From ac431c0815ba25a7e073db63dbd5da4bec432efa Mon Sep 17 00:00:00 2001 From: christophergandrud Date: Mon, 14 Apr 2025 16:37:09 +0200 Subject: [PATCH 1/7] update documentation links --- DESCRIPTION | 7 ++++--- NEWS.md | 4 ++++ R/networkD3.R | 2 +- R/utils.R | 6 +++--- man/JS.Rd | 2 +- man/MisLinks.Rd | 4 +++- man/MisNodes.Rd | 6 ++++-- man/SchoolsJournals.Rd | 4 +++- man/as_treenetdf.data.frame.Rd | 10 ++++++++-- man/as_treenetdf.list.Rd | 3 +-- man/chordNetwork.Rd | 21 +++++++++++++++------ man/dendroNetwork.Rd | 22 +++++++++++++++++----- man/diagonalNetwork.Rd | 17 +++++++++++++---- man/forceNetwork.Rd | 34 ++++++++++++++++++++++++++-------- man/igraph_to_networkD3.Rd | 2 +- man/networkD3-package.Rd | 2 +- man/radialNetwork.Rd | 17 +++++++++++++---- man/sankeyNetwork.Rd | 26 +++++++++++++++++++++----- man/simpleNetwork.Rd | 18 +++++++++++++++--- man/treeNetwork.Rd | 16 +++++++++++++--- 20 files changed, 167 insertions(+), 56 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f5378ca6..e26ffbce 100644 --- 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 index c23dc8b5..73a5cdb8 100644 --- 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/networkD3.R b/R/networkD3.R index bd832e95..d00e7bf5 100644 --- 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/utils.R b/R/utils.R index d7ecad29..34c2b493 100644 --- 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 diff --git a/man/JS.Rd b/man/JS.Rd index 9235d0ae..699fba36 100644 --- a/man/JS.Rd +++ b/man/JS.Rd @@ -5,7 +5,7 @@ \title{Create character strings that will be evaluated as JavaScript} \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. } \usage{ diff --git a/man/MisLinks.Rd b/man/MisLinks.Rd index 13542742..1cc76274 100644 --- a/man/MisLinks.Rd +++ b/man/MisLinks.Rd @@ -4,7 +4,9 @@ \name{MisLinks} \alias{MisLinks} \title{Les Miserables character links} -\format{A data set with 254 observations of 3 variables.} +\format{ +A data set with 254 observations of 3 variables. +} \source{ See Mike Bostock \url{http://bl.ocks.org/mbostock/4062045}. } diff --git a/man/MisNodes.Rd b/man/MisNodes.Rd index c7cb5663..8cca267e 100644 --- a/man/MisNodes.Rd +++ b/man/MisNodes.Rd @@ -4,8 +4,10 @@ \name{MisNodes} \alias{MisNodes} \title{Les Miserables character nodes} -\format{A data set with 77 observations of 2 variables, plus made up -node size variable.} +\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}. } diff --git a/man/SchoolsJournals.Rd b/man/SchoolsJournals.Rd index 2ba5483e..cabcba5e 100644 --- a/man/SchoolsJournals.Rd +++ b/man/SchoolsJournals.Rd @@ -5,7 +5,9 @@ \alias{SchoolsJournals} \title{Edge list of REF (2014) journal submissions for Politics and International Relations} -\format{A data set with 2732 rows and 3 variables.} +\format{ +A data set with 2732 rows and 3 variables. +} \source{ See REF 2014 \url{http://results.ref.ac.uk/DownloadSubmissions/ByUoa/21}. } diff --git a/man/as_treenetdf.data.frame.Rd b/man/as_treenetdf.data.frame.Rd index 3f108840..7cd4b436 100644 --- a/man/as_treenetdf.data.frame.Rd +++ b/man/as_treenetdf.data.frame.Rd @@ -4,8 +4,14 @@ \alias{as_treenetdf.data.frame} \title{Convert a data.frame to a \code{treenetdf}} \usage{ -\method{as_treenetdf}{data.frame}(data, cols = setNames(names(data), - names(data)), df_type = "treenetdf", subset = names(data), root, ...) +\method{as_treenetdf}{data.frame}( + data, + cols = setNames(names(data), names(data)), + df_type = "treenetdf", + subset = names(data), + root, + ... +) } \arguments{ \item{data}{a tree network description in one of numerous forms (see diff --git a/man/as_treenetdf.list.Rd