initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rhistory
+.Rproj*
+test/*
+*.Rproj

DESCRIPTION

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+Package: scholarnetwork
+Type: Package
+Title: Extract and Visualize Google Scholar Collaboration Networks
+Version: 0.1
+Date: 2015-10-11
+Author: Pablo Barbera <[email protected]>
+Maintainer: Pablo Barbera <[email protected]>
+Description: Extracts publication information from Google Scholar, create network of
+  collaborators based on co-authored projects, and visualize network using
+  a force-directed layout algorithm.
+License: GPL-2
+LazyData: TRUE
+Depends: igraph, scholar, stringr, networkD3

NAMESPACE

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+# Generated by roxygen2 (4.1.1): do not edit by hand
+
+export(extractNetwork)
+export(plotNetwork)
+import(igraph)
+import(networkD3)
+import(scholar)
+importFrom(stringr,str_trim)

R/extract-network.R

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+#' extractNetwork
+#' @export
+#'
+#' @title
+#' Extract collaborators network from Google Scholar page
+#'
+#' @description
+#' Uses \code{scholar} package to scrape Google Scholar page of an author
+#' (determined by ID) and returns a list with a list of edges and a data frame
+#' with node-level information
+#'
+#' @param id Character string specifying the Google Scholar ID.
+#' @param n Maximum number of publications to retrieve.
+#' @param largest_component If \code{TRUE}, keep only largest component in network
+#' @param ... Other options to pass to \code{get_publications} function
+#'
+#' @examples \dontrun{
+#' ## Download Google Scholar network data for a sample user
+#' d <- extractNetwork(id="jGLKJUoAAAAJ", n=500)
+#' ## Plot network into file called \code{network.html}
+#' plotNetwork(d$nodes, d$edges, file="network.html")
+#' }
+#'
+
+extractNetwork <- function(id, n=500, largest_component=TRUE, ...){
+
+  # downloading publications
+  pubs <- scholar::get_publications(id=id, pagesize=n, ...)
+
+  # converting to edges
+  edges <- lapply(pubs$author, extractAuthors)
+  edges <- do.call(rbind, edges)
+  edges <- aggregate(edges$weight,
+                     by=list(node1=edges$node1, node2=edges$node2),
+                     FUN=function(x) sum(x))
+  names(edges)[3] <- "weight"
+
+  ### SELECT LARGEST COMPONENT
+
+  # extracting node-level information
+  network <- igraph::graph.edgelist(as.matrix(edges[,c("node1", "node2")]), directed=FALSE)
+  igraph::edge_attr(network, "weight") <- edges$weight
+  fc <- igraph::walktrap.community(network)
+  nodes <- data.frame(label = igraph::V(network)$name,
+                      degree=igraph::strength(network), group=fc$membership,
+                      stringsAsFactors=F)
+  nodes <- nodes[order(nodes$label),]
+
+  return(list(nodes=nodes, edges=edges))
+
+}
+
+extractAuthors <- function(x){
+  authors <- unlist(stringr::str_split(x, ","))
+  # deleting empty authors
+  authors <- authors[grepl('[A-Za-z]+', authors)]
+  # cleaning author list
+  authors <- stringr::str_trim(authors)
+  # if more than one author, create edge list
+  if (length(authors)>1){
+    edges <- as.data.frame(t(combn(x=authors, m=2)), stringsAsFactors=F)
+    names(edges) <- c("node1", "node2")
+    edges$weight <- 1/length(authors)
+    return(edges)
+  }
+  if (length(authors)<=1) return(NULL)
+}
+

R/plot-network.R

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+#' plotNetwork
+#' @export
+#'
+#' @title
+#' Plot collaborators network from Google Scholar page
+#'
+#' @description
+#' Takes value from \code{extractNetwork} function and visualizes network
+#' using networkD3.
+#'
+#' @param nodes Data frame with node information returned by \code{extractNetwork}.
+#' @param edges Data frame with edge list returned by \code{extractNetwork}.
+#' @param file File where network visualization will be exported to.
+#' @param width numeric width for the network graph's frame area in pixels
+#' @param height numeric height for the network graph's frame area in pixels.
+#' @param opacity numeric value of the proportion opaque you would like the graph elements to be.
+#' @param fontsize numeric font size in pixels for the node text labels.
+#' @param charge numeric value indicating either the strength of the node repulsion (negative value) or attraction (positive value).
+#' @param ... Other options to pass to \code{networkD3} function
+#'
+#' #' @examples \dontrun{
+#' ## Download Google Scholar network data for a sample user
+#' d <- extractNetwork(id="jGLKJUoAAAAJ", n=500)
+#' ## Plot network into file called \code{network.html}
+#' plotNetwork(d$nodes, d$edges, file="network.html")
+#' }
+#'
+
+plotNetwork <- function(nodes, edges, file='network.html', width=550,
+                        height=400, opacity = .75, fontsize=10,
+                         charge=-400,...){
+
+  df <- data.frame(
+    Source=as.numeric(factor(edges$node1, levels=nodes$label))-1,
+    Target=as.numeric(factor(edges$node2, levels=nodes$label))-1,
+    value=edges$weight)
+
+  output <- networkD3::forceNetwork(Links = df, Nodes = nodes, Source="Source", Target="Target",
+               NodeID = "label", Group = "group",linkWidth = 1,
+               Nodesize = "degree", fontSize=fontsize,
+               opacity = opacity, charge=charge,
+               width = width, height = height, ...)
+
+  saveNetwork(output, file, selfcontained = FALSE)
+
+}
+
+#d3Network::d3ForceNetwork(
+#  Links = df, Nodes = nodes, Source="Source", Target="Target",
+#  NodeID = "label", Group="group", width = width, height = height,
+#  opacity = opacity, file=file, fontsize=fontsize,
+#  linkDistance=linkDistance, ...)

R/scholarnetwork-package.R

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+#' Extract and Visualize Google Scholar Collaboration Networks
+#'
+#' This package provides functions to extracts publication information from
+#' Google Scholar, create network of collaborators based on co-authored projects,
+#' and visualize these networks using a force-directed layout algorithm.
+#'
+#' @seealso \code{\link{extractNetwork}}, \code{\link{plotNetwork}}
+#' @name scholarnetwork-package
+#' @aliases scholarnetwork
+#' @docType package
+#' @author Pablo Barbera \email{pablo.barbera@@nyu.edu}
+#' @import scholar igraph networkD3
+#' @importFrom stringr str_trim
+NULL

README.md

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+<script src="https://raw.githubusercontent.com/ramnathv/htmlwidgets/master/inst/www/htmlwidgets.js"></script>
+<script src="https://raw.githubusercontent.com/mbostock/d3/master/d3.min.js" charset="utf-8"></script>
+<script src="https://raw.githubusercontent.com/christophergandrud/networkD3/master/inst/htmlwidgets/forceNetwork.js"></script>
+
+
+# Extract and Visualize Google Scholar Collaboration Networks
+
+**scholarnetwork** is an R package that provides functions to extracts publication information from Google Scholar, create network of collaborators based on co-authored projects, and visualize these networks using a force-directed layout algorithm.
+
+## Installation ##
+
+An initial release of this package is available in this repository (eventually maybe also on CRAN), and can be installed directly using Hadley Wickham's [devtools](http://cran.r-project.org/web/packages/devtools/index.html) package:
+
+```
+if(!require("devtools")) install.packages("devtools")
+library("devtools")
+install_github("pablobarbera/scholarnetwork")
+```
+
+## Examples ##
+
+For now, the package consists of two functions, `extractNetwork` and `plotNetwork`, which correspond to the data collection and data visualization steps.
+
+`extractNetwork` wraps the `get_publications` function from the scholar package, which extracts the list of publications on a Google Scholar profile, cleans it, and then parses the results into a format that is more suitable for network analysis: 
+
+- a data frame of __weighted edges__, where each edge is a collaboration in a publication, and the weight is one divided by number of co-authors; and 
+
+- a data frame with __node-level information__, which includes the group resulting from running a walktrap community detection algorithm. 
+
+```r
+d <- extractNetwork(id="jGLKJUoAAAAJ", n=500)
+str(d)
+```
+```
+List of 2
+ $ nodes:'data.frame':	40 obs. of  3 variables:
+  ..$ label : chr [1:40] "A Boydstun" "A Valeriani" "A Venetz" "C Roca Cuberes" ...
+  ..$ degree: num [1:40] 0.75 1.69 0.75 0.667 1.69 ...
+  ..$ group : num [1:40] 11 7 10 8 7 1 3 4 5 13 ...
+ $ edges:'data.frame':	106 obs. of  3 variables:
+  ..$ node1 : chr [1:106] "P Barberá" "C Vaccari" "K Ackermann" "P Barberá" ...
+  ..$ node2 : chr [1:106] "A Boydstun" "A Valeriani" "A Venetz" "A Venetz" ...
+  ..$ weight: num [1:106] 0.25 0.31 0.25 0.25 0.25 ...
+```
+
+`plotNetwork` takes the lists of nodes and edges returned by `extractNetwork` and visualizes it using `networkD3`. The output of this function is an html file with the network visualization. Note that this function will also work with any other set of edge and node lists.
+
+```r
+plotNetwork(d$nodes, d$edges, file="network.html")
+```
+<div id="htmlwidget_container">
+  <div id="htmlwidget-491" style="width:550px;height:400px;" class="forceNetwork"></div>
+</div>
+<script type="application/json" data-for="htmlwidget-491">{"x":{"links":{"source":[26,4,21,26,31,11,16,22,25,23,26,26,29,26,26,36,26,5,6,22,23,26,32,0,1,4,5,13,20,22,24,26,27,32,35,33,1,4,6,11,13,14,20,23,24,25,26,27,32,26,30,34,14,20,26,17,26,30,34,1,4,24,26,27,32,26,31,26,26,11,1,3,4,5,6,22,23,28,29,30,31,38,26,32,3,7,26,1,4,5,14,18,20,22,24,26,26,30,0,26,26,38,39,26,26,38],"target":[0,1,2,2,2,5,5,5,5,6,7,8,8,9,10,10,12,13,13,13,13,13,13,14,14,14,14,14,14,14,14,14,14,14,14,15,16,16,16,16,16,16,16,16,16,16,16,16,16,17,17,17,18,18,18,19,19,19,19,20,20,20,20,20,20,21,21,22,24,25,26,26,26,26,26,26,26,26,26,26,26,26,27,27,28,30,30,32,32,32,32,32,32,32,32,32,34,34,35,35,36,36,36,37,39,39]},"nodes":{"name":["A