From 43539b47412a4864dacff75e6bca952082e9019a Mon Sep 17 00:00:00 2001 From: "George G. Vega Yon" Date: Sun, 30 Jun 2024 13:53:58 -0600 Subject: [PATCH] Addressing CRAN comments --- DESCRIPTION | 1 - R/.Rhistory | 512 ------------------------------------------ R/gexf.R | 2 +- R/manipulation.R | 4 +- R/read.gexf.R | 2 +- R/rgexf-package.R | 6 +- README.md | 32 +-- README.qmd | 2 +- inst/CITATION | 8 +- man/add.gexf.node.Rd | 2 +- man/gexf-class.Rd | 2 +- man/new.gexf.graph.Rd | 2 +- man/read.gexf.Rd | 2 +- man/rgexf-package.Rd | 6 +- vignettes/rgexf.Rmd | 2 +- 15 files changed, 35 insertions(+), 550 deletions(-) delete mode 100644 R/.Rhistory diff --git a/DESCRIPTION b/DESCRIPTION index 23042b3..0091f3a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,6 @@ Type: Package Encoding: UTF-8 Title: Build, Import, and Export GEXF Graph Files Version: 0.16.3 -Date: 2024-06-27 Authors@R: c( person("George", "Vega Yon", email="g.vegayon@gmail.com", role=c("aut", "cre"), comment = structure("0000-0002-3171-0844", .Names = "ORCID")), diff --git a/R/.Rhistory b/R/.Rhistory deleted file mode 100644 index 3a5eff6..0000000 --- a/R/.Rhistory +++ /dev/null @@ -1,512 +0,0 @@ -my.app2 <- function(env){ -res <- Response$new() -res$write(gexf.object$graph) -res$finish() -} -s$add(app=my.app2, name='data') -# jquery -jquery <- readLines("../inst/sigmajs/jquery.min.js", warn=FALSE) -my.app3 <- function(env){ -res <- Response$new() -res$write(paste(jquery , collapse="\n ")) -res$finish() -} -s$add(app=my.app3, name='jquery.js') -# sigmajs -sigmajs <- readLines("../inst/sigmajs/sigma.min.js", warn=FALSE) -my.app4 <- function(env){ -res <- Response$new() -res$write(paste(sigmajs , collapse="\n ")) -res$finish() -} -s$add(app=my.app4, name='sigmajs') -# sigmajs -sigma.parseGexf <- readLines("../inst/sigmajs/sigma.parseGexf.js", warn=FALSE) -my.app5 <- function(env){ -res <- Response$new() -res$write(paste(sigma.parseGexf , collapse="\n ")) -res$finish() -} -s$add(app=my.app5, name='sigmaparseGexfjs') -s$browse('plot') -gexf.object2 <- write.gexf(nodes=data.frame(id=1:4, label=c("juan", "pedro", "matthew", "carlos"), stringsAsFactors=F), -edges=data.frame(source=c(1,1,1,2,3,4,2,4,4), target=c(4,2,3,3,4,2,4,1,1)), -edgesAtt=data.frame(letrafavorita=letters[1:9], numbers=1:9, stringsAsFactors=F), -nodesAtt=data.frame(letrafavorita=c(letters[1:3],"hola"), numbers=1:4, stringsAsFactors=F)) -library(Rook) -# system.file(package="rgexf") -library(sna) -nNodes <- nrow(gexf.object$nodes) -links <- matrix(rep(0, nNodes*nNodes), ncol = nNodes) -relations <- gexf.object$edges[,c(3,4)] -for(edge in 1:ncol(relations)){ -links[(relations[edge,]$target), (relations[edge,]$source)] <- 1 -} -positions <- gplot.layout.kamadakawai(links, layout.par=list()) -positions <- cbind(positions, 0) # needs a z axis -library(sna) -nNodes <- nrow(gexf.object$nodes) -links <- matrix(rep(0, nNodes*nNodes), ncol = nNodes) -relations <- gexf.object$edges[,c(3,4)] -for(edge in 1:ncol(relations)){ -links[(relations[edge,]$target), (relations[edge,]$source)] <- 1 -} -positions <- gplot.layout.kamadakawai(links, layout.par=list()) -positions <- cbind(positions, 0) # needs a z axis -positions -nodecolors <- data.frame(r = rep(0, nNodes), -g = rep(0, nNodes), -b = rep(0, nNodes), -a = rep(0, nNodes)) -nodecolors -gexg.object <- write.gexf(nodes=gexf.object$nodes, -edges=gexf.object$edges[,c(3,4)], -nodesVizAtt=list( -color=nodecolors, -position=positions -)) -gexf.object$edges[,c(3,4)] -gexf.object$edges -gexf.object2 <- write.gexf(nodes=data.frame(id=1:4, label=c("juan", "pedro", "matthew", "carlos"), stringsAsFactors=F), -edges=data.frame(source=c(1,1,1,2,3,4,2,4,4), target=c(4,2,3,3,4,2,4,1,1)), -edgesAtt=data.frame(letrafavorita=letters[1:9], numbers=1:9, stringsAsFactors=F), -nodesAtt=data.frame(letrafavorita=c(letters[1:3],"hola"), numbers=1:4, stringsAsFactors=F)) -gexf.object <- gexf.object2 -library(Rook) -library(sna) -nNodes <- nrow(gexf.object$nodes) -links <- matrix(rep(0, nNodes*nNodes), ncol = nNodes) -relations <- gexf.object$edges[,c(3,4)] -for(edge in 1:ncol(relations)){ -links[(relations[edge,]$target), (relations[edge,]$source)] <- 1 -} -positions <- gplot.layout.kamadakawai(links, layout.par=list()) -positions <- cbind(positions, 0) # needs a z axis -nodecolors <- data.frame(r = rep(0, nNodes), -g = rep(0, nNodes), -b = rep(0, nNodes), -a = rep(0, nNodes)) -gexg.object <- write.gexf(nodes=gexf.object$nodes, -edges=gexf.object$edges[,c("source","target")], -nodesVizAtt=list( -color=nodecolors, -position=positions -)) -if(!is.null(gexf.object$node.att)){ -# dev -html <- readLines("../inst/sigmajs/index_att.html", warn=FALSE) -} else { -# dev -html <- readLines("../inst/sigmajs/index.html", warn=FALSE) -} -html <- gsub("EdgeTypePar", EdgeType, html) -s <- Rhttpd$new() -s$start(listen='127.0.0.1') -# html -my.app <- function(env){ -res <- Response$new() -res$write(paste(html, collapse="\n")) -res$finish() -} -s$add(app=my.app, name='plot') -# graph -my.app2 <- function(env){ -res <- Response$new() -res$write(gexf.object$graph) -res$finish() -} -s$add(app=my.app2, name='data') -# jquery -jquery <- readLines("../inst/sigmajs/jquery.min.js", warn=FALSE) -my.app3 <- function(env){ -res <- Response$new() -res$write(paste(jquery , collapse="\n ")) -res$finish() -} -s$add(app=my.app3, name='jquery.js') -# sigmajs -sigmajs <- readLines("../inst/sigmajs/sigma.min.js", warn=FALSE) -my.app4 <- function(env){ -res <- Response$new() -res$write(paste(sigmajs , collapse="\n ")) -res$finish() -} -s$add(app=my.app4, name='sigmajs') -# sigmajs -sigma.parseGexf <- readLines("../inst/sigmajs/sigma.parseGexf.js", warn=FALSE) -my.app5 <- function(env){ -res <- Response$new() -res$write(paste(sigma.parseGexf , collapse="\n ")) -res$finish() -} -s$add(app=my.app5, name='sigmaparseGexfjs') -s$browse('plot') -gexf.object$nodes -gexf.object$edges[,c("source","target")] -nodecolors -positions -gexg.object <- write.gexf(nodes=gexf.object$nodes, -edges=gexf.object$edges[,c("source","target")], -nodesVizAtt=list( -color=nodecolors, -position=positions -)) -gexf.object <- write.gexf(nodes=gexf.object$nodes, -edges=gexf.object$edges[,c("source","target")], -nodesVizAtt=list( -color=nodecolors, -position=positions -)) -if(!is.null(gexf.object$node.att)){ -# dev -html <- readLines("../inst/sigmajs/index_att.html", warn=FALSE) -} else { -# dev -html <- readLines("../inst/sigmajs/index.html", warn=FALSE) -} -html <- gsub("EdgeTypePar", EdgeType, html) -s <- Rhttpd$new() -s$start(listen='127.0.0.1') -# html -my.app <- function(env){ -res <- Response$new() -res$write(paste(html, collapse="\n")) -res$finish() -} -s$add(app=my.app, name='plot') -# graph -my.app2 <- function(env){ -res <- Response$new() -res$write(gexf.object$graph) -res$finish() -} -s$add(app=my.app2, name='data') -# jquery -jquery <- readLines("../inst/sigmajs/jquery.min.js", warn=FALSE) -my.app3 <- function(env){ -res <- Response$new() -res$write(paste(jquery , collapse="\n ")) -res$finish() -} -s$add(app=my.app3, name='jquery.js') -# sigmajs -sigmajs <- readLines("../inst/sigmajs/sigma.min.js", warn=FALSE) -my.app4 <- function(env){ -res <- Response$new() -res$write(paste(sigmajs , collapse="\n ")) -res$finish() -} -s$add(app=my.app4, name='sigmajs') -# sigmajs -sigma.parseGexf <- readLines("../inst/sigmajs/sigma.parseGexf.js", warn=FALSE) -my.app5 <- function(env){ -res <- Response$new() -res$write(paste(sigma.parseGexf , collapse="\n ")) -res$finish() -} -s$add(app=my.app5, name='sigmaparseGexfjs') -s$browse('plot') -nodecolors <- data.frame(r = rep(255, nNodes), -g = rep(255, nNodes), -b = rep(255, nNodes), -a = rep(255, nNodes)) -gexf.object <- write.gexf(nodes=gexf.object$nodes, -edges=gexf.object$edges[,c("source","target")], -nodesVizAtt=list( -color=nodecolors, -position=positions -)) -if(!is.null(gexf.object$node.att)){ -# dev -html <- readLines("../inst/sigmajs/index_att.html", warn=FALSE) -} else { -# dev -html <- readLines("../inst/sigmajs/index.html", warn=FALSE) -} -html <- gsub("EdgeTypePar", EdgeType, html) -s <- Rhttpd$new() -s$start(listen='127.0.0.1') -# html -my.app <- function(env){ -res <- Response$new() -res$write(paste(html, collapse="\n")) -res$finish() -} -s$add(app=my.app, name='plot') -# graph -my.app2 <- function(env){ -res <- Response$new() -res$write(gexf.object$graph) -res$finish() -} -s$add(app=my.app2, name='data') -# jquery -jquery <- readLines("../inst/sigmajs/jquery.min.js", warn=FALSE) -my.app3 <- function(env){ -res <- Response$new() -res$write(paste(jquery , collapse="\n ")) -res$finish() -} -s$add(app=my.app3, name='jquery.js') -# sigmajs -sigmajs <- readLines("../inst/sigmajs/sigma.min.js", warn=FALSE) -my.app4 <- function(env){ -res <- Response$new() -res$write(paste(sigmajs , collapse="\n ")) -res$finish() -} -s$add(app=my.app4, name='sigmajs') -# sigmajs -sigma.parseGexf <- readLines("../inst/sigmajs/sigma.parseGexf.js", warn=FALSE) -my.app5 <- function(env){ -res <- Response$new() -res$write(paste(sigma.parseGexf , collapse="\n ")) -res$finish() -} -s$add(app=my.app5, name='sigmaparseGexfjs') -s$browse('plot') -system.file(package="rgexf") -system.file("inst/sigmajs/index_att.html",package="rgexf") -system.file("inst/sigmajs/index_att.html", package="rgexf") -system.file("/inst/sigmajs/index_att.html", package="rgexf") -install_bitbucket(repo="rgexf", username="gvegayon") -library(devtools) -install_bitbucket(repo="rgexf", username="gvegayon") -library(devtools) -install_bitbucket(repo="rgexf", username="gvegayon") -system.file("/inst/sigmajs/index_att.html", package="rgexf") -plot.gexf <- function(gexf.object, EdgeType = c("line", "curve")){ -library(Rook) -if(!is.null(gexg.object$positions)){ -library(sna) -nNodes <- nrow(gexf.object$nodes) -links <- matrix(rep(0, nNodes*nNodes), ncol = nNodes) -relations <- gexf.object$edges[,c(3,4)] -for(edge in 1:ncol(relations)){ -links[(relations[edge,]$target), (relations[edge,]$source)] <- 1 -} -positions <- gplot.layout.kamadakawai(links, layout.par=list()) -positions <- cbind(positions, 0) # needs a z axis -} -nodecolors <- data.frame(r = rep(255, nNodes), -g = rep(255, nNodes), -b = rep(255, nNodes), -a = rep(255, nNodes)) -gexf.object <- write.gexf(nodes=gexf.object$nodes, -edges=gexf.object$edges[,c("source","target")], -nodesVizAtt=list( -color=nodecolors, -position=positions -)) -if(!is.null(gexf.object$node.att)){ -# dev -html <- readLines("../inst/sigmajs/index_att.html", warn=FALSE) -system.file("/inst/sigmajs/index_att.html", package="rgexf") -} else { -# dev -html <- readLines("../inst/sigmajs/index.html", warn=FALSE) -} -html <- gsub("EdgeTypePar", EdgeType, html) -s <- Rhttpd$new() -s$start(listen='127.0.0.1') -# html -my.app <- function(env){ -res <- Response$new() -res$write(paste(html, collapse="\n")) -res$finish() -} -s$add(app=my.app, name='plot') -# graph -my.app2 <- function(env){ -res <- Response$new() -res$write(gexf.object$graph) -res$finish() -} -s$add(app=my.app2, name='data') -# jquery -my.app3 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/jquery.min.js", warn=FALSE), collapse="\n ")) -res$finish() -} -s$add(app=my.app3, name='jquery.js') -# sigmajs -my.app4 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/sigma.min.js", warn=FALSE) , collapse="\n ")) -res$finish() -} -s$add(app=my.app4, name='sigmajs') -# sigmajs -my.app5 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/sigma.parseGexf.js", warn=FALSE), collapse="\n ")) -res$finish() -} -s$add(app=my.app5, name='sigmaparseGexfjs') -s$browse('plot') -} -gexf.object <- write.gexf(nodes=data.frame(id=1:4, label=c("juan", "pedro", "matthew", "carlos"), stringsAsFactors=F), -edges=data.frame(source=c(1,1,1,2,3,4,2,4,4), target=c(4,2,3,3,4,2,4,1,1))) -plot.gexf(gexf.object) -library(rgexf) -plot.gexf(gexf.object) -gexf.object <- read.gexf("http://sigmajs.org/data/les_miserables.gexf") -plot.gexf(gexf.object) -gexf.object -gexf.object$positions -plot.gexf <- function(gexf.object, EdgeType = c("line", "curve")){ -library(Rook) -if(!is.null(gexf.object$positions)){ -library(sna) -nNodes <- nrow(gexf.object$nodes) -links <- matrix(rep(0, nNodes*nNodes), ncol = nNodes) -relations <- gexf.object$edges[,c(3,4)] -for(edge in 1:ncol(relations)){ -links[(relations[edge,]$target), (relations[edge,]$source)] <- 1 -} -positions <- gplot.layout.kamadakawai(links, layout.par=list()) -positions <- cbind(positions, 0) # needs a z axis -} -nodecolors <- data.frame(r = rep(255, nNodes), -g = rep(255, nNodes), -b = rep(255, nNodes), -a = rep(255, nNodes)) -gexf.object <- write.gexf(nodes=gexf.object$nodes, -edges=gexf.object$edges[,c("source","target")], -nodesVizAtt=list( -color=nodecolors, -position=positions -)) -if(!is.null(gexf.object$node.att)){ -# dev -html <- readLines("../inst/sigmajs/index_att.html", warn=FALSE) -system.file("/inst/sigmajs/index_att.html", package="rgexf") -} else { -# dev -html <- readLines("../inst/sigmajs/index.html", warn=FALSE) -} -html <- gsub("EdgeTypePar", EdgeType, html) -s <- Rhttpd$new() -s$start(listen='127.0.0.1') -# html -my.app <- function(env){ -res <- Response$new() -res$write(paste(html, collapse="\n")) -res$finish() -} -s$add(app=my.app, name='plot') -# graph -my.app2 <- function(env){ -res <- Response$new() -res$write(gexf.object$graph) -res$finish() -} -s$add(app=my.app2, name='data') -# jquery -my.app3 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/jquery.min.js", warn=FALSE), collapse="\n ")) -res$finish() -} -s$add(app=my.app3, name='jquery.js') -# sigmajs -my.app4 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/sigma.min.js", warn=FALSE) , collapse="\n ")) -res$finish() -} -s$add(app=my.app4, name='sigmajs') -# sigmajs -my.app5 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/sigma.parseGexf.js", warn=FALSE), collapse="\n ")) -res$finish() -} -s$add(app=my.app5, name='sigmaparseGexfjs') -s$browse('plot') -} -plot.gexf(gexf.object) -gexf.object <- write.gexf(nodes=data.frame(id=1:4, label=c("juan", "pedro", "matthew", "carlos"), stringsAsFactors=F), -edges=data.frame(source=c(1,1,1,2,3,4,2,4,4), target=c(4,2,3,3,4,2,4,1,1))) -plot.gexf(gexf.object) -plot.gexf <- function(gexf.object, EdgeType = c("line", "curve")){ -library(Rook) -# if(!is.null(gexf.object$positions)){ -# library(sna) -# nNodes <- nrow(gexf.object$nodes) -# links <- matrix(rep(0, nNodes*nNodes), ncol = nNodes) -# relations <- gexf.object$edges[,c(3,4)] -# -# for(edge in 1:ncol(relations)){ -# links[(relations[edge,]$target), (relations[edge,]$source)] <- 1 -# } -# -# positions <- gplot.layout.kamadakawai(links, layout.par=list()) -# positions <- cbind(positions, 0) # needs a z axis -# } -# -# nodecolors <- data.frame(r = rep(255, nNodes), -# g = rep(255, nNodes), -# b = rep(255, nNodes), -# a = rep(255, nNodes)) -# -# gexf.object <- write.gexf(nodes=gexf.object$nodes, -# edges=gexf.object$edges[,c("source","target")], -# nodesVizAtt=list( -# color=nodecolors, -# position=positions -# )) -# -if(!is.null(gexf.object$node.att)){ -# dev -html <- readLines("../inst/sigmajs/index_att.html", warn=FALSE) -system.file("/inst/sigmajs/index_att.html", package="rgexf") -} else { -# dev -html <- readLines("../inst/sigmajs/index.html", warn=FALSE) -} -html <- gsub("EdgeTypePar", EdgeType, html) -s <- Rhttpd$new() -s$start(listen='127.0.0.1') -# html -my.app <- function(env){ -res <- Response$new() -res$write(paste(html, collapse="\n")) -res$finish() -} -s$add(app=my.app, name='plot') -# graph -my.app2 <- function(env){ -res <- Response$new() -res$write(gexf.object$graph) -res$finish() -} -s$add(app=my.app2, name='data') -# jquery -my.app3 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/jquery.min.js", warn=FALSE), collapse="\n ")) -res$finish() -} -s$add(app=my.app3, name='jquery.js') -# sigmajs -my.app4 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/sigma.min.js", warn=FALSE) , collapse="\n ")) -res$finish() -} -s$add(app=my.app4, name='sigmajs') -# sigmajs -my.app5 <- function(env){ -res <- Response$new() -res$write(paste(readLines("../inst/sigmajs/sigma.parseGexf.js", warn=FALSE), collapse="\n ")) -res$finish() -} -s$add(app=my.app5, name='sigmaparseGexfjs') -s$browse('plot') -} -gexf.object <- read.gexf("http://sigmajs.org/data/les_miserables.gexf") -plot.gexf(gexf.object) -gexf.object <- read.gexf("http://sigmajs.org/data/les_miserables.gexf") -plot.gexf(gexf.object) diff --git a/R/gexf.R b/R/gexf.R index 4984415..42d9b1a 100644 --- a/R/gexf.R +++ b/R/gexf.R @@ -102,7 +102,7 @@ #' #' Jorge Fabrega Lacoa #' @seealso [new.gexf.graph()] -#' @references The GEXF project website: https://gephi.org/gexf/format/ +#' @references The GEXF project website: http://gexf.net/format/ #' @keywords IO #' @examples #' diff --git a/R/manipulation.R b/R/manipulation.R index e1a494d..610cf4f 100644 --- a/R/manipulation.R +++ b/R/manipulation.R @@ -35,7 +35,7 @@ #' @author George Vega Yon #' #' Jorge Fabrega Lacoa -#' @references The GEXF project website: https://gephi.org/gexf/format/ +#' @references The GEXF project website: http://gexf.net/format/ #' @keywords manip #' @examples #' @@ -244,7 +244,7 @@ add.gexf.edge <- function( #' @author George Vega Yon #' #' Jorge Fabrega Lacoa -#' @references The GEXF project website: https://gephi.org/gexf/format/ +#' @references The GEXF project website: http://gexf.net/format/ #' @keywords manip #' @examples #' diff --git a/R/read.gexf.R b/R/read.gexf.R index 124dd8c..3bd17ae 100644 --- a/R/read.gexf.R +++ b/R/read.gexf.R @@ -10,7 +10,7 @@ #' @author George Vega Yon #' #' Jorge Fabrega Lacoa -#' @references The GEXF project website: https://gephi.org/gexf/format/ +#' @references The GEXF project website: http://gexf.net/format/ #' @keywords IO #' @examples #' diff --git a/R/rgexf-package.R b/R/rgexf-package.R index 7aa630f..e5c55a8 100644 --- a/R/rgexf-package.R +++ b/R/rgexf-package.R @@ -140,12 +140,12 @@ NULL #' @name rgexf-package #' @aliases rgexf-package rgexf gephi #' @note See the GEXF primer for details on the GEXF graph format: -#' \url{https://gephi.org/gexf/1.2draft/gexf-12draft-primer.pdf} +#' \url{http://gexf.net/1.2draft/gexf-12draft-primer.pdf} #' @references \itemize{ \item rgexf project site: #' \url{https://github.com/gvegayon/rgexf} \item Gephi project site: -#' \url{https://gephi.org/} \item GEXF project site: \url{https://gephi.org/gexf/format//} +#' \url{https://gephi.org/} \item GEXF project site: \url{http://gexf.net/format//} #' \item gexf-js project website: \url{https://github.com/raphv/gexf-js} -#' \item Sigmasj project site: \url{http://sigmajs.org/} +#' \item Sigmasj project site: \url{https://www.sigmajs.org/} #' } #' @keywords package #' @examples diff --git a/README.md b/README.md index 262473d..4182740 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ website](https://github.com/gvegayon/rgexf/actions/workflows/website.yml/badge.s [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/gvegayon/rgexf?branch=master&svg=true.png)](https://ci.appveyor.com/project/gvegayon/rgexf) [![Coverage -Status](https://img.shields.io/codecov/c/github/gvegayon/rgexf/master.svg)](https://codecov.io/github/gvegayon/rgexf?branch=master) +Status](https://img.shields.io/codecov/c/github/gvegayon/rgexf/master.svg)](https://app.codecov.io/github/gvegayon/rgexf?branch=master) [![DOI](https://joss.theoj.org/papers/10.21105/joss.03456/status.svg)](https://doi.org/10.21105/joss.03456) [![Sponsor](https://img.shields.io/badge/-Sponsor-fafbfc?logo=GitHub%20Sponsors.png)](https://github.com/sponsors/gvegayon) @@ -241,7 +241,7 @@ write.gexf(people, relations) - + NodosChile A GEXF file written in R with "rgexf" GEXF, NodosChile, R, rgexf, Gephi @@ -250,22 +250,22 @@ write.gexf(people, relations) - + - + - + - + @@ -302,7 +302,7 @@ write.gexf(people, relations, nodeDynamic=time) - + NodosChile A GEXF file written in R with "rgexf" GEXF, NodosChile, R, rgexf, Gephi @@ -311,7 +311,7 @@ write.gexf(people, relations, nodeDynamic=time) - + @@ -321,12 +321,12 @@ write.gexf(people, relations, nodeDynamic=time) - + - + @@ -405,7 +405,7 @@ write.gexf(nodes=people, edges=relations, edgeDynamic=time.edges, - + NodosChile A GEXF file written in R with "rgexf" GEXF, NodosChile, R, rgexf, Gephi @@ -426,7 +426,7 @@ write.gexf(nodes=people, edges=relations, edgeDynamic=time.edges, - + @@ -435,7 +435,7 @@ write.gexf(nodes=people, edges=relations, edgeDynamic=time.edges, - + @@ -444,7 +444,7 @@ write.gexf(nodes=people, edges=relations, edgeDynamic=time.edges, - + @@ -453,7 +453,7 @@ write.gexf(nodes=people, edges=relations, edgeDynamic=time.edges, - + @@ -528,7 +528,7 @@ devtools::session_info() collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Denver - date 2024-06-27 + date 2024-06-30 pandoc 3.1.1 @ /usr/bin/ (via rmarkdown) ─ Packages ─────────────────────────────────────────────────────────────────── diff --git a/README.qmd b/README.qmd index 04a1888..89290cd 100644 --- a/README.qmd +++ b/README.qmd @@ -12,7 +12,7 @@ knitr::opts_chunk$set(fig.path = "man/figures/", warning = FALSE) [![R CI](https://github.com/gvegayon/rgexf/actions/workflows/ci.yml/badge.svg)](https://github.com/gvegayon/rgexf/actions/workflows/ci.yml) [![rgexf website](https://github.com/gvegayon/rgexf/actions/workflows/website.yml/badge.svg)](https://github.com/gvegayon/rgexf/actions/workflows/website.yml) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/gvegayon/rgexf?branch=master&svg=true)](https://ci.appveyor.com/project/gvegayon/rgexf) -[![Coverage Status](https://img.shields.io/codecov/c/github/gvegayon/rgexf/master.svg)](https://codecov.io/github/gvegayon/rgexf?branch=master) +[![Coverage Status](https://img.shields.io/codecov/c/github/gvegayon/rgexf/master.svg)](https://app.codecov.io/github/gvegayon/rgexf?branch=master) [![DOI](https://joss.theoj.org/papers/10.21105/joss.03456/status.svg)](https://doi.org/10.21105/joss.03456) [![Sponsor](https://img.shields.io/badge/-Sponsor-fafbfc?logo=GitHub%20Sponsors)](https://github.com/sponsors/gvegayon) diff --git a/inst/CITATION b/inst/CITATION index 0630aa5..41c3208 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,10 +1,8 @@ year <- sub("-.