science-for-nature-and-people/bibscan

R package to batch download PDFs from a Web of Science search

BibScan

An R package to batch download PDFs from a .bib file

Installing

To install this package from GitHub you first need to install and run the devtools package.

install.packages("devtools")

To install the package, you can then execute

devtools::install_github("Science-for-Nature-and-People/BibScan")

Getting your token with Publishers

Before being able to use BibScan, you will have to get an authtetification token with CrossRef to be able to access content from Willey and Elsevier. Here are the intructions from crminer package on how to do this: https://github.com/ropensci/crminer#authentication

We recommend you to add your token to your R environement by editing your .Renviron file adding the variable name: CROSSREF_TDM= followed by your token.

Downloading files

To download files you need to be on a server that has a license to download from journal websites. The success rate of this package depends on the institutional access of the institution whose server you are on.

First, download a .bib file from a Web of Science search. Make sure that your .bib file includes a DOI.

You can then run

article_pdf_download(indir, outdir)

This will download PDFs from the .bib files in the director indir and save those PDFs in the director outdir.

Downloading files from Colandr

This tool has been designed to download files from literature reviews in the Colandr tool. The tool reads in a directory of .bib files that were imported into Colandr. The match argument can be used to specify the location of a .csv exported from Colandr. When this is specified, only the titles included in the .csv--which are a subset of the .bib file--will be downloaded.

article_pdf_download(indir='~/Documents/bibdir', '~/Documents/outdir', '~/Documents/sorted-papers.csv')

License

This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

Authors

• Stephen Wood - Creator, Author - swood-ecology
• Julien Brun - Author - brunj7
• Timothy Nguyen - Author - timothydnguyen