Boydstun","A Valeriani","A Venetz","C Roca Cuberes","C Vaccari","D Penfold-Brown","E Borra","E Dinas","G Rivero","G Sood","H Schmitt","I Cioroianu","J Arregui","J Jost","J Nagler","J Subirats","J Tucker","JA Mayoral","JA Tucker","JR Montero","JT Jost","K Ackermann","M Metzger","N Hassanpour","N Wang","NYU Jonathan Nagler","P Barberá","P Egan","P Estelrich Arce","P Fernández-Vázquez","P Riera","PC Bauer","R Bonneau","R Gallego","R Gómez","S Linn","SA Popa","T Zeitzoff","Y Theocharis","Z Fazekas"],"group":[11,7,10,8,7,1,3,4,5,13,2,1,14,3,7,12,3,9,7,9,7,10,6,3,7,1,6,7,8,5,4,10,7,12,9,11,2,15,2,2],"nodesize":[0.75,1.69047619047619,0.75,0.666666666666667,1.69047619047619,1.58333333333333,0.8,0.666666666666667,1.66666666666667,0.5,0.666666666666667,0.75,0.5,1.63333333333333,5.74047619047619,0.5,4.07380952380952,0.8,0.8,0.8,4.15714285714286,0.75,2.33333333333333,0.8,0.833333333333333,0.75,15.5071428571429,0.833333333333333,0.666666666666667,0.666666666666667,1.46666666666667,0.75,4.99047619047619,0.5,0.8,0.75,1.41666666666667,0.5,0.75,0.75]},"options":{"NodeID":"label","Group":"group","colourScale":"d3.scale.category20()","fontSize":10,"fontFamily":"serif","clickTextSize":25,"linkDistance":50,"linkWidth":"1","charge":-500,"linkColour":"#666","opacity":0.75,"zoom":false,"legend":false,"nodesize":true,"radiusCalculation":" Math.sqrt(d.nodesize)+6","bounded":false,"opacityNoHover":0,"clickAction":null}},"evals":[]}</script>
+<script type="application/htmlwidget-sizing" data-for="htmlwidget-491">{"viewer":{"width":550,"height":400,"padding":10,"fill":false},"browser":{"width":550,"height":400,"padding":10,"fill":false}}</script>
+
+
+
+The output of the `extractNetwork` function can also be used to generate a static version of this visualization with e.g. `ggplot2`:
+
+```r
+library(ggplot2)
+library(igraph)
+# cleaning network data
+network <- graph_from_data_frame(d$edges, directed=FALSE)
+set.seed(123)
+l <- layout.fruchterman.reingold(network, niter=1500) # layout
+fc <- walktrap.community(network) # community detection
+
+# node locations
+nodes <- data.frame(l); names(nodes) <- c("x", "y")
+nodes$cluster <- factor(fc$membership)
+nodes$label <- fc$names
+nodes$degree <- degree(network)
+
+# edge locations
+edgelist <- get.edgelist(network, names=FALSE)
+edges <- data.frame(nodes[edgelist[,1],c("x", "y")], nodes[edgelist[,2],c("x", "y")])
+names(edges) <- c("x1", "y1", "x2", "y2")
+
+# and now visualizing it...
+p <- ggplot(nodes, aes(x=x, y=y, color=cluster, label=label, size=degree))
+pq <- p + geom_text(color="black", aes(label=label, size=degree),
+                    show_guide=FALSE) +
+  # nodes
+  geom_point(color="grey20", aes(fill=cluster),
+             shape=21, show_guide=FALSE, alpha=1/2) +
+  # edges
+  geom_segment(
+    aes(x=x1, y=y1, xend=x2, yend=y2, label=NA),
+    data=edges, size=0.25, color="grey20", alpha=1/5) +
+  ## note that here I add a border to the points
+  scale_fill_discrete(labels=labels) +
+  scale_size_continuous(range = c(5, 8)) +
+  theme(
+    panel.background = element_rect(fill = "white"),
+    plot.background = element_rect(fill="white"),
+    axis.line = element_blank(), axis.text = element_blank(),
+    axis.ticks = element_blank(),
+    axis.title = element_blank(), panel.border = element_blank(),
+    panel.grid.major = element_blank(),
+    panel.grid.minor = element_blank(),
+    legend.background = element_rect(colour = F, fill = "black"),
+    legend.key = element_rect(fill = "black", colour = F),
+    legend.title = element_text(color="white"),
+    legend.text = element_text(color="white")
+  ) +
+  ## changing size of points in legend
+  guides(fill = guide_legend(override.aes = list(size=5)))
+
+pq
+```
+
+<center><img src="img/network.png" style="width: 550px;"/></center>
+
+However, it is difficult to make sure labels do not overlap. A probably better option is to export the network data to a format that Gephi can read, and then edit it manually in Gephi, as shown below.
+
+```r
+df <- data.frame(Source = d$edges$node1, Target = d$edges$node2)
+write.csv(df, file="edgelist-gephi.csv", row.names=FALSE)
+```
+
+<center><img src="img/collaborator-network.png" style="width: 550px;"/></center>