*", "", meta$Date) note <- sprintf("R package version %s", meta$Version) -citHeader("To cite rgexf in publications use the following paper:") - -citEntry( - entry = "Article", +bibentry( + bibtype = "Article", title = "Building, Importing, and Exporting GEXF Graph Files with rgexf", author = c( person("George", "Vega Yon") @@ -16,7 +14,7 @@ citEntry( doi = "10.21105/joss.03456", url = "https://doi.org/10.21105/joss.03456", pages = "3456", - textVersion = "Vega Yon, G. G., (2021). Building, Importing, and Exporting GEXF Graph Files with rgexf. Journal of Open Source Software, 6(64), 3456, https://doi.org/10.21105/joss.03456" + header = "To cite rgexf in publications use the following paper:" ) bibentry(bibtype = "Manual", diff --git a/man/add.gexf.node.Rd b/man/add.gexf.node.Rd index 1d2747b..7452e58 100644 --- a/man/add.gexf.node.Rd +++ b/man/add.gexf.node.Rd @@ -153,7 +153,7 @@ g } \references{ -The GEXF project website: https://gephi.org/gexf/format/ +The GEXF project website: http://gexf.net/format/ } \author{ George Vega Yon diff --git a/man/gexf-class.Rd b/man/gexf-class.Rd index f16fbb0..f7fe51d 100644 --- a/man/gexf-class.Rd +++ b/man/gexf-class.Rd @@ -179,7 +179,7 @@ if (interactive()) { } \references{ -The GEXF project website: https://gephi.org/gexf/format/ +The GEXF project website: http://gexf.net/format/ } \seealso{ \code{\link[=new.gexf.graph]{new.gexf.graph()}} diff --git a/man/new.gexf.graph.Rd b/man/new.gexf.graph.Rd index 24cab4a..5e7ef53 100644 --- a/man/new.gexf.graph.Rd +++ b/man/new.gexf.graph.Rd @@ -31,7 +31,7 @@ if (interactive()) { } \references{ -The GEXF project website: https://gephi.org/gexf/format/ +The GEXF project website: http://gexf.net/format/ } \author{ George Vega Yon diff --git a/man/read.gexf.Rd b/man/read.gexf.Rd index c77bed0..42da31b 100644 --- a/man/read.gexf.Rd +++ b/man/read.gexf.Rd @@ -26,7 +26,7 @@ By the time attributes and viz-attributes aren't supported. } \references{ -The GEXF project website: https://gephi.org/gexf/format/ +The GEXF project website: http://gexf.net/format/ } \author{ George Vega Yon diff --git a/man/rgexf-package.Rd b/man/rgexf-package.Rd index da0ccea..23ef17b 100644 --- a/man/rgexf-package.Rd +++ b/man/rgexf-package.Rd @@ -28,7 +28,7 @@ Please visit the project home for more information: } \note{ See the GEXF primer for details on the GEXF graph format: -\url{https://gephi.org/gexf/1.2draft/gexf-12draft-primer.pdf} +\url{http://gexf.net/1.2draft/gexf-12draft-primer.pdf} } \examples{ @@ -50,9 +50,9 @@ if (interactive()) { \references{ \itemize{ \item rgexf project site: \url{https://github.com/gvegayon/rgexf} \item Gephi project site: -\url{https://gephi.org/} \item GEXF project site: \url{https://gephi.org/gexf/format//} +\url{https://gephi.org/} \item GEXF project site: \url{http://gexf.net/format//} \item gexf-js project website: \url{https://github.com/raphv/gexf-js} -\item Sigmasj project site: \url{http://sigmajs.org/} +\item Sigmasj project site: \url{https://www.sigmajs.org/} } } \seealso{ diff --git a/vignettes/rgexf.Rmd b/vignettes/rgexf.Rmd index f4f47d9..8a9025d 100644 --- a/vignettes/rgexf.Rmd +++ b/vignettes/rgexf.Rmd @@ -15,7 +15,7 @@ knitr::opts_chunk$set(fig.width = 7) # Introduction -The `rgexf` package provides a way to interact with [GEXF files](https://gephi.org/gexf/format/). +The `rgexf` package provides a way to interact with [GEXF files](http://gexf.net/format/). The GEXF standard was developed by the [Gephi](https://gephi.org/)--"Like Photoshop for graphs"--core team, and can be used to save static and dynamic networks.