Fix deprecations and warnings in ggplot

.Rbuildignore

@@ -9,3 +9,7 @@ README.md
 ^cran-comments\.md$
 ^CRAN-RELEASE$
 ^codecov\.yml$
+^revdep$
+^CRAN-SUBMISSION$
+^doc$
+^Meta$

.gitignore

@@ -4,3 +4,5 @@
 .Ruserdata
 docs
 inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: ggdendro
-Version: 0.1.23
+Version: 0.1.23.9000
 Title: Create Dendrograms and Tree Diagrams Using 'ggplot2'
 Description: This is a set of tools for dendrograms and
     tree plots using 'ggplot2'.  The 'ggplot2' philosophy is to
@@ -32,7 +32,7 @@ Suggests:
     rmarkdown,
     covr
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Language: en-US
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS → NEWS.md

@@ -1,17 +1,19 @@
-ggdendro 0.1.23 (Release date: 2022-02-15)
-===============
+# ggdendro 0.1.23.9000
+
+- Fix deprecated ggplot aes usage
+
+
+# ggdendro 0.1.23
 
 * No functional changes.  Minor changes only to comply with CRAN policy.
 
-ggdendro 0.1.22 (Release date: 2020-09-13)
-===============
+# ggdendro 0.1.22 
 
 * No functional changes
 * Update tests to conform with `testthat_3.0.0`
 
 
-ggdendro 0.1.21 (Release date: 2020-08-08)
-===============
+# ggdendro 0.1.21 
 
 Bug fixes:
 
@@ -24,18 +26,16 @@ Other changes
 * Added spellcheck and fixed spelling mistakes
 
 
-ggdendro 0.1-20 (Release date: 2016-04-27)
-===============
+# ggdendro 0.1-20 
 
 Enhancements:
 
 * Don't open plot device during calculation of segment data #25
 
 
-ggdendro 0.1-19 (Release date: 2016-04-27)
-===============
+# ggdendro 0.1-19 
 
-Bug fix release
+Bug fix release.
 
 Functional changes:
 
@@ -48,8 +48,7 @@ Bug fixes:
 * Fixed issue #22: Margin not working for `dendro_data.rpart`
 
 
-ggdendro 0.1-16 (Release date: 2016-09-06)
-===============
+# ggdendro 0.1-16 
 
 New functionality:
 
@@ -59,20 +58,19 @@ Fixes:
 - Many small changes and improvements to documentation
 
 
-ggdendro 0.1-15 (Release date: 29/09/2014)
-===============
+# ggdendro 0.1-15 
 
 New functionality:
 - None
 
 Changes:
+
 - Some bug fixes
 - Unit tests now run during R CMD check
 - Modified vignette to use knitr instead of SWeave
 
 
-ggdendro 0.1-14 (Release date: 2013-09-03)
-===============
+# ggdendro 0.1-14 
 
 New functionality
 * Added support for rpart
@@ -84,8 +82,7 @@ Changes:
 
 
 
-ggdendro 0.1-12 (Release date: 2013-01-27)
-===============
+# ggdendro 0.1-12 
 
 New functionality
 * None
@@ -94,8 +91,7 @@ Changes:
 * ggdendro now imports MASS, tree and ggplot2 (rather than suggests)
 * Added Brian D. Ripley as author (original author of package tree)
 
-ggdendro 0.1-09 (Release date: 2012-12-25)
-===============
+# ggdendro 0.1-09 
 
 New functionality
 * None
@@ -104,28 +100,29 @@ Changes:
 * Removed support for rpart
 * Changed Licence from GPL (>=2) to GPL-2|GPL-3 to conform with rtree license conditions
 
-ggdendro 0.1-07 (Release date: 2012-08-30)
-===============
+# ggdendro 0.1-07 
+
+New functionality:
 
-New functionality
 * None
 
 Changes:
+
 * Modified code to conform to `ggplot2` v0.9.2
 
 
-ggdendro 0.1-04 (Release date: 2012-02-02)
-===============
+# ggdendro 0.1-04 
+
+New functionality:
 
-New functionality
 * None
 * Modified examples to conform to ggplot2 v0.9
 
 
-ggdendro 0.1-02 (Release date: 19/10/2011)
-===============
+# ggdendro 0.1-02 
+
+New functionality:
 