man/extractNetwork.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/extract-network.R
+\name{extractNetwork}
+\alias{extractNetwork}
+\title{Extract collaborators network from Google Scholar page}
+\usage{
+extractNetwork(id, n = 500, largest_component = TRUE, ...)
+}
+\arguments{
+\item{id}{Character string specifying the Google Scholar ID.}
+
+\item{n}{Maximum number of publications to retrieve.}
+
+\item{largest_component}{If \code{TRUE}, keep only largest component in network}
+
+\item{...}{Other options to pass to \code{get_publications} function}
+}
+\description{
+Uses \code{scholar} package to scrape Google Scholar page of an author
+(determined by ID) and returns a list with a list of edges and a data frame
+with node-level information
+}
+\details{
+extractNetwork
+}
+\examples{
+\dontrun{
+## Download Google Scholar network data for a sample user
+d <- extractNetwork(id="jGLKJUoAAAAJ", n=500)
+## Plot network into file called \\code{network.html}
+plotNetwork(d$nodes, d$edges, file="network.html")
+}
+}
+

man/plotNetwork.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/plot-network.R
+\name{plotNetwork}
+\alias{plotNetwork}
+\title{Plot collaborators network from Google Scholar page}
+\usage{
+plotNetwork(nodes, edges, file = "network.html", width = 550,
+  height = 400, opacity = 0.75, fontsize = 10, charge = -500, ...)
+}
+\arguments{
+\item{nodes}{Data frame with node information returned by \code{extractNetwork}.}
+
+\item{edges}{Data frame with edge list returned by \code{extractNetwork}.}
+
+\item{file}{File where network visualization will be exported to.}
+
+\item{width}{numeric width for the network graph's frame area in pixels}
+
+\item{height}{numeric height for the network graph's frame area in pixels.}
+
+\item{opacity}{numeric value of the proportion opaque you would like the graph elements to be.}
+
+\item{fontsize}{numeric font size in pixels for the node text labels.}
+
+\item{charge}{numeric value indicating either the strength of the node repulsion (negative value) or attraction (positive value).}
+
+\item{...}{Other options to pass to \code{networkD3} function
+
+#'}
+}
+\description{
+Takes value from \code{extractNetwork} function and visualizes network
+using networkD3.
+}
+\details{
+plotNetwork
+}
+\examples{
+\dontrun{
+## Download Google Scholar network data for a sample user
+d <- extractNetwork(id="jGLKJUoAAAAJ", n=500)
+## Plot network into file called \\code{network.html}
+plotNetwork(d$nodes, d$edges, file="network.html")
+}
+}
+

man/scholarnetwork-package.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/scholarnetwork-package.R
+\docType{package}
+\name{scholarnetwork-package}
+\alias{scholarnetwork}
+\alias{scholarnetwork-package}
+\title{Extract and Visualize Google Scholar Collaboration Networks}
+\description{
+This package provides functions to extracts publication information from
+Google Scholar, create network of collaborators based on co-authored projects,
+and visualize these networks using a force-directed layout algorithm.
+}
+\author{
+Pablo Barbera \email{pablo.barbera@nyu.edu}
+}
+\seealso{
+\code{\link{extractNetwork}}, \code{\link{plotNetwork}}
+}
+