Update repo tools

.Rbuildignore

@@ -1,19 +1,20 @@
-^\.DS_Store$
 ^\.Rproj\.user$
 ^.+\.Rproj$
 ^\.gitignore$
 ^\.git$
 ^\.github$
+^\.DS_Store$
 ^Makefile$
 ^\.Rprofile$
 ^revdep$
 ^codecov\.yml$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
 ^CODE_OF_CONDUCT\.md$
 ^FAQ\.md$
 ^LICENSE\.md$
 ^README\.Rmd$
-^README\.Rmd$
+^README\.md$
 ^TODO\.md$
-^_pkgdown\.yml$
-^pkgdown$
-^docs$
+data-raw

.github/workflows/test-coverage.yaml

@@ -13,6 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4
@@ -28,10 +29,12 @@ jobs:
 
       - name: Test coverage
         run: |
+          token <- Sys.getenv("CODECOV_TOKEN", "")
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
+            token = if (token != "") token
           )
         shell: Rscript {0}
 

.gitignore

@@ -55,3 +55,4 @@ rsconnect/
 # More files
 inst/doc
 docs
+Meta

DESCRIPTION

@@ -13,38 +13,38 @@ Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
 Depends:
     R (>= 4.2.0),
     ggplot2 (>= 3.0),
-    lattice
+    lattice (>= 0.21.0)
 Imports:
-    cowplot,
-    data.io,
-    ggplotify,
-    ggpubr,
-    graphics,
-    grDevices,
-    latticeExtra,
-    pryr,
-    rlang,
-    scales,
-    stats,
-    utils,
-    viridis,
-    svMisc
+    cowplot (>= 1.1.1),
+    data.io (>= 1.5.0),
+    ggplotify (>= 0.1.0),
+    ggpubr (>= 0.6.0),
+    graphics (>= 4.2.0),
+    grDevices (>= 4.2.0),
+    latticeExtra (>= 0.6.30),
+    pryr (>= 0.1.6),
+    rlang (>= 1.1.1),
+    scales (>= 1.2.1),
+    stats (>= 4.2.0),
+    svMisc (>= 1.4.0),
+    utils (>= 4.2.0),
+    viridis (>= 0.6.2)
 Suggests:
-    MASS,
-    knitr,
-    rmarkdown,
-    spelling,
+    MASS (>= 7.3.58.3),
+    knitr (>= 1.42),
+    rmarkdown (>= 2.21),
+    spelling (>= 2.2.1),
     testthat (>= 3.0.0)
 Remotes:
     SciViews/data.io,
     SciViews/svMisc
 License: MIT + file LICENSE
 URL: https://github.com/SciViews/chart, https://www.sciviews.org/chart/
 BugReports: https://github.com/SciViews/chart/issues
-ByteCompile: yes
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Config/testthat/edition: 3
 VignetteBuilder: knitr
 Encoding: UTF-8
 Language: en-US
+ByteCompile: yes
+Config/testthat/edition: 3

NEWS.md

@@ -1,6 +1,6 @@
 # chart 1.5.2
 
--   Documentation (vignettes et README file) are completed.
+-   Documentation (vignettes and README file) are completed.
 
 -   License change to MIT for better reusability.
 

R/chart-package.R

@@ -5,7 +5,11 @@
 #'
 #' @section Important functions:
 #'
-#'- [chart()] constructs a `Chart` object.
+#'- [chart()] constructs a **Chart** object.
+#'
+#'- [combine_charts()] combines multiple **Chart** objects into a single plot.
+#'
+#'- [f_aes()] creates a formula for aesthetics mapping (use it instead of [ggplot2::aes()].
 #'
 #' @docType package
 #' @name chart-package

