Package API
- pub_tabularize
- pub_guess_publisher
- pub_sections
- pub_chunks
- pub_providers
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.
Working with files
pub_chunks(x, "abstract")
#> <pub chunks>
#> from: file
#> publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#> sections: abstract
#> showing up to first 5:
#> abstract (n=1): Abstract
#>
#> This pa ...
pub_chunks(x, "title")
#> <pub chunks>
#> from: file
#> publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#> sections: title
#> showing up to first 5:
#> title (n=1): On the driving of a piston with a rigid collar int ...
pub_chunks(x, "authors")
#> <pub chunks>
#> from: file
#> publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#> sections: authors
#> showing up to first 5:
#> authors (n=1): Chetaev, D.N
pub_chunks(x, c("title", "refs"))
#> <pub chunks>
#> from: file
#> publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#> sections: title, refs
#> showing up to first 5:
#> title (n=1): On the driving of a piston with a rigid collar int ...
#> refs (n=6): 1.G.N.WatsonTeoriia besselevykh funktsiiTheory ofThe 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 xml2 class object
xml <- paste0(readLines(x), collapse = "")
xml <- xml2::read_xml(xml)
pub_chunks(xml, "title")
#> <pub chunks>
#> from: xml_document
#> publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#> sections: title
#> showing up to first 5:
#> title (n=1): On the driving of a piston with a rigid collar int ...Working with output of fulltext::ft_get()
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
#> publisher/journal: plos/PLoS ONE
#> sections: authors
#> showing up to first 5:
#> authors (n=4): nested list
#>
#>
#> attr(,"ft_data")
#> [1] TRUECoerce 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 elifeGet 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$URL[1], (i <- tempfile(fileext = ".xml")))
pub_chunks(i)
#> <pub chunks>
#> from: file
#> publisher/journal: scientific_research_publishing/Open Journal of Social Sciences
#> sections: all
#> showing up to first 5:
#> front (n=2): nested list
#> body (n=40): Educational behaviors refer to the activities or a
#> back (n=1): nested list
#> title (n=1): Inspection on Reality of Kindergarten Teachers’ Ed ...
#> doi (n=1): 10.4236/jss.2014.29048
download.file(links$URL[13], (j <- tempfile(fileext = ".xml")))
pub_chunks(j)
#> <pub chunks>
#> from: file
#> publisher/journal: hindawi/Case Reports in Gastrointestinal Medicine
#> sections: all
#> showing up to first 5:
#> front (n=2): nested list
#> body (n=12): The American Association for the Study of Liver Di
#> back (n=4): nested list
#> title (n=1): Yogi Detox Tea: A Potential Cause of Acute Liver F ...
#> doi (n=1): 10.1155/2017/3540756
download.file(links$URL[20], (k <- tempfile(fileext = ".xml")))
pub_chunks(k)
#> <pub chunks>
#> from: file
#> publisher/journal: hindawi/Advances in Materials Science and Engineering
#> sections: all
#> showing up to first 5:
#> front (n=2): nested list
#> body (n=74): Nowadays, most of the service bridges are close or
#> back (n=3): nested list
#> title (n=1): Cubic Function-Based Bayesian Dynamic Linear Predi ...
#> doi (n=1): 10.1155/2017/7460378Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
pubchunks:citation(package = 'pubchunks') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
