pubchunks

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. Build Status codecov rstudio mirror downloads cran version

Get chunks of XML articles

Package API

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

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

devtools::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>
#>   from: character
#>   sections: abstract
#>    abstract (n=1): Abstract
#>                
#>                   This pa ...
pub_chunks(x, "title")
#> <pub chunks>
#>   from: character
#>   sections: title
#>    title (n=1): On the driving of a piston with a rigid collar int ...
pub_chunks(x, "authors")
#> <pub chunks>
#>   from: character
#>   sections: authors
#>    authors (n=1): Chetaev, D.N
pub_chunks(x, c("title", "refs"))
#> <pub chunks>
#>   from: character
#>   sections: title, refs
#>    title (n=1): On the driving of a piston with a rigid collar int ...
#>    refs (n=6): 1.G.N.WatsonTeoriia besselevykh funktsiiTheory of

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")
#> <pub chunks>
#>   from: character
#>   sections: title
#>    title (n=1): On the driving of a piston with a rigid collar int ...

Working with xml2 class object

xml <- paste0(readLines(x), collapse = "")
xml <- xml2::read_xml(xml)
pub_chunks(xml, "title")
#> <pub chunks>
#>   from: xml_document
#>   sections: title
#>    title (n=1): On the driving of a piston with a rigid collar int ...

Working with output of fulltext::ft_get()

install.packages("fulltext")
library("fulltext")
x <- fulltext::ft_get('10.1371/journal.pone.0086169', from='plos')
pub_chunks(fulltext::ft_collect(x), sections="authors")
#> $plos
#> $plos$`10.1371/journal.pone.0086169`
#> <pub chunks>
#>   from: xml_document
#>   sections: authors
#>    authors (n=4): nested list
#> 
#> 
#> attr(,"ft_data")
#> [1] TRUE

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)
#>                   doi                                          title
#> 1 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 2 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 3 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 4 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 5 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 6 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#>                       keywords .publisher
#> 1                     microRNA      elife
#> 2            nonsense mutation      elife
#> 3 nonsense-mediated mRNA decay      elife
#> 4                          APC      elife
#> 5             intron retention      elife
#> 6  premature termination codon      elife

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