README.Rmd

@@ -7,8 +7,8 @@ output: github_document
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/SciViews/chart/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SciViews/chart/actions/workflows/R-CMD-check.yaml) [![Coverage status](https://img.shields.io/codecov/c/github/SciViews/chart/master.svg)](https://codecov.io/github/SciViews/chart?branch=main) [![CRAN status](https://www.r-pkg.org/badges/version/chart)](https://cran.r-project.org/package=chart) [![License](https://img.shields.io/badge/license-GPL-blue.svg)](https://www.gnu.org/licenses/gpl-2.0.html) [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
-[![Codecov test coverage](https://codecov.io/gh/SciViews/chart/branch/main/graph/badge.svg)](https://app.codecov.io/gh/SciViews/chart?branch=main)
+[![R-CMD-check](https://github.com/SciViews/chart/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SciViews/chart/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/SciViews/chart/branch/main/graph/badge.svg)](https://app.codecov.io/gh/SciViews/chart?branch=main) [![CRAN status](https://www.r-pkg.org/badges/version/chart)](https://cran.r-project.org/package=chart) [![r-universe status](https://sciviews.r-universe.dev/badges/chart)](https://sciviews.r-universe.dev/chart) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
+
 <!-- badges: end -->
 
 ```{r setup, include=FALSE}
@@ -18,7 +18,7 @@ library(chart)
 ```
 
 
-{chart} provides an alternate formula interface to {ggplot2}, and it also homogenize plot outputs from base R plots, {lattice} and {ggplot}. If labels and/or units attributes are defined for variables in the data, they are used automatically to construct the label (with units) of the axes. See <https://www.sciviews.org/chart/> for more details.
+The {chart} package  provides an alternate formula interface to {ggplot2}, and it also homogenize plot outputs from base R plots, {lattice} and {ggplot}. If labels and/or units attributes are defined for variables in the data, they are used automatically to construct the label (with units) of the axes. See <https://www.sciviews.org/chart/> for more details.
 
 ## Installation
 
@@ -57,7 +57,6 @@ airquality <- data.io::labelise(airquality, label = list(
 ))
 ```
 
-
 here is a first {chart}:
 
 ```{r}
@@ -80,4 +79,4 @@ vignette("chart") # Not installed with install_github()
 
 ## Code of Conduct
 
-Please note that the {chart} package is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+Please note that the {chart} package is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

README.md

@@ -1,26 +1,30 @@
-Chart - Unified Interface (with Formula) for R Plots
+Unified Interface (with Formula) for R Plots
 <a href='https://www.sciviews.org/chart'><img src='man/figures/logo.png' align='right' height='139'/></a>
 ================
 
 <!-- Do not edit the README.md file directly. It is generated from README.Rmd. -->
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/SciViews/chart/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SciViews/chart/actions/workflows/R-CMD-check.yaml)
-[![Coverage
-status](https://img.shields.io/codecov/c/github/SciViews/chart/master.svg)](https://codecov.io/github/SciViews/chart?branch=main)
+[![Codecov test
+coverage](https://codecov.io/gh/SciViews/chart/branch/main/graph/badge.svg)](https://app.codecov.io/gh/SciViews/chart?branch=main)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/chart)](https://cran.r-project.org/package=chart)
-[![License](https://img.shields.io/badge/license-GPL-blue.svg)](https://www.gnu.org/licenses/gpl-2.0.html)
+[![r-universe
+status](https://sciviews.r-universe.dev/badges/chart)](https://sciviews.r-universe.dev/chart)
+[![License:
+MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Lifecycle:
-stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
+stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 
 <!-- badges: end -->
 
-{chart} provides an alternate formula interface to {ggplot2}, and it
-also homogenize plot outputs from base R plots, {lattice} and {ggplot}.
-If labels and/or units attributes are defined for variables in the data,
-they are used automatically to construct the label (with units) of the
-axes. See <https://www.sciviews.org/chart/> for more details.
+The {chart} package provides an alternate formula interface to
+{ggplot2}, and it also homogenize plot outputs from base R plots,
+{lattice} and {ggplot}. If labels and/or units attributes are defined
+for variables in the data, they are used automatically to construct the
+label (with units) of the axes. See <https://www.sciviews.org/chart/>
+for more details.
 