b/man/as_treenetdf.list.Rd index e6ec2ee3..05fada3d 100644 --- a/man/as_treenetdf.list.Rd +++ b/man/as_treenetdf.list.Rd @@ -4,8 +4,7 @@ \alias{as_treenetdf.list} \title{Convert a nested list to \code{treenetdf}} \usage{ -\method{as_treenetdf}{list}(data, children_name = "children", - node_name = "name", ...) +\method{as_treenetdf}{list}(data, children_name = "children", node_name = "name", ...) } \arguments{ \item{data}{a tree network description in one of numerous forms (see diff --git a/man/chordNetwork.Rd b/man/chordNetwork.Rd index 6b6d71c1..1f343454 100644 --- a/man/chordNetwork.Rd +++ b/man/chordNetwork.Rd @@ -7,12 +7,21 @@ Mike Bostock: \url{https://github.com/mbostock/d3/wiki/Chord-Layout}. } \usage{ -chordNetwork(Data, height = 500, width = 500, initialOpacity = 0.8, - useTicks = 0, colourScale = c("#1f77b4", "#aec7e8", "#ff7f0e", "#ffbb78", - "#2ca02c", "#98df8a", "#d62728", "#ff9896", "#9467bd", "#c5b0d5", "#8c564b", - "#c49c94", "#e377c2", "#f7b6d2", "#7f7f7f", "#c7c7c7", "#bcbd22", "#dbdb8d", - "#17becf", "#9edae5"), padding = 0.1, fontSize = 14, - fontFamily = "sans-serif", labels = c(), labelDistance = 30) +chordNetwork( + Data, + height = 500, + width = 500, + initialOpacity = 0.8, + useTicks = 0, + colourScale = c("#1f77b4", "#aec7e8", "#ff7f0e", "#ffbb78", "#2ca02c", "#98df8a", + "#d62728", "#ff9896", "#9467bd", "#c5b0d5", "#8c564b", "#c49c94", "#e377c2", + "#f7b6d2", "#7f7f7f", "#c7c7c7", "#bcbd22", "#dbdb8d", "#17becf", "#9edae5"), + padding = 0.1, + fontSize = 14, + fontFamily = "sans-serif", + labels = c(), + labelDistance = 30 +) } \arguments{ \item{Data}{A square matrix or data frame whose (n, m) entry represents diff --git a/man/dendroNetwork.Rd b/man/dendroNetwork.Rd index feeb8fb9..6bd14c25 100644 --- a/man/dendroNetwork.Rd +++ b/man/dendroNetwork.Rd @@ -9,11 +9,23 @@ Mike Bostock: \url{http://bl.ocks.org/mbostock/4063570}. Fabio Nelli: \url{http://www.meccanismocomplesso.org/en/dendrogramma-d3-parte1/} } \usage{ -dendroNetwork(hc, height = 500, width = 800, fontSize = 10, - linkColour = "#ccc", nodeColour = "#fff", nodeStroke = "steelblue", - textColour = "#111", textOpacity = 0.9, textRotate = NULL, - opacity = 0.9, margins = NULL, linkType = c("elbow", "diagonal"), - treeOrientation = c("horizontal", "vertical"), zoom = FALSE) +dendroNetwork( + hc, + height = 500, + width = 800, + fontSize = 10, + linkColour = "#ccc", + nodeColour = "#fff", + nodeStroke = "steelblue", + textColour = "#111", + textOpacity = 0.9, + textRotate = NULL, + opacity = 0.9, + margins = NULL, + linkType = c("elbow", "diagonal"), + treeOrientation = c("horizontal", "vertical"), + zoom = FALSE +) } \arguments{ \item{hc}{a hierarchical (\code{hclust}) cluster object.} diff --git a/man/diagonalNetwork.Rd b/man/diagonalNetwork.Rd index 2bc47050..4d054457 100644 --- a/man/diagonalNetwork.Rd +++ b/man/diagonalNetwork.Rd @@ -10,10 +10,19 @@ IEEE Transactions on Software Engineering, SE-7(2), 223-228. Mike Bostock: \url{http://bl.ocks.org/mbostock/4339083}. } \usage{ -diagonalNetwork(List, height = NULL, width = NULL, fontSize = 10, - fontFamily = "serif", linkColour = "#ccc", nodeColour = "#fff", - nodeStroke = "steelblue", textColour = "#111", opacity = 0.9, - margin = NULL) +diagonalNetwork( + List, + height = NULL, + width = NULL, + fontSize = 10, + fontFamily = "serif", + linkColour = "#ccc", + nodeColour = "#fff", + nodeStroke = "steelblue", + textColour = "#111", + opacity = 0.9, + margin = NULL +) } \arguments{ \item{List}{a hierarchical list object with a root node and children.} diff --git a/man/forceNetwork.Rd b/man/forceNetwork.Rd index 2b97ba15..66875b56 100644 --- a/man/forceNetwork.Rd +++ b/man/forceNetwork.Rd @@ -9,15 +9,33 @@ specifically for force directed networks \url{https://github.com/d3/d3/blob/master/API.md#forces-d3-force}. } \usage{ -forceNetwork(Links, Nodes, Source, Target, Value, NodeID, Nodesize, Group, - height = NULL, width = NULL, - colourScale = JS("d3.scaleOrdinal(d3.schemeCategory20);"), fontSize = 7, - fontFamily = "serif", linkDistance = 50, +forceNetwork( + Links, + Nodes, + Source, + Target, + Value, + NodeID, + Nodesize, + Group, + height = NULL, + width = NULL, + colourScale = JS("d3.scaleOrdinal(d3.schemeCategory20);"), + fontSize = 7, + fontFamily = "serif", + linkDistance = 50, linkWidth = JS("function(d) { return Math.sqrt(d.value); }"), - radiusCalculation = JS(" Math.sqrt(d.nodesize)+6"), charge = -30, - linkColour = "#666", opacity = 0.6, zoom = FALSE, legend = FALSE, - arrows = FALSE, bounded = FALSE, opacityNoHover = 0, - clickAction = NULL) + radiusCalculation = JS(" Math.sqrt(d.nodesize)+6"), + charge = -30, + linkColour = "#666", + opacity = 0.6, + zoom = FALSE, + legend = FALSE, + arrows = FALSE, + bounded = FALSE, + opacityNoHover = 0, + clickAction = NULL +) } \arguments{ \item{Links}{a data frame object with the links between the nodes. It should diff --git a/man/igraph_to_networkD3.Rd b/man/igraph_to_networkD3.Rd index 30950f10..666578ab 100644 --- a/man/igraph_to_networkD3.Rd +++ b/man/igraph_to_networkD3.Rd @@ -10,7 +10,7 @@ igraph_to_networkD3(g, group, what = "both") \item{g}{an \code{igraph} class graph object} \item{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.} \item{what}{a character string specifying what to return. If \code{what = 'links'} or \code{what = 'nodes'} only the links or nodes are diff --git a/man/networkD3-package.Rd b/man/networkD3-package.Rd index 108a786c..43ec5a5a 100644 --- a/man/networkD3-package.Rd +++ b/man/networkD3-package.Rd @@ -1,9 +1,9 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/networkD3.R -\docType{package} \name{networkD3-package} \alias{networkD3-package} \alias{networkD3} +\alias{_PACKAGE} \title{Tools for Creating D3 Network Graphs from R} \description{ Creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R. diff --git a/man/radialNetwork.Rd b/man/radialNetwork.Rd index 84313b2c..2b3f507e 100644 --- a/man/radialNetwork.Rd +++ b/man/radialNetwork.Rd @@ -10,10 +10,19 @@ IEEE Transactions on Software Engineering, SE-7(2), 223-228. Mike Bostock: \url{http://bl.ocks.org/mbostock/4063550}. } \usage{ -radialNetwork(List, height = NULL, width = NULL, fontSize = 10, - fontFamily = "serif", linkColour = "#ccc", nodeColour = "#fff", - nodeStroke = "steelblue", textColour = "#111", opacity = 0.9, - margin = NULL) +radialNetwork( + List, + height = NULL, + width = NULL, + fontSize = 10, + fontFamily = "serif", + linkColour = "#ccc", + nodeColour = "#fff", + nodeStroke = "steelblue", + textColour = "#111", + opacity = 0.9, + margin = NULL +) } \arguments{ \item{List}{a hierarchical list object with a root node and children.} diff --git a/man/sankeyNetwork.Rd b/man/sankeyNetwork.Rd index 45445951..dc3fe556 100644 --- a/man/sankeyNetwork.Rd +++ b/man/sankeyNetwork.Rd @@ -8,11 +8,27 @@ 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/}. } \usage{ -sankeyNetwork(Links, Nodes, Source, Target, Value, NodeID, NodeGroup = NodeID, - LinkGroup = NULL, units = "", - colourScale = JS("d3.scaleOrdinal(d3.schemeCategory20);"), fontSize = 7, - fontFamily = NULL, nodeWidth = 15, nodePadding = 10, margin = NULL, - height = NULL, width = NULL, iterations = 32, sinksRight = TRUE) +sankeyNetwork( + Links, + Nodes, + Source, + Target, + Value, + NodeID, + NodeGroup = NodeID, + LinkGroup = NULL, + units = "", + colourScale = JS("d3.scaleOrdinal(d3.schemeCategory20);"), + fontSize = 7, + fontFamily = NULL, + nodeWidth = 15, + nodePadding = 10, + margin = NULL, + height = NULL, + width = NULL, + iterations = 32, + sinksRight = TRUE +) } \arguments{ \item{Links}{a data frame object with the links between the nodes. It should diff --git a/man/simpleNetwork.Rd b/man/simpleNetwork.Rd index 217573b5..e96b1f4f 100644 --- a/man/simpleNetwork.Rd +++ b/man/simpleNetwork.Rd @@ -9,9 +9,21 @@ D3.js was created by Michael Bostock. See \url{http://d3js.org/} and, \url{https://github.com/d3/d3/blob/master/API.md#forces-d3-force} } \usage{ -simpleNetwork(Data, Source = 1, Target = 2, height = NULL, width = NULL, - linkDistance = 50, charge = -30, fontSize = 7, fontFamily = "serif", - linkColour = "#666", nodeColour = "#3182bd", opacity = 0.6, zoom = F) +simpleNetwork( + Data, + Source = 1, + Target = 2, + height = NULL, + width = NULL, + linkDistance = 50, + charge = -30, + fontSize = 7, + fontFamily = "serif", + linkColour = "#666", + nodeColour = "#3182bd", + opacity = 0.6, + zoom = F +) } \arguments{ \item{Data}{a data frame object with three columns. The first two are the diff --git a/man/treeNetwork.Rd b/man/treeNetwork.Rd index 76f13030..22264de3 100644 --- a/man/treeNetwork.Rd +++ b/man/treeNetwork.Rd @@ -4,9 +4,19 @@ \alias{treeNetwork} \title{Create collapsible tree network diagrams.} \usage{ -treeNetwork(data, width = NULL, height = NULL, treeType = "tidy", - direction = "right", linkType = "diagonal", defaults = NULL, - mouseover = "", mouseout = "", inbrowser = FALSE, ...) +treeNetwork( + data, + width = NULL, + height = NULL, + treeType = "tidy", + direction = "right", + linkType = "diagonal", + defaults = NULL, + mouseover = "", + mouseout = "", + inbrowser = FALSE, + ... +) } \arguments{ \item{data}{a tree network description in one of numerous forms (see details)} From a01fb4f38efb32b5a3d448dc074278d69f9dcb81 Mon Sep 17 00:00:00 2001 From: christophergandrud Date: Mon, 14 Apr 2025 17:39:50 +0200 Subject: [PATCH 2/7] remove bad urls --- R/chordNetwork.R | 2 +- R/data-definitions.R | 6 +++--- R/dendroNetwork.R | 4 ++-- R/forceNetwork.R | 2 +- R/sankeyNetwork.R | 6 +++--- R/simpleNetwork.R | 2 +- README.md | 6 +++--- man/MisLinks.Rd | 2 +- man/MisNodes.Rd | 2 +- man/chordNetwork.Rd | 2 +- man/dendroNetwork.Rd | 4 ++-- man/forceNetwork.Rd | 2 +- man/sankeyNetwork.Rd | 6 +++--- man/simpleNetwork.Rd | 2 +- 14 files changed, 24 insertions(+), 24 deletions(-) diff --git a/R/chordNetwork.R b/R/chordNetwork.R index 971e93fc..02c007f0 100644 --- 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 index 195c5c31..c5fe9d9d 100644 --- a/R/data-definitions.R +++ b/R/data-definitions.R @@ -5,7 +5,7 @@ #' #' @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 @@ -13,12 +13,12 @@ #' 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 index bec82c1c..aebb9351 100644 --- 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 index 8bf8d136..07b3e215 100755 --- 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/sankeyNetwork.R b/R/sankeyNetwork.R index 31f99ded..5ad19d85 100644 --- 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 index 6ee58aba..9360f922 100644 --- 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/README.md b/README.md index e03f2f18..e372382c 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ 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) +Status](https://travis-ci.org/christophergandrud/networkD3.svg?branch=master)](https://app.travis-ci.com/christophergandrud/networkD3) ![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 +42,7 @@ 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 +55,7 @@ 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/MisLinks.Rd b/man/MisLinks.Rd index 1cc76274..6571b9f8 100644 --- a/man/MisLinks.Rd +++ b/man/MisLinks.Rd @@ -8,7 +8,7 @@ A data set with 254 observations of 3 variables. } \source{ -See Mike Bostock \url{http://bl.ocks.org/mbostock/4062045}. +See Mike Bostock \url{https://bl.ocks.org/mbostock/4062045}. } \usage{ MisLinks diff --git a/man/MisNodes.Rd b/man/MisNodes.Rd index 8cca267e..20461d64 100644 --- a/man/MisNodes.Rd +++ b/man/MisNodes.Rd @@ -9,7 +9,7 @@ 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}. +See Mike Bostock \url{https://bl.ocks.org/mbostock/4062045}. } \usage{ MisNodes diff --git a/man/chordNetwork.Rd b/man/chordNetwork.Rd index 1f343454..20d3a156 100644 --- a/man/chordNetwork.Rd +++ b/man/chordNetwork.Rd @@ -4,7 +4,7 @@ \alias{chordNetwork} \title{Create Reingold-Tilford Tree network diagrams.} \source{ -Mike Bostock: \url{https://github.com/mbostock/d3/wiki/Chord-Layout}. +Mike Bostock: \url{https://github.com/d3/d3/wiki/Chord-Layout}. } \usage{ chordNetwork( diff --git a/man/dendroNetwork.Rd b/man/dendroNetwork.Rd index 6bd14c25..72a6a74d 100644 --- a/man/dendroNetwork.Rd +++ b/man/dendroNetwork.Rd @@ -4,9 +4,9 @@ \alias{dendroNetwork} \title{Create hierarchical cluster network diagrams.} \source{ -Mike Bostock: \url{http://bl.ocks.org/mbostock/4063570}. +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/ } \usage{ dendroNetwork( diff --git a/man/forceNetwork.Rd b/man/forceNetwork.Rd index 66875b56..2991e6e7 100644 --- a/man/forceNetwork.Rd +++ b/man/forceNetwork.Rd @@ -4,7 +4,7 @@ \alias{forceNetwork} \title{Create a D3 JavaScript force directed network graph.} \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}. } diff --git a/man/sankeyNetwork.Rd b/man/sankeyNetwork.Rd index dc3fe556..a1f697c3 100644 --- a/man/sankeyNetwork.Rd +++ b/man/sankeyNetwork.Rd @@ -4,8 +4,8 @@ \alias{sankeyNetwork} \title{Create a D3 JavaScript Sankey diagram} \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/}. } \usage{ sankeyNetwork( @@ -96,7 +96,7 @@ Create a D3 JavaScript Sankey diagram } \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') diff --git a/man/simpleNetwork.Rd b/man/simpleNetwork.Rd index e96b1f4f..2dee439f 100644 --- a/man/simpleNetwork.Rd +++ b/man/simpleNetwork.Rd @@ -4,7 +4,7 @@ \alias{simpleNetwork} \title{Function for creating simple D3 JavaScript force directed network graphs.} \source{ -D3.js was created by Michael Bostock. See \url{http://d3js.org/} and, +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} } From 9ace3f576bc3ea0687ccba95211fcbbd24cf485a Mon Sep 17 00:00:00 2001 From: christophergandrud Date: Mon, 14 Apr 2025 17:51:03 +0200 Subject: [PATCH 3/7] minor link change --- R/utils.R | 2 +- man/SchoolsJournals.Rd | 2 +- man/igraph_to_networkD3.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/utils.R b/R/utils.R index 34c2b493..554670be 100644 --- a/R/utils.R +++ b/R/utils.R @@ -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/man/SchoolsJournals.Rd b/man/SchoolsJournals.Rd index cabcba5e..49647b07 100644 --- a/man/SchoolsJournals.Rd +++ b/man/SchoolsJournals.Rd @@ -9,7 +9,7 @@ Relations} A data set with 2732 rows and 3 variables. } \source{ -See REF 2014 \url{http://results.ref.ac.uk/DownloadSubmissions/ByUoa/21}. +See REF 2014 \url{https://results.ref.ac.uk/DownloadSubmissions/ByUoa/21}. } \usage{ SchoolsJournals diff --git a/man/igraph_to_networkD3.Rd b/man/igraph_to_networkD3.Rd