Displayr · pull · Apr 14, 2025 · Apr 14, 2025 · Apr 14, 2025 · Apr 18, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,7 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^JSONdata
-.travis.yml
 .sass-cache
 ^.*\.o$
 ^README\.Rmd$

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+name: R-CMD-check
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest, r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,51 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+name: test-coverage
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## Install package
+          R CMD INSTALL .
+          ## Run tests
+          Rscript -e 'testthat::test_package("networkD3")'
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,8 +3,8 @@ Type: Package
 Title: D3 JavaScript Network Graphs from R
 Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
     graphs from 'R'.
-Version: 0.4.9000
-Date: 2017-06-18
+Version: 0.4.1
+Date: 2025-04-14
 Authors@R: c(
     person("J.J.", "Allaire", role = "aut"),
     person("Peter", "Ellis", role = "ctb"),
@@ -33,6 +33,7 @@ Imports:
 Suggests:
     htmltools (>= 0.2.6),
     tibble
+Encoding: UTF-8
 Enhances: knitr, shiny
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,10 @@
 [Pull Request](https://github.com/christophergandrud/networkD3/pulls) number.
 Please see those for more details.
 
+# 0.4.1
+
+- Minor link changes
+
 # 0.4
 
 ## Major changes

diff --git a/R/chordNetwork.R b/R/chordNetwork.R
@@ -47,7 +47,7 @@
 #'
 #' @source 
 #'
-#' Mike Bostock: \url{https://github.com/mbostock/d3/wiki/Chord-Layout}.
+#' Mike Bostock: \url{https://github.com/d3/d3/wiki/Chord-Layout}.
 #'
 #' @export
 #'

diff --git a/R/data-definitions.R b/R/data-definitions.R
@@ -5,20 +5,20 @@
 #'
 #' @format A data set with 77 observations of 2 variables, plus made up
 #' node size variable.
-#' @source See Mike Bostock \url{http://bl.ocks.org/mbostock/4062045}.
+#' @source See Mike Bostock \url{https://bl.ocks.org/mbostock/4062045}.
 "MisNodes"
 
 #' Les Miserables character links
 #'
 #' A data file of links from Knuth's Les Miserables characters data base.
 #'
 #' @format A data set with 254 observations of 3 variables.
-#' @source See Mike Bostock \url{http://bl.ocks.org/mbostock/4062045}.
+#' @source See Mike Bostock \url{https://bl.ocks.org/mbostock/4062045}.
 "MisLinks"
 
 #' Edge list of REF (2014) journal submissions for Politics and International
 #' Relations
 #' 
 #' @format A data set with 2732 rows and 3 variables.
-#' @source See REF 2014 \url{http://results.ref.ac.uk/DownloadSubmissions/ByUoa/21}.
+#' @source See REF 2014 \url{https://results.ref.ac.uk/DownloadSubmissions/ByUoa/21}.
 "SchoolsJournals"
diff --git a/R/dendroNetwork.R b/R/dendroNetwork.R
@@ -46,9 +46,9 @@
 #'                treeOrientation = "vertical")
 #' }
 #'
-#' @source Mike Bostock: \url{http://bl.ocks.org/mbostock/4063570}.
+#' @source Mike Bostock: \url{https://bl.ocks.org/mbostock/4063570}.
 #'
-#' Fabio Nelli: \url{http://www.meccanismocomplesso.org/en/dendrogramma-d3-parte1/}
+#' Fabio Nelli: https://www.meccanismocomplesso.org/en/dendrogramma-d3-parte1/
 #'
 #' @importFrom stats setNames
 #' @importFrom utils modifyList

diff --git a/R/forceNetwork.R b/R/forceNetwork.R
@@ -139,7 +139,7 @@
 #'
 
 #' @source
-#' D3.js was created by Michael Bostock. See \url{http://d3js.org/} and, more
+#' D3.js was created by Michael Bostock. See \url{https://d3js.org/} and, more
 #' specifically for force directed networks
 #' \url{https://github.com/d3/d3/blob/master/API.md#forces-d3-force}.
 #' @seealso \code{\link{JS}}.

diff --git a/R/networkD3.R b/R/networkD3.R
@@ -5,7 +5,7 @@
 #'
 #' @name networkD3-package
 #' @aliases networkD3
-#' @docType package
+#' _PACKAGE
 NULL
 
 

diff --git a/R/sankeyNetwork.R b/R/sankeyNetwork.R
@@ -44,7 +44,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' # Recreate Bostock Sankey diagram: http://bost.ocks.org/mike/sankey/
+#' # Recreate Bostock Sankey diagram: https://bost.ocks.org/mike/sankey/
 #' # Load energy projection data
 #' URL <- paste0('https://cdn.rawgit.com/christophergandrud/networkD3/',
 #'               'master/JSONdata/energy.json')
@@ -65,8 +65,8 @@
 #'
 #' }
 #' @source
-#' D3.js was created by Michael Bostock. See \url{http://d3js.org/} and, more
-#' specifically for Sankey diagrams \url{http://bost.ocks.org/mike/sankey/}.
+#' D3.js was created by Michael Bostock. See \url{https://d3js.org/} and, more
+#' specifically for Sankey diagrams \url{https://bost.ocks.org/mike/sankey/}.
 #'
 #' @seealso \code{\link{JS}}
 #'

