tableParser (1.0.3)

Converts HTML-tables and character matrices into a text vector and extracts and checks statistical standard test results.

The package contains several functions to extract, unify and parse content from scientific tables into a human readable text format by simulating the experience of a screen reader for visually impaired users. It can process HTML-encoded tables, as well as native R character matrices. The functions table2matrix(), table2text() and table2stats() can be applied on documents in HTML, HML, XML, as well as DOCX and PDF file format. The table extraction from DOCX files is performed with the function docx2matrix(), tables in PDF documents are extracted with the 'tabulapdf' package.

The textual representation of characters in matrix content can be unified with unifyMatrix() before parsing. The function table2stats() extracts tabled statistical results. The function further unifies the parsed text, which is then processed with JATSdecoder::standardStats(), in order to extract all statistical standard results (t, Z, χ2, F, r, d, β, SE, r, d, η2, ω2, OR, RR, p), the coded p-values and recompute p-values if possible.

Important note: Due to the great variability in table structures and complexity, parsing accuracy may vary. For best results, it is recommended to work with simple, accessible, and barrier-free table structures to minimize parsing errors.

How does it work?

The following process tree is a simplified representation of the conversion of HTML tables into the extracted statistical standard results. The HTML table is first transposed into a matrix. The matrix is then parsed into text lines, considering the detected legend codings within the caption and foot notes (e.g. '*' for p<.05). The representations of the numerical results within the text lines are further unified and then processed with JATSdecoder's function standardStats() to detect all statistical standard results and recompute p-values if possible.

The parsing of the matrix content to text is based on the decision of the classifier. In the case of correlation matrices, the reported sample size specified within the caption or footnote is subtracted by two and then imputed as degrees of freedom. This process enables a subsequent recomputation of the p-values.

Installation

# latest CRAN release
install.packages("tableParser")

# latest github version
if(require(devtools)!=TRUE) install.packages("devtools")
devtools::install_github("ingmarboeschen/tableParser")

Examples for table processing in docx, html and pdf documents

I have prepared a document with several example table structures to demonstrate tableParser's capabilities. You may manually download the examples in three file formats, or use the following lines to only store them within the temporary folder.

# Load the package
library(tableParser)

# prepare temporary file path
docxFilePath<-paste0(tempdir(),"/","tableExamples.docx")
htmlFilePath<-paste0(tempdir(),"/","tableExamples.html")
pdfFilePath<-paste0(tempdir(),"/","tableExamples.pdf")

# Download example files with tables from this repo to temp directory
download.file("https://github.com/ingmarboeschen/tableParser/raw/refs/heads/main/tableExamples.docx",docxFilePath)
download.file("https://github.com/ingmarboeschen/tableParser/raw/refs/heads/main/tableExamples.html",htmlFilePath)
download.file("https://github.com/ingmarboeschen/tableParser/raw/refs/heads/main/tableExamples.pdf",pdfFilePath)

## Extract tables from example files
table2matrix(docxFilePath)
table2matrix(htmlFilePath,rm.html=TRUE)
table2matrix(pdfFilePath)
# Note: The extraction of tables with the tablulapdf package does not work properly here.
# Also, the table's caption and footnotes cannot be used for decoding (e.g., p-values).
# This affects all further processes and results.

## Parse tabled content from example files
table2text(docxFilePath)
table2text(htmlFilePath,decodeP=TRUE)
table2text(pdfFilePath,decodeP=TRUE,standardPcoding=TRUE,noSign2p=TRUE)

## Extract the detected statistical standard results and validate the reported and coded p-values
#ä with the recaluclated p-values
table2stats(docxFilePath,checkP=TRUE,estimateZ=T)
table2stats(htmlFilePath,checkP=TRUE,estimateZ=T,noSign2p=T,alpha=.01)
table2stats(pdfFilePath,checkP=TRUE,estimateZ=T,standardPcoding=TRUE)
 

Web application

Test tableParser without installation here: http://134.100.146.165:3838/tableParser/

Reference

@Manual{,
    title = {tableParser: Parse Tabled Content to Text Vector and Extract Statistical Standard Results},
    author = {Ingmar Böschen},
    year = {2026},
    note = {R package version 1.0.3},
    url = {https://github.com/ingmarboeschen/tableParser},
  }