Type: Package
Title: Extract Tables and Sentences from PDFs with User Interface
Version: 1.4.10
Author: Erik Stricker [aut, cre]
Maintainer: Erik Stricker <erik.stricker@gmx.com>
Description: The PDE (Pdf Data Extractor) allows the extraction of information and tables optionally based on search words from PDF (Portable Document Format) files and enables the visualization of the results, both by providing a convenient user-interface.
License: GPL-3 | file LICENSE
Encoding: UTF-8
Imports: tcltk
Depends: tcltk2 (≥ 1.2.11), R (≥ 3.5)
SystemRequirements: XPDF (4.02)(https://github.com/erikstricker/PDE/tree/master/inst/examples/bin)
RoxygenNote: 7.3.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-06-11 17:25:29 UTC; Erik
Repository: CRAN
Date/Publication: 2024-06-11 18:10:06 UTC

PDE: Extract Tables and Sentences from PDF Files.

Description

The package includes two main components: 1) The PDE analyzer performs the sentence and table extraction while 2) the PDE reader allows the user-friendly visualization and quick-processing of the obtained results.

PDE functions

PDE_analyzer, PDE_analyzer_i, PDE_extr_data_from_pdfs, PDE_pdfs2table, PDE_pdfs2table_searchandfilter,PDE_pdfs2txt_searchandfilter, PDE_reader_i, PDE_install_Xpdftools4.02, PDE_check_Xpdf_install

_PACKAGE

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)
}

Deprecated functions in package ‘PDE’

Description

These functions are provided for compatibility with older versions of ‘PDE’ only, and will be defunct at the next release.

Details

The following functions are deprecated and will be made defunct; use the replacement indicated below:

Extracting data from PDF (Portable Document Format) files

Description

The PDE_analyzer allows the sentence and table extraction from multiple PDF files.

Usage

PDE_analyzer(PDE_parameters_file_path = NA, verbose = TRUE)

Arguments

PDE_parameters_file_path

String. This file includes all parameters to run PDE_extr_data_from_pdfs on multiple PDF files. If PDE_parameters_file_path does not exist or is NA a dialog box is opened prompting the user to select the parameter file.

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.

Details

The parameter file (also referred to as .tsv file) can either manually or with the help of the PDE_analyzer_i interface be filled.

Note

A detailed description of the parameters in the TSV file can be found in the markdown file (README_PDE.md) and in the description of PDE_extr_data_from_pdfs.

See Also

PDE_extr_data_from_pdfs

Examples

 if(PDE_check_Xpdf_install() == TRUE){
   PDE_analyzer(paste0(system.file(package = "PDE"),
   "/examples/tsvs/PDE_parameters_v1.4_all_files+-0.tsv"))
 }

## Not run: 
 ## requires user file choice:
 PDE_analyzer()

## End(Not run)

Extracting data from PDF (Portable Document Format) files using a user interface

Description

The PDE_analyzer_i provides a user interface for the sentence and table extraction from multiple PDF files.

Usage

PDE_analyzer_i(verbose = TRUE)

Arguments

verbose

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

Note

A detailed description of the elements in the user interface can be found in the markdown file (README_PDE.md).

Examples


PDE_analyzer_i()

Check if the Xpdftools are installed an in the system path

Description

PDE_check_Xpdf_install runs a version test for pdftotext, pdftohtml and pdftopng.

Usage

PDE_check_Xpdf_install(sysname = NULL, verbose = TRUE)

Arguments

sysname

String. In case the function returns "Unknown OS" the sysname can be set manually. Allowed options are "Windows", "Linux", "SunOS" for Solaris, and "Darwin" for Mac. Default: NULL.

verbose

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

Value

The function returns a Boolean for the installation status and a message in case the commands are not detected.

Examples


PDE_check_Xpdf_install()

Extracting data from PDF (Portable Document Format) files

Description

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

Usage

PDE_extr_data_from_pdfs(
  pdfs,
  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,
  regex.sw = TRUE,
  save.tab.by.category = FALSE,
  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

pdfs

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

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.

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.

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 files 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_pdfs(pdfs = c(paste0(system.file(package = "PDE"),
                                                 "/examples/Methotrexate/29973177_!.pdf"),
                                                 paste0(system.file(package = "PDE"),
                                                 "/examples/Methotrexate/31083238_!.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_pdfs(pdfs = c(paste0(system.file(package = "PDE"),
                                                 "/examples/Methotrexate/29973177_!.pdf"),
                                                  paste0(system.file(package = "PDE"),
                                                 "/examples/Methotrexate/31083238_!.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]],
 regex.sw = TRUE,
 ignore.case.sw = FALSE,
 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)
}

Install the Xpdf command line tools 4.02

Description

PDE_install_Xpdftools4.02 downloads and installs the XPDF command line tools 4.02.

Usage

PDE_install_Xpdftools4.02(
  sysname = NULL,
  bin = NULL,
  verbose = TRUE,
  permission = 0
)

Arguments

sysname

String. In case the function returns "Unknown OS" the sysname can be set manually. Allowed options are "Windows", "Linux", "SunOS" for Solaris, and "Darwin" for Mac. Default: NULL.

bin

String. In case the function returns "Unknown OS" the bin of the operational system can be set manually. Allowed options are "64", and "32". Default: NULL.

verbose

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

permission

Numerical. If set to 0 the user is ask for a permission to download Xpdftools. If set to 1, no user input is required. Default: 0.

Value

The function returns a Boolean for the installation status and a message in case the commands are not installed.

Examples

## Not run: 

PDE_install_Xpdftools4.02()


## End(Not run)

Export the installation path the PDE (PDF Data Extractor) package

Description

PDE_path is deprecated. Please run system.file(package = "PDE") instead.

Usage

PDE_path()

Value

The function returns a potential path for the PDE package. If the PDE tool was not correctly installed it returns "".

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)
}

Extracting tables from a PDF (Portable Document Format) file

Description

PDE_pdfs2table_searchandfilter extracts tables from a single PDF file according to filter and search words and writes output in the corresponding folder.

Usage

PDE_pdfs2table_searchandfilter(
  pdfs,
  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,
  write.table.locations = FALSE,
  exp.nondetc.tabs = TRUE,
  write.tab.doc.file = TRUE,
  delete = TRUE,
  cpy_mv = "nocpymv",
  verbose = TRUE
)

Arguments

pdfs

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

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.

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.

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_extr_data_from_pdfs, PDE_pdfs2table

Examples


## Running a simple analysis with filter and search words to extract tables
if(PDE_check_Xpdf_install() == TRUE){
 outputtables <- PDE_pdfs2table_searchandfilter(pdf = paste0(system.file(package = "PDE"),
                                   "/examples/Methotrexate/29973177_!.pdf"),
 out = paste0(system.file(package = "PDE"),"/examples/29973177_tables/"),
 filter.words = strsplit("cohort;case-control;group;study population;study participants", ";")[[1]],
 regex.fw = FALSE,
 ignore.case.fw = TRUE,
 search.words = strsplit("(M|m)ethotrexate;(T|t)rexal;(R|r)heumatrex;(O|o)trexup", