README.md

In inSileco/refR: An R package to get and manage BibTeX/YAML/JSON references

refR

Overview

The package refR retrieves author references from Scopus Search and Crossref APIs and returns references as BibTeX files (function getRefs()). It also allows to convert BibTeX files in more readable formats (i.e. YAML and JSON) by calling the software pandoc-citeproc (functions getRefs(), bib2yaml() and bib2json()). Informations in references files can be cleaned using the function cleanRefs(). This function translates special characters (accented characters and other LaTeX tags) and also cleans author names (detection of particle in family names, removal of uppercase except for each first letter of family and given names, and shorten given name).

System requirements

The refR package works well on both Unix and Windows platforms. This only requirement is that user has to install the wonderful software Pandoc, the swiss-army knife of the documents formats conversion. Do not forget to also install pandoc-citeproc.

Installation

To install the package refR from GitHub, first install the package devtools from the CRAN.

# Install the < devtools > package
install.packages("devtools", dependencies = TRUE)

# Load the < devtools > package
library(devtools)

Then install the refR package:

# Install the < refR > package from GitHub
devtools::install_github("inSileco/refR", build_vignettes = TRUE)

# Load the < refR > package
library(refR)

Getting started

Some useful command lines to get started:

# List the content (objects and functions) of the < refR > package
ls("package:refR")

# Open the < refR > package home page
help(package = "refR")

# Open the help file of a specific function
help(getRefs)

# Open the vignette (coming soon)
# browseVignettes(package = "refR")

Usage and workflow

# Create a folder to store references
path <- "references/"
dir.create(path, showWarnings = FALSE)

# Scopus Search API Key (get freely your own) https://blog.scopus.com/topics/api
api_key   <- "9zz9z999zz99z9999zz999zz999zz999"

# Author Scopus ID
author_id <- "99999999999"

# Retrieve references from Scopus and Crossref
refs <- refR::getRefs(
  api_key   = api_key,
  author_id = author_id,
  date      = NULL,
  sort      = "pubyear",
  sleep     = 5,
  folder    = path,
  format    = c("bibtex", "yaml"),
  erase     = FALSE
)

# Print the first reference (BibTeX) in memory
cat(refs[[1]])

# List all exported YAMLs
yamls <- list.files(
  path       = path,
  pattern    = "\\.yml$",
  full.names = TRUE
)

# Import the first YAML
(ref <- yaml.load_file(yamls[1]))

# Clean all YAML references
refR::cleanRefs(files = yamls)

# Re-import the first YAML (cleaned)
(ref <- yaml.load_file(yamls[1]))

# Make bibliography
# Coming soon...

# See also
?bib2yaml

To do list

• [ ] Add JSON and BibTeX formats in cleanRefs()
• [ ] Add a function bib2json()
• [ ] Add a function json2bib()
• [ ] Add a function yaml2bib()
• [ ] Add a function makeBiblio()
• [ ] Make a connexion with rscimap
• [ ] Write a vignette with a complete working example

inSileco/refR documentation built on May 28, 2019, 9:55 p.m.