JATSdecoder: JATSdecoder

Description

Function to extract and restructure NISO-JATS coded XML file or text into a list with metadata and text as selectable elements. Use CERMINE to convert PDF to CERMXML files.

Usage

JATSdecoder(
  x,
  sectionsplit = c("intro", "method", "result", "study", "experiment", "conclu",
    "implica", "discussion"),
  grepsection = "",
  sentences = FALSE,
  paragraph = FALSE,
  abstract2sentences = TRUE,
  output = "all",
  letter.convert = TRUE,
  unify.country.name = TRUE,
  greek2text = FALSE,
  warning = TRUE,
  countryconnection = FALSE,
  authorconnection = FALSE
)

Value

List with extracted meta data, sectioned text and references.

Arguments

x: a NISO-JATS coded XML file or text.
sectionsplit: search patterns for section split of text parts (forced to lower case), e.g. c("intro", "method", "result", "discus").
grepsection: search pattern in regex to reduce text to specific section only.
sentences: Logical. IF TRUE text is returned as sectioned list with sentences.
paragraph: Logical. IF TRUE "<New paragraph>" is added at the end of each paragraph to enable manual splitting at paragraphs.
abstract2sentences: Logical. IF TRUE abstract is returned as vector with sentences.
output: selection of specific results to output c("all", "title", "author", "affiliation", "journal", "volume", "editor", "doi", "type", "history", "country", "subject", "keywords", "abstract", "sections", "text", "tables", "captions", "references").
letter.convert: Logical. If TRUE converts hexadecimal and HTML coded characters to Unicode.
unify.country.name: Logical. If TRUE tries to unify country name/s with list of country names from worldmap().
greek2text: Logical. If TRUE converts and unifies several greek letters to textual representation, e.g.: "alpha".
warning: Logical. If TRUE outputs a warning if processing CERMINE converted PDF files.
countryconnection: Logical. If TRUE outputs country connections as vector c("A - B","A - C", ...).
authorconnection: Logical. If TRUE outputs connections of a maximum of 50 involved authors as vector c("A - B","A - C", ...).

References

Böschen (2021). "Software review: The JATSdecoder package - extract metadata, abstract and sectioned text from NISO-JATS coded XML documents; Insights to PubMed Central’s open access database.” Scientometrics. doi: 10.1007/s1119202104162z.

Examples

Run this code

# download example XML file via URL
x<-"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0114876&type=manuscript"
# file name
file<-paste0(tempdir(),"/file.xml")
# download URL as "file.xml" in tempdir() if a connection is possible
tryCatch({
readLines(x,n=1)
download.file(x,file)
},
warning = function(w) message(
  "Something went wrong. Check your internet connection and the link address."),
error = function(e) message(
  "Something went wrong. Check your internet connection and the link address."))
# convert full article to list with metadata, sectioned text and reference list
if(file.exists(file)) JATSdecoder(file)
# extract specific content (here: abstract and text)
if(file.exists(file)) JATSdecoder(file,output=c("abstract","text"))
# or use specific functions, e.g.:
if(file.exists(file)) get.abstract(file)
if(file.exists(file)) get.text(file)