get.abstract

Extracts abstract tag from NISO-JATS coded XML file or text as vector of abstracts.

Provides a function collection to extract metadata, sectioned text and study characteristics from scientific articles in 'NISO-JATS' format. Articles in PDF format can be converted to 'NISO-JATS' with the 'Content ExtRactor and MINEr' ('CERMINE', <https://github.com/CeON/CERMINE>). For convenience, two functions bundle the extraction heuristics: JATSdecoder() converts 'NISO-JATS'-tagged XML files to a structured list with elements title, author, journal, history, 'DOI', abstract, sectioned text and reference list. study.character() extracts multiple study characteristics like number of included studies, statistical methods used, alpha error, power, statistical results, correction method for multiple testing, software used. An estimation of the involved sample size is performed based on reports within the abstract and the reported degrees of freedom within statistical results. In addition, the package contains some useful functions to process text (text2sentences(), text2num(), ngram(), strsplit2(), grep2()). See Böschen, I. (2021) <doi:10.1007/s11192-021-04162-z> Böschen, I. (2021) <doi:10.1038/s41598-021-98782-3> and Böschen, I (2023) <doi:10.1038/s41598-022-27085-y>.

Ingmar Böschen

JATSdecoder

A Metadata and Text Extraction and Manipulation Tool Set

get.abstract function

<dl><dt>x</dt>
<dd>a NISO-JATS coded XML file or text.</dd>
<dt>sentences</dt>
<dd>Logical. If TRUE abstract is returned as vector of sentences.</dd>
<dt>remove.title</dt>
<dd>Logical. If TRUE removes section titles in abstract.</dd>
<dt>letter.convert</dt>
<dd>Logical. If TRUE converts hexadecimal and HTML coded characters to Unicode.</dd>
<dt>cermine</dt>
<dd>Logical. If TRUE and if 'letter.convert=TRUE' CERMINE specific letter correction is carried out (e.g. inserting of missing operators to statistical results).</dd></dl>

Arguments

get.abstract — get.abstract

<dl>

<dt>x</dt>
<dd>a NISO-JATS coded XML file or text.</dd>


<dt>sentences</dt>
<dd>Logical. If TRUE abstract is returned as vector of sentences.</dd>


<dt>remove.title</dt>
<dd>Logical. If TRUE removes section titles in abstract.</dd>


<dt>letter.convert</dt>
<dd>Logical. If TRUE converts hexadecimal and HTML coded characters to Unicode.</dd>


<dt>cermine</dt>
<dd>Logical. If TRUE and if 'letter.convert=TRUE' CERMINE specific letter correction is carried out (e.g. inserting of missing operators to statistical results).</dd>

</dl>

get.abstract: get.abstract

Description

Usage

Value

Arguments

See Also

Examples