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_Bibliography.Rmd
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_Bibliography.Rmd
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# Bibliography
A brief introduction to bibliometrix
https://cran.r-project.org/web/packages/bibliometrix/vignettes/bibliometrix-vignette.html
Bibliographic Network Visualization for Academic Literature Reviews
http://www.mburnamfink.com/blog/bibliographic-network-visualization-for-academic-literature-reviews
https://embed.kumu.io/0b991b02bb20975fde904f4bf7433333#jpsp-top-50?s=%23doi-101037-0022-35147451252
More Than Words? Computer-Aided Text Analysis in Organizational Behavior and Psychology Research
https://www.annualreviews.org/doi/10.1146/annurev-orgpsych-032117-104622
https://www.kumu.io/nicholasjkelley/jpsp-top-50
# knitcitations
https://github.com/cboettig/knitcitations
```
{r eval=FALSE, include=FALSE, echo=TRUE}
# library(devtools)
# install_github( cboettig/knitcitations )
install.packages( knitcitations )
```
```
{r eval=FALSE, include=FALSE, echo=TRUE}
library( knitcitations )
cleanbib()
options( citation_format = pandoc )
```
```
{r eval=FALSE, include=FALSE, echo=TRUE}
knitcitations::citep( 10.1890/11-0011.1 )
```
```
citation r citep( 10.1890/11-0011.1 ) in text
```
```
{r eval=FALSE, include=FALSE, echo=TRUE}
knitcitations::citet( 10.1098/rspb.2013.1372 )
```
```
citation r citet( 10.1098/rspb.2013.1372 ) in text
```
```
{r eval=FALSE, include=FALSE, echo=TRUE}
knitcitations::citep( http://knowledgeblog.org/greycite )
```
```
write.bibtex(file= references.bib )
```
# rcrossref
https://github.com/ropensci/rcrossref
# rorcid tutorial
https://ropensci.org/tutorials/rorcid_tutorial/
# rentrez tutorial
https://ropensci.org/tutorials/rentrez_tutorial/
# WebSciCorpus
https://www.clarehooper.net/WebSciCorpus/
# WEB OF SCIENCE (WOS) CORPUS | PARSING SCRIPT
https://docs.cortext.net/question/web-of-science-wos-corpus-parsing-script-2/
# T-LAB PLUS 2019
https://tlab.it/en/allegati/help_en_online/mmappe2.htm
# Tools for bibliometric analyses
https://ju.se/library/research--teaching-support/bibliometrics/tools-for-bibliometric-analyses.html
# evidencepartners
https://www.evidencepartners.com/
# R script for creating a cross-citation network
https://www.researchgate.net/publication/327790285_R_script_for_creating_a_cross-citation_network
Repository: https://github.com/arsiders/citation-network
```
# RCitation - Quick Citation Network
# Fall 2018
# A.R. Siders (siders@alumni.stanford.edu)
# Creates a network of the citations among a set of academic papers.
# Rationale: If full title of Article 2 is present in text of Article 1, Article 1 cites Article 2.
# NOTE: Will only work in fields where full, unabbreviated titles are used in reference/bibliography citation format.
# NOTE: Will have high error rate if titles are very short or comprised of common words (e.g., paper Vulnerability produced many false positives). Some errors result from authors using a shortened version of a title (e.g., only text before a colon) or incorrect citations or typos. Citation networks produced are therefore approximate and to be used primarily for exploration of the data.
# NOTE: Error rate may be reduced by using only reference sections of the articles of interest, rather than full texts, but this will increase work required to prepare articles.
# ==> FIVE STEPS TO CITATION NETWORK
# STEP 1. FORMAT INPUT
# a. Papers: Folder of papers in txt format (UTF-8) organized *in SAME ORDER* as Titles
# b. Titles: Column of paper titles in csv spreadsheet (Column #1) *in SAME ORDER* as documents in Papers folder. Need a header cell or top title will be removed.
# Recommend naming all texts in Papers folder using author last name listed alphabetically. Organize Titles using same order.