index 666578ab..6be34092 100644 --- a/man/igraph_to_networkD3.Rd +++ b/man/igraph_to_networkD3.Rd @@ -44,7 +44,7 @@ forceNetwork(Links = karate_d3$links, Nodes = karate_d3$nodes, \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 From 5d425099dc8fa37c0c6db9ca74f75c4d23806770 Mon Sep 17 00:00:00 2001 From: christophergandrud Date: Fri, 18 Apr 2025 08:17:22 +0200 Subject: [PATCH 4/7] Remove Travis CI configuration and references --- .Rbuildignore | 1 - .travis.yml | 2 -- README.Rmd | 1 - README.md | 5 +---- 4 files changed, 1 insertion(+), 8 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index d9db7619..7aadd213 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,7 +1,6 @@ ^.*\.Rproj$ ^\.Rproj\.user$ ^JSONdata -.travis.yml .sass-cache ^.*\.o$ ^README\.Rmd$ diff --git a/.travis.yml b/.travis.yml index 468cc477..e69de29b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,2 +0,0 @@ -language: r -cache: packages diff --git a/README.Rmd b/README.Rmd index 0fe4afd2..c8d01ead 100644 --- a/README.Rmd +++ b/README.Rmd @@ -6,7 +6,6 @@ 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) ![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 index e372382c..de6200c0 100644 --- 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://app.travis-ci.com/christophergandrud/networkD3) -![CRAN Monthly +Version](http://www.r-pkg.org/badges/version/networkD3)](https://CRAN.R-project.org/package=networkD3) ![CRAN Monthly Downloads](http://cranlogs.r-pkg.org/badges/last-month/networkD3) ![CRAN Total Downloads](http://cranlogs.r-pkg.org/badges/grand-total/networkD3) From 6ef1f0016178ee9fd779ddbef7080c1d64c1de24 Mon Sep 17 00:00:00 2001 From: christophergandrud Date: Fri, 18 Apr 2025 08:18:37 +0200 Subject: [PATCH 5/7] remove travis --- .travis.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index e69de29b..00000000 From 9146254dca2ee296757fbfc49b1be5c9e5ad1a10 Mon Sep 17 00:00:00 2001 From: christophergandrud Date: Fri, 18 Apr 2025 08:22:21 +0200 Subject: [PATCH 6/7] Add GitHub Actions CI workflows to replace Travis CI --- .github/workflows/R-CMD-check.yaml | 50 +++++++++++++++++++++++++++ .github/workflows/test-coverage.yaml | 51 ++++++++++++++++++++++++++++ README.Rmd | 1 + README.md | 2 +- 4 files changed, 103 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/R-CMD-check.yaml create mode 100644 .github/workflows/test-coverage.yaml diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 00000000..941d1536 --- /dev/null +++ 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 new file mode 100644 index 00000000..ae9b6578 --- /dev/null +++ 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@v3 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/README.Rmd b/README.Rmd index c8d01ead..c54ffdd8 100644 --- a/README.Rmd +++ b/README.Rmd @@ -6,6 +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) +[![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 index de6200c0..dd1f58d9 100644 --- a/README.md +++ b/README.md @@ -2,7 +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) ![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) From b67747003682b16f776ad621a2cd45f79bacb0d9 Mon Sep 17 00:00:00 2001 From: christophergandrud Date: Fri, 18 Apr 2025 08:24:43 +0200 Subject: [PATCH 7/7] Update actions/upload-artifact to v4 --- .github/workflows/test-coverage.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index ae9b6578..fa106c32 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -45,7 +45,7 @@ jobs: - name: Upload test results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-test-failures path: ${{ runner.temp }}/package