-New functionality
 * Added support for classification trees using `package:rpart` 
 
 Fixed bugs:
@@ -135,15 +132,13 @@ Changes in API
 * Fixed inconsistencies in the names of the `data.frame` segments.  The names are now always `x`, `y`, `xend` and `yend`
 
 
-ggdendro 0.0-7 (Release date: 2011-08-12)
-==============
+# ggdendro 0.0-7 
 
 New functionality
 * Included the `ggdendrogram` function that conveniently creates a `ggplot` dendrogram in a single line of code.
 * Created `theme_dendro`, an almost blank theme
 
-ggdendro 0.0
-============
+# ggdendro 0.0
 
 Experimental release of package.
 

R/ggdendrogram.R

@@ -62,13 +62,13 @@ ggdendrogram <- function(data,
   if (segments && !is.null(data$segments)) {
     p <- p + geom_segment(
       data = segment(data),
-      aes_string(x = "x", y = "y", xend = "xend", yend = "yend")
+      aes(x = .data[["x"]], y = .data[["y"]], xend = .data[["xend"]], yend = .data[["yend"]])
     )
   }
   if (leaf_labels && !is.null(data$leaf_labels)) {
     p <- p + geom_text(
       data = leaf_label(data),
-      aes_string(x = "x", y = "y", label = "label"), hjust = hjust, angle = angle, ...
+      aes(x = .data[["x"]], y = .data[["y"]], label = .data[["label"]]), hjust = hjust, angle = angle, ...
     )
   }
   if (labels) {

README.Rmd

@@ -19,9 +19,9 @@ Provides functions for creating dendrograms and tree plots using `ggplot2`.
 
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/andrie/ggdendro/workflows/R-CMD-check/badge.svg)](https://github.com/andrie/ggdendro/actions)
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#inactive)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/ggdendro)](http://cran.r-project.org/package=ggdendro)
+[![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
+[![CRAN status](https://www.r-pkg.org/badges/version/ggdendro)](https://CRAN.R-project.org/package=ggdendro)
+[![R-CMD-check](https://github.com/andrie/ggdendro/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/andrie/ggdendro/actions/workflows/R-CMD-check.yaml)
 [![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/ggdendro)](http://www.r-pkg.org/pkg/ggdendro)
 [![Codecov test coverage](https://codecov.io/gh/andrie/ggdendro/branch/main/graph/badge.svg)](https://app.codecov.io/gh/andrie/ggdendro?branch=main)
 <!-- badges: end -->

README.md

@@ -8,11 +8,13 @@ Provides functions for creating dendrograms and tree plots using
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/andrie/ggdendro/workflows/R-CMD-check/badge.svg)](https://github.com/andrie/ggdendro/actions)
-[![Project Status: Active - The project has reached a stable, usable
-state and is being actively
-developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#inactive)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/ggdendro)](http://cran.r-project.org/package=ggdendro)
+[![Project Status: Inactive – The project has reached a stable, usable
+state but is no longer being actively developed; support/maintenance
+will be provided as time
+allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
+[![CRAN
+status](https://www.r-pkg.org/badges/version/ggdendro)](https://CRAN.R-project.org/package=ggdendro)
+[![R-CMD-check](https://github.com/andrie/ggdendro/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/andrie/ggdendro/actions/workflows/R-CMD-check.yaml)
 [![CRAN RStudio mirror
 downloads](http://cranlogs.r-pkg.org/badges/ggdendro)](http://www.r-pkg.org/pkg/ggdendro)
 [![Codecov test
@@ -22,23 +24,23 @@ coverage](https://codecov.io/gh/andrie/ggdendro/branch/main/graph/badge.svg)](ht
 The `ggdendro` package offers a generic function to extract data and
 text from the various clustering models:
 
--   `dendro_data()` extracts cluster information from the model object,
-    e.g. cluster allocation, line segment data or label data.
+- `dendro_data()` extracts cluster information from the model object,
+  e.g. cluster allocation, line segment data or label data.
 
 The `dendro_data` object has methods for the following classes:
 
--   `tree`
--   `hclust`
--   `dendrogram`
--   `rpart`
+- `tree`
+- `hclust`
+- `dendrogram`
+- `rpart`
 
 These methods create an object of class `dendro`, which is essentially a
 list of data frames. To extract the relevant data frames from the list,
 use the three accessor functions:
 
--   `segment()` for the line segment data
--   `label()` for the text for each end segment
--   `leaf_label()` for the leaf labels of a tree diagram
+- `segment()` for the line segment data
+- `label()` for the text for each end segment
+- `leaf_label()` for the leaf labels of a tree diagram
 
 The results of these functions can then be passed to `ggplot()` for
 plotting.
@@ -65,6 +67,7 @@ ggplot() +
 <img src="man/figures/README-unnamed-chunk-2-1.png" width="100%" />
 
 ``` r
+
 ### demonstrate plotting directly from object class hclust
 ggdendrogram(hc)
 ```
@@ -78,6 +81,7 @@ ggdendrogram(hc, rotate = TRUE)
 <img src="man/figures/README-unnamed-chunk-2-3.png" width="100%" />
 
 ``` r
+
 ### demonstrate converting hclust to dendro using dendro_data first
 hcdata <- dendro_data(hc)
 ggdendrogram(hcdata, rotate = TRUE) +

inst/WORDLIST

@@ -1,19 +1,25 @@
 CMD
+Codecov
+Licence
 RStudio
+SWeave
 Vries
 agnes
 arg
 args
-cran
+behaviour
 de
-dendextend
 dendro
 diana
+ggdendrogram
 ggplot
 hclust
-https
+knitr
 minbranch
 minlength
 nleaves
+pkgdown
 rpart
+rtree
+tidyverse
 treeco

inst/examples/example_dendro_tree.R

@@ -8,7 +8,7 @@ if (require(tree)) {
                    data = cpus)
   tree_data <- dendro_data(cpus.ltr)
   ggplot(segment(tree_data)) +
-    geom_segment(aes(x = x, y = y, xend = xend, yend = yend, size = n),
+    geom_segment(aes(x = x, y = y, xend = xend, yend = yend, linewidth = n),
       colour = "lightblue"
     ) +
     scale_size("n") +

vignettes/ggdendro.Rmd

@@ -1,8 +1,8 @@
 ---
-title: "Introduction to ggdendro"
+title: "Using 'ggdendro' to plot dendrograms"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Introduction to ggdendro}
+  %\VignetteIndexEntry{Using 'ggdendro' to plot dendrograms}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -15,8 +15,6 @@ knitr::opts_chunk$set(
 ```
 
 
-# Using the `ggdendro` package to plot dendrograms
-
 The `ggdendro` package makes it easy to extract dendrogram and tree diagrams into a list of data frames.  You can then use this list to recreate these types of plots using the `ggplot2` package.
 
 ## Introduction
@@ -44,7 +42,7 @@ library(ggplot2)
 library(ggdendro)
 ```
 
-## Using the `ggdendrogram()` wrapper
+## Using the 'ggdendrogram()' wrapper
 
 The `ggdendro` package extracts the plot data from dendrogram objects.  Sometimes it is useful to have fine-grained control over the plot.  Other times it might be more convenient to have a simple wrapper around `ggplot()` to produce a dendrogram with a small amount of code.
 
@@ -58,7 +56,7 @@ ggdendrogram(hc, rotate = FALSE, size = 2)
 
 The next section shows how to take full control over the data extraction and subsequent plotting.
 
-## Extracting the dendrogram plot data using `dendro_data()`
+## Extracting the dendrogram plot data using 'dendro_data()'
 
 The `hclust()` and `dendrogram()` functions in R makes it easy to plot the results of hierarchical cluster analysis and other dendrograms in R.  However, it is hard to extract the data from this analysis to customize these plots, since the `plot()` functions for both these classes prints directly without the option of returning the plot data.  
 
@@ -144,7 +142,7 @@ if(require(rpart)){
 ```
 
 
-## Twins diagrams: agnes and diana
+## Twins diagrams: 'agnes' and 'diana'
 
 The `cluster` package allows you to draw `agnes` and `diana` diagrams.