# STEP 2. PREP
# set working directory
setwd( C:\[name of working space] ) # make sure \ not / in name
setwd( C:/Users/User/OneDrive/Adaptive Capacity Text Mining/Citation Network Test/CitationNetwork Test Data )
# load packages
install.packages(c( tm , plyr ))
library(tm)
library(plyr)
# STEP 3. LOAD INPUTS
# a. Papers
papers<-Corpus(DirSource( [name of folder where papers located] ))
papers<-Corpus(DirSource( Papers ))
# b. Titles
titletable<-read.csv( [name of titles file].csv ) #make sure column has a header
titletable<-read.csv( TestTitles.csv )
titles<-as.vector(titletable[,1])
# load functions at bottom of this script (below Step 5)
length(papers)
length(titles)
# STEP 4. RUN FUNCTION
CitationNetwork<-CreateCitationNetwork(papers,titles)
# add date
currentDate <- Sys.Date()
csvFileName <- paste( CitationEdges ,currentDate, .csv ,sep= )
# save results
write.csv(CitationNetwork, file=csvFileName)
# STEP 5. VISUALIZE NETWORK
# Install Gephi or other network visualization software and load CitationEdges.csv
# Load list of titles or other spreadsheet as nodes to visualize network
# Gephi available at https://gephi.org/
# ===> FUNCTIONS TO LOAD
CreateCitationNetwork<-function(papers,titles){
# prep papers corpus
papers<-tm_map(papers, content_transformer(tolower))
papers<-tm_map(papers, removePunctuation)
papers<-tm_map(papers, removeNumbers)
papers<-tm_map(papers, stripWhitespace)
# prep titles
titles<-removePunctuation(titles)
titles<-stripWhitespace(titles)
titles<-tolower(titles)
# create citation true/false matrix
Cites.TF<-CiteMatrix(titles, papers)
# format matrix into edges file
CitationEdges<-EdgesFormat(Cites.TF, titles)
return(CitationEdges)
}
# format true/false matrix into edges file
EdgesFormat<-function(Cites.TF, titles){
#create an empty object to put information in
edges<-data.frame(matrix(NA), nrow=NA, ncol=NA)
colnames(edges)<- c( Source , Target , Weight )
for (i in 1:length(Cites.TF)){
#for each document, run through all titles accross columns
for (j in 1:ncol(Cites.TF)){
# for each title, see if document [row] cited that title [column]
if (Cites.TF[i,j]==TRUE){ #if document is cited
temp<-data.frame(matrix(NA), nrow=NA, ncol=NA)
colnames(temp)<- c( Source , Target , Weight )
# first column <- document doing the citing
temp[1,1]<-titles[i]
# second column <- document being cited
temp[1,2]<-titles[j]
# third column the yes/no [weight]
temp[1,3]<-1
temp[1,4]<- Directed
edges<-rbind(edges,temp)
}
}
}
return(edges[-1,]) #-1 removes initial row of null values
}
# Citation true/false matrix
CiteMatrix<-function(search.vector, Ref.corpus){
# Creates a csv matrix with True/False for citation patterns
citations<-data.frame(matrix(NA, nrow = length(Ref.corpus), ncol=length(search.vector)))
#Columns are the document being cited
colnames(citations)<-search.vector
#Rows are the document doing the citing
rownames(citations)<-search.vector
for (i in 1:length(search.vector)){
searchi<-search.vector[i]
papercite<-grepl(searchi, Ref.corpus$content, fixed=TRUE)
citations[,i]<-papercite
}
return(citations)
}
```
- The application of methods of social network analysis in bibliometrics and webometrics. Measures and tools
https://www.researchgate.net/publication/327817518_The_application_of_methods_of_social_network_analysis_in_bibliometrics_and_webometrics_Measures_and_tools
# ScientoMiner ICR
https://zenodo.org/record/1432557#.XItjfxO2k1J
# onodo
https://onodo.org/dashboard
https://onodo.org/tutorials
# BibExcel
https://homepage.univie.ac.at/juan.gorraiz/bibexcel/
# Scientometric Portal
https://sites.google.com/site/hjamali/scientometric-portal
# leydesdorff
https://www.leydesdorff.net/software.htm
# Publish or Perish
https://harzing.com/resources/publish-or-perish
# Pajek: analysis and visualization of large networks
http://mrvar.fdv.uni-lj.si/pajek/