 ## Installation
 
@@ -108,5 +112,5 @@ vignette("chart") # Not installed with install_github()
 
 Please note that the {chart} package is released with a [Contributor
 Code of
-Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
 By contributing to this project, you agree to abide by its terms.

_pkgdown.yml

@@ -7,6 +7,7 @@ development:
 
 template:
   package: svPkgdown
+  bootstrap: 5
   params:
     bootswatch: spacelab
     mathjax: true

chart.Rproj

@@ -1,7 +1,7 @@
 Version: 1.0
 
-RestoreWorkspace: Default
-SaveWorkspace: Default
+RestoreWorkspace: No
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
@@ -14,8 +14,14 @@ LaTeX: XeLaTeX
 
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
 
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace,vignette
+
+QuitChildProcessesOnExit: Yes
+
+SpellingDictionary: en_US

inst/CITATION

@@ -1,16 +1,17 @@
-citHeader("To cite SciViews-R in publications, please use:")
+citHeader("To cite SciViews-R in publications use:")
 
 citEntry(
   entry        = "Manual",
   title        = "SciViews::R",
-  author       = personList(as.person("Philippe Grosjean")),
+  author       = personList(as.person("Philippe Grosjean"),
+                            as.person("Guyliann Engels")),
   organization = "UMONS",
   address      = "MONS, Belgium",
   year         = version$year,
   url          = "https://sciviews.r-universe.dev/",
 
   textVersion =
-    paste("Grosjean, Ph. (", version$year, "). ",
+    paste("Grosjean, Ph. & Engels, G. (", version$year, "). ",
       "SciViews::R. ",
       "UMONS, Mons, Belgium. ",
       "URL https://sciviews.r-universe.dev/.",

inst/WORDLIST

@@ -1,10 +1,14 @@
 aes
 appveyor
+customizable
 devtools
+exploreit
 ggplot
 GitHub
+modelit
 OSX
 pipeable
+reusability
 subsettable
 thetics
 viridis

tests/testthat/test-chart.R

@@ -1,4 +1,4 @@
-test_that("chart creates 'Chart' objects", {
+test_that("chart() creates Chart objects", {
   dtf <- data.frame(x = 1:2, y = 1:2)
   expect_s3_class(chart(dtf, y ~ x), 'Chart')
 })

vignettes/chart.R

@@ -0,0 +1,4 @@
+## ----setup, include=FALSE-----------------------------------------------------
+knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
+library(chart)
+

vignettes/chart.Rmd

@@ -1,23 +1,20 @@
 ---
-title: "Chart - Unified Interface (with Formula) for R Plots"
-author: "Philippe Grosjean (phgrosjean@sciviews.org)"
+title: "Unified Interface (with Formula) for R Plots"
+author: "Philippe Grosjean"
 date: "`r Sys.Date()`"
 output:
   rmarkdown::html_vignette:
     toc: true
     toc_depth: 3
+    fig_caption: yes
 vignette: >
-  %\VignetteIndexEntry{Chart - Unified Interface (with Formula) for R Plots}
+  %\VignetteIndexEntry{Unified Interface (with Formula) for R Plots}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
-  \usepackage[utf8]{inputenc}
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
+knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 library(chart)
 ```
 
@@ -28,11 +25,11 @@ In R, there are several plotting engines, but the three major ones are the base
 The goal of {chart} is:
 
 -   to provide a unified interface to the three major plotting engines in R;
--   to make all three types of plots intercompatible in a composite figure;
+-   to make all three types of plots compatible in a composite figure;
 -   to propose a default style for the plots that is consistent across the three engines and close enough to a publication-ready style;
 -   to use automatically labels and units for axes, when possible;
 -   to expose an formula-base interface as an alternative for {ggplot2} users;
--   to implement various (customisable) plot types for different R objects.
+-   to implement various (customizable) plot types for different R objects.
 
 
 ## {chart} for {ggplot2} users