PDE_pdfs2table {PDE}

Extracting all tables from a PDF (Portable Document Format) file

Description

PDE_pdfs2table extracts all tables from a single PDF file and writes output in the corresponding folder.

Usage

PDE_pdfs2table(
  pdfs,
  out = ".",
  table.heading.words = "",
  ignore.case.th = FALSE,
  out.table.format = ".csv (WINDOWS-1252)",
  dev_x = 20,
  dev_y = 9999,
  write.table.locations = FALSE,
  exp.nondetc.tabs = TRUE,
  delete = TRUE,
  verbose = TRUE
)

Arguments

pdfs

String. A list of paths to the PDF files to be analyzed.

out

String. Directory chosen to save tables in. Default: ".".

table.heading.words

List of strings. Different than standard (TABLE, TAB or table plus number) headings to be detected. Regex rules apply (see also https://github.com/erikstricker/PDE/blob/master/inst/examples/cheatsheets/regex.pdf). Default = "".

ignore.case.th

Logical. Are the additional table headings (see table.heading.words) case-sensitive (does capitalization matter)? Default = FALSE.

out.table.format

String. Output file format. Either comma separated file .csv or tab separated file .tsv. The encoding indicated in parantheses should be selected according to the operational system exported tables are opened in, i.e., Windows: "(WINDOWS-1252)"; Mac: (macintosh); Linux: (UTF-8). Default: ".csv" and encoding depending on the operational system.

dev_x

Numeric. For a table the size of indention which would be considered the same column. Default: 20.

dev_y

Numeric. For a table the vertical distance which would be considered the same row. Can be either a number or set to dynamic detection [9999], in which case the font size is used to detect which words are in the same row. Default: 9999.

write.table.locations

Logical. If TRUE, a separate file with the headings of all tables, their relative location in the generated html and txt files, as well as information if search words were found will be generated. Default: FALSE.

exp.nondetc.tabs

Logical. If TRUE, if a table was detected in a PDF file but is an image or cannot be read, the page with the table with be exported as a png. Default: FALSE.

delete

Logical. If TRUE, the intermediate txt, keeplayouttxt and html copies of the PDF file will be deleted. Default: TRUE.

verbose

Logical. Indicates whether messages will be printed in the console. Default: TRUE.

See Also

PDE_extr_data_from_pdfs,PDE_pdfs2table_searchandfilter

Examples

## Running a simple table extraction
if(PDE_check_Xpdf_install() == TRUE){
outputtables <- PDE_pdfs2table(pdf = paste0(system.file(package = "PDE"),
                 "/examples/Methotrexate/29973177_!.pdf"),
 out = paste0(system.file(package = "PDE"),"/examples/29973177_tables/"))
}

## Running a the same table extraction as above with all paramaters shown
if(PDE_check_Xpdf_install() == TRUE){
 outputtables <- PDE_pdfs2table(pdf = paste0(system.file(package = "PDE"),
                                 "/examples/Methotrexate/29973177_!.pdf"),
 out = paste0(system.file(package = "PDE"),"/examples/29973177_tables/"),
 dev_x = 20,
 dev_y = 9999,
 table.heading.words = "",
 ignore.case.th = FALSE,
 out.table.format = ".csv (WINDOWS-1252)",
 write.table.locations = FALSE,
 exp.nondetc.tabs = FALSE,
 delete = TRUE)
}