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.
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> #> 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 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 #> 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 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()
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 #> publisher/journal: plos/PLoS ONE #> sections: authors #> showing up to first 5: #> 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
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$URL[1], (i <- tempfile(fileext = ".xml"))) pub_chunks(i) #> <pub chunks> #> from: file #> publisher/journal: unknown/NA #> sections: all #> showing up to first 5: #> front (n=0): #> body (n=0): #> back (n=0): #> title (n=0): #> doi (n=0): download.file(links$URL[13], (j <- tempfile(fileext = ".xml"))) pub_chunks(j) #> <pub chunks> #> from: file #> publisher/journal: scientific_research_publishing/Journal of Electromagnetic Analysis and Applications #> sections: all #> showing up to first 5: #> front (n=2): nested list #> body (n=122): Conventional theoretical physics and its Standard #> back (n=1): nested list #> title (n=1): Impacts of Revised Quantum Electrodynamics on Fund ... #> doi (n=1): 10.4236/jemaa.2018.105008 download.file(links$URL[20], (k <- tempfile(fileext = ".xml"))) pub_chunks(k) #> <pub chunks> #> from: file #> publisher/journal: hindawi/BioMed Research International #> sections: all #> showing up to first 5: #> front (n=2): nested list #> body (n=14): Neospora caninum is an obligate intracellular prot #> back (n=5): nested list #> title (n=1): First Report of Seroprevalence and Risk Factors of ... #> doi (n=1): 10.1155/2018/2098908
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.
