.PDE_extr_data_from_pdf {PDE}

Extracting data from a PDF (Protable Document Format) file

Description

PDE_extr_data_from_pdf extracts sentences or tables from a single PDF file and writes output in the corresponding folder.

Usage

.PDE_extr_data_from_pdf(
  pdf,
  whattoextr,
  out = ".",
  filter.words = "",
  regex.fw = TRUE,
  ignore.case.fw = FALSE,
  filter.word.times = "0.2%",
  table.heading.words = "",
  ignore.case.th = FALSE,
  search.words,
  search.word.categories = NULL,
  save.tab.by.category = FALSE,
  regex.sw = TRUE,
  ignore.case.sw = FALSE,
  eval.abbrevs = TRUE,
  out.table.format = ".csv (WINDOWS-1252)",
  dev_x = 20,
  dev_y = 9999,
  context = 0,
  write.table.locations = FALSE,
  exp.nondetc.tabs = TRUE,
  write.tab.doc.file = TRUE,
  write.txt.doc.file = TRUE,
  delete = TRUE,
  cpy_mv = "nocpymv",
  verbose = TRUE
)

Arguments

pdf

String. Path to the PDF file to be analyzed.

whattoextr

String. Either txt, tab, or tabandtxt for PDFS2TXT (extract sentences from a PDF file) or PDFS2TABLE (table of a PDF file to a Microsoft Excel file) extraction. tab allows the extraction of tables with and without search words while txt and tabandtxt require search words.

out

String. Directory chosen to save analysis results in. Default: ".".

filter.words

List of strings. The list of filter words. If not NA or "" a hit will be counted every time a word from the list is detected in the article. Default: "".

regex.fw

Logical. If TRUE filter words will follow the regex rules (see https://github.com/erikstricker/PDE/blob/master/inst/examples/cheatsheets/regex.pdf). Default = TRUE.

ignore.case.fw

Logical. Are the filter words case-sensitive (does capitalization matter)? Default: FALSE.

filter.word.times

Numeric or string. Can either be expressed as absolute number or percentage of the total number of words (by adding the " filter.words for a paper to be further analyzed. Default: 0.2%.

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.

search.words

List of strings. List of search words. To extract all tables from the PDF file leave search.words = "".

search.word.categories

List of strings. List of categories with the same length as the list of search words. Accordingly, each search word can be assigned to a category, of which the word counts will be summarized in the PDE_analyzer_word_stats.csv file. If search.word.categories is a different length than search.words the parameter will be ignored. Default: NULL.

save.tab.by.category

Logical. Can only be used with search.word.categories. If set to TRUE, tables that carry search words will be saved in sub-folders according to the search word category of the detected search word. Default: FALSE.

regex.sw

Logical. If TRUE search words will follow the regex rules (see https://github.com/erikstricker/PDE/blob/master/inst/examples/cheatsheets/regex.pdf). Default = TRUE.

ignore.case.sw

Logical. Are the search words case-sensitive (does capitalization matter)? Default: FALSE.

eval.abbrevs

Logical. Should abbreviations for the search words be automatically detected and then replaced with the search word + "$*"? Default: TRUE.

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.

context

Numeric. Number of sentences extracted before and after the sentence with the detected search word. If 0 only the sentence with the search word is extracted. Default: 0.

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: TRUE.

write.tab.doc.file

Logical. If TRUE, if search words are used for table detection and no search words were found in the tables of a PDF file, a no.table.w.search.words. Default: TRUE.

write.txt.doc.file

Logical. If TRUE, if no search words were found in the sentences of a PDF file, a file will be created with the PDF filename followed by no.txt.w.search.words. If the PDF file is empty, a file will be created with the PDF filename followed by no.content.detected. If the filter word threshold is not met, a file will be created with the PDF filename followed by no.txt.w.filter.words. Default: TRUE.

delete

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

cpy_mv

String. Either "nocpymv", "cpy", or "mv". If filter words are used in the analyses, the processed PDF files will either be copied ("cpy") or moved ("mv") into the /pdf/ subfolder of the output folder. Default: "nocpymv".

verbose

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

Value

If tables were extracted from the PDF file the function returns a list of following tables/items: 1) htmltablelines, 2) txttablelines, 3) keeplayouttxttablelines, 4) id, 5) out_msg. The tablelines are tables that provide the heading and position of the detected tables. The id provide the name of the PDF file. The out_msg includes all messages printed to the console or the suppressed messages if verbose=FALSE.

See Also

PDE_pdfs2table,PDE_pdfs2table_searchandfilter, PDE_pdfs2txt_searchandfilter

Examples

## Running a simple analysis with filter and search words to extract sentences and tables
if(PDE_check_Xpdf_install() == TRUE){
 outputtables <- .PDE_extr_data_from_pdf(pdf = "/examples/Methotrexate/29973177_!.pdf",
 whattoextr = "tabandtxt",
 out = paste0(system.file(package = "PDE"),"/examples/MTX_output+-0_test/"),
 filter.words = strsplit("cohort;case-control;group;study population;study participants", ";")[[1]],
 ignore.case.fw = TRUE,
 regex.fw = FALSE,
 search.words = strsplit("(M|m)ethotrexate;(T|t)rexal;(R|r)heumatrex;(O|o)trexup", ";")[[1]],
 ignore.case.sw = FALSE,
 regex.sw = TRUE)
}

## Running an advanced analysis with filter and search words to
## extract sentences and tables and obtain documentation files
if(PDE_check_Xpdf_install() == TRUE){
 outputtables <- .PDE_extr_data_from_pdf(pdf = paste0(system.file(package = "PDE"),
                       "/examples/Methotrexate/29973177_!.pdf"),
 whattoextr = "tabandtxt",
 out = paste0(system.file(package = "PDE"),"/examples/MTX_output+-1_test/"),
 context = 1,
 dev_x = 20,
 dev_y = 9999,
 filter.words = strsplit("cohort;case-control;group;study population;study participants", ";")[[1]],
 ignore.case.fw = TRUE,
 regex.fw = FALSE,
 filter.word.times = "0.2%",
 table.heading.words = "",
 ignore.case.th = FALSE,
 search.words = strsplit("(M|m)ethotrexate;(T|t)rexal;(R|r)heumatrex;(O|o)trexup", ";")[[1]],
 ignore.case.sw = FALSE,
 regex.sw = TRUE,
 eval.abbrevs = TRUE,
 out.table.format = ".csv (WINDOWS-1252)",
 write.table.locations = TRUE,
 write.tab.doc.file = TRUE,
 write.txt.doc.file = TRUE,
 exp.nondetc.tabs = TRUE,
 cpy_mv = "nocpymv",
 delete = TRUE)
}