pCheck

Wrapper function for a standardStats data frame to check extracted and recalculated p-value for consistency

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

pCheck function

<dl><dt>stats</dt>
<dd>Data frame. A data frame object of standard stats that was created by get.stats() or standardStats()</dd>
<dt>alpha</dt>
<dd>Numeric. Set the alpha level of tests.</dd>
<dt>criticalDif</dt>
<dd>Numeric. Defines the absolute threshold of absolute differences in extracted and recalculated p-value to be labeled as inconsistency.</dd>
<dt>add</dt>
<dd>Logical. If TRUE the result of Pcheck are added to the input data frame.</dd>
<dt>warnings</dt>
<dd>Logical. If FALSE warning messages are omitted.</dd></dl>

Arguments

pCheck — pCheck

<dl>

<dt>stats</dt>
<dd>Data frame. A data frame object of standard stats that was created by get.stats() or standardStats()</dd>


<dt>alpha</dt>
<dd>Numeric. Set the alpha level of tests.</dd>


<dt>criticalDif</dt>
<dd>Numeric. Defines the absolute threshold of absolute differences in extracted and recalculated p-value to be labeled as inconsistency.</dd>


<dt>add</dt>
<dd>Logical. If TRUE the result of Pcheck are added to the input data frame.</dd>


<dt>warnings</dt>
<dd>Logical. If FALSE warning messages are omitted.</dd>

</dl>

pCheck: pCheck

Description

Usage

Value

Arguments

Examples