diff --git a/R/simpleNetwork.R b/R/simpleNetwork.R
@@ -41,7 +41,7 @@
 #' simpleNetwork(NetworkData)
 #' simpleNetwork(NetworkData, fontFamily = "sans-serif")
 #'
-#' @source D3.js was created by Michael Bostock. See \url{http://d3js.org/} and,
+#' @source D3.js was created by Michael Bostock. See \url{https://d3js.org/} and,
 #'   more specifically for directed networks
 #'   \url{https://github.com/d3/d3/blob/master/API.md#forces-d3-force}
 #'

diff --git a/R/utils.R b/R/utils.R
@@ -3,7 +3,7 @@
 #' @param ... character string to evaluate
 #'
 #' @source A direct import of \code{JS} from Ramnath Vaidyanathan, Yihui Xie,
-#' JJ Allaire, Joe Cheng and Kenton Russell (2015). \link{htmlwidgets}: HTML
+#' JJ Allaire, Joe Cheng and Kenton Russell (2015). htmlwidgets: HTML
 #' Widgets for R. R package version 0.4.
 #'
 #' @export
@@ -33,7 +33,7 @@ toJSONarray <- function(dtf){
 
   name.value <- function(i){
     quote <- '';
-    if(class(dtf[, i])!='numeric' && class(dtf[, i])!='integer'){
+    if (!inherits(dtf[, i], "numeric") && !inherits(dtf[, i], "integer")){
       quote <- '"';
     }
     paste('"', i, '" : ', quote, dtf[,i], quote, sep='')
@@ -104,7 +104,7 @@ margin_handler <- function(margin){
 #'
 #' @param g an \code{igraph} class graph object
 #' @param group an object that contains node group values, for example, those
-#' created with igraph's \code{\link{membership}} function.
+#' created with igraph's \code{\link[igraph]{membership}} function.
 #' @param what a character string specifying what to return. If
 #' \code{what = 'links'} or \code{what = 'nodes'} only the links or nodes are
 #' returned as data frames, respectively. If \code{what = 'both'} then both
@@ -133,7 +133,7 @@ margin_handler <- function(margin){
 #' \dontrun{
 #' # Example with data from data frame
 #' # Load data
-#' ## Original data from http://results.ref.ac.uk/DownloadSubmissions/ByUoa/21
+#' ## Original data from https://results.ref.ac.uk/DownloadSubmissions/ByUoa/21
 #' data('SchoolsJournals')
 #'
 #' # Convert to igraph

diff --git a/README.Rmd b/README.Rmd
@@ -6,7 +6,7 @@ output: md_document
 
 Development version: `r packageVersion("networkD3")`
 [![CRAN Version](http://www.r-pkg.org/badges/version/networkD3)](https://CRAN.R-project.org/package=networkD3)
-[![Build Status](https://travis-ci.org/christophergandrud/networkD3.svg?branch=master)](https://travis-ci.org/christophergandrud/networkD3)
+[![R-CMD-check](https://github.com/christophergandrud/networkD3/workflows/R-CMD-check/badge.svg)](https://github.com/christophergandrud/networkD3/actions)
 ![CRAN Monthly Downloads](http://cranlogs.r-pkg.org/badges/last-month/networkD3)
 ![CRAN Total Downloads](http://cranlogs.r-pkg.org/badges/grand-total/networkD3)
 

diff --git a/README.md b/README.md
@@ -2,10 +2,7 @@ D3 JavaScript Network Graphs from R
 ===================================
 
 Development version: 0.4.9000 [![CRAN
-Version](http://www.r-pkg.org/badges/version/networkD3)](https://CRAN.R-project.org/package=networkD3)
-[![Build
-Status](https://travis-ci.org/christophergandrud/networkD3.svg?branch=master)](https://travis-ci.org/christophergandrud/networkD3)
-![CRAN Monthly
+Version](http://www.r-pkg.org/badges/version/networkD3)](https://CRAN.R-project.org/package=networkD3) [![R-CMD-check](https://github.com/christophergandrud/networkD3/workflows/R-CMD-check/badge.svg)](https://github.com/christophergandrud/networkD3/actions) ![CRAN Monthly
 Downloads](http://cranlogs.r-pkg.org/badges/last-month/networkD3) ![CRAN
 Total Downloads](http://cranlogs.r-pkg.org/badges/grand-total/networkD3)
 
@@ -42,7 +39,7 @@ Here's `forceNetwork`:
 
 Here's `sankeyNetwork` using a downloaded JSON data file:
 
-    # Recreate Bostock Sankey diagram: http://bost.ocks.org/mike/sankey/
+    # Recreate Bostock Sankey diagram: https://bost.ocks.org/mike/sankey/
     # Load energy projection data
     URL <- paste0("https://cdn.rawgit.com/christophergandrud/networkD3/",
                   "master/JSONdata/energy.json")
@@ -55,7 +52,7 @@ Here's `sankeyNetwork` using a downloaded JSON data file:
 
 ### Interacting with igraph
 
-You can use [igraph](http://igraph.org/r/) to create network graph data
+You can use [igraph](https://igraph.org/r/) to create network graph data
 that can be plotted with **networkD3**. The `igraph_to_networkD3`
 function converts igraph graphs to lists that work well with
 **networkD3**. For example:

diff --git a/man/JS.Rd b/man/JS.Rd
diff --git a/man/MisLinks.Rd b/man/MisLinks.Rd
diff --git a/man/MisNodes.Rd b/man/MisNodes.Rd
diff --git a/man/SchoolsJournals.Rd b/man/SchoolsJournals.Rd
diff --git a/man/as_treenetdf.data.frame.Rd b/man/as_treenetdf.data.frame.Rd
diff --git a/man/as_treenetdf.list.Rd b/man/as_treenetdf.list.Rd