In ropensci/pubchunks: Fetch Sections of XML Scholarly Articles

knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  warning = FALSE,
  message = FALSE,
  cache.path = "inst/cache/"
)

pubchunks

Get chunks of XML articles

Package API

cat(paste(" -", paste(getNamespaceExports("pubchunks"), collapse = "\n - ")))

The main workhorse function is pub_chunks(). It allows you to pull out sections of articles from many different publishers (see next section below) WITHOUT having to know how to parse/navigate XML. XML has a steep learning curve, and can require quite a bit of Googling to sort out how to get to different parts of an XML document.

The other main function is pub_tabularize() - which takes the output of pub_chunks() and coerces into a data.frame for easier downstream processing.

Supported publishers/sources

• eLife
• PLOS
• Entrez/Pubmed
• Elsevier
• Hindawi
• Pensoft
• PeerJ
• Copernicus
• Frontiers
• F1000 Research

If you know of other publishers or sources that provide XML let us know by opening an issue.

We'll continue adding additional publishers.

Installation

Stable version

install.packages("pubchunks")

Development version from GitHub

remotes::install_github("ropensci/pubchunks")

Load library

library('pubchunks')

Working with files

x <- system.file("examples/10_1016_0021_8928_59_90156_x.xml", 
  package = "pubchunks")

pub_chunks(x, "abstract")
pub_chunks(x, "title")
pub_chunks(x, "authors")
pub_chunks(x, c("title", "refs"))

The output of pub_chunks() is a list with an S3 class pub_chunks to make internal work in the package easier. You can easily see the list structure by using unclass().

Working with the xml already in a string

xml <- paste0(readLines(x), collapse = "")
pub_chunks(xml, "title")

Working with xml2 class object

xml <- paste0(readLines(x), collapse = "")
xml <- xml2::read_xml(xml)
pub_chunks(xml, "title")

Working with output of fulltext::ft_get()

install.packages("fulltext")

library("fulltext")
x <- fulltext::ft_get('10.1371/journal.pone.0086169')
pub_chunks(fulltext::ft_collect(x), sections="authors")

Coerce pub_chunks output into data.frame's

x <- system.file("examples/elife_1.xml", package = "pubchunks")
res <- pub_chunks(x, c("doi", "title", "keywords"))
pub_tabularize(res)

Get a random XML article

library(rcrossref)
library(dplyr)

res <- cr_works(filter = list(
    full_text_type = "application/xml", 
    license_url="http://creativecommons.org/licenses/by/4.0/"))
links <- bind_rows(res$data$link) %>% filter(content.type == "application/xml")
download.file(links$URL[1], (i <- tempfile(fileext = ".xml")))
pub_chunks(i)
download.file(links$URL[13], (j <- tempfile(fileext = ".xml")))
pub_chunks(j)
download.file(links$URL[20], (k <- tempfile(fileext = ".xml")))
pub_chunks(k)

unlink(i)
unlink(j)
unlink(k)

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for pubchunks: citation(package = 'pubchunks')
• Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

ropensci/pubchunks documentation built on Sept. 14, 2022, 7:48 a.m.