expect_silent({
     pg <- ggmatrix_gtable(pm)
   })
-  expect_warning({
+  lifecycle::expect_deprecated({
     ggmatrix_gtable(pm, progress = TRUE)
   })
-  expect_warning({
+  lifecycle::expect_deprecated({
     ggmatrix_gtable(pm, progress_format = "asdfasdf :plot_i")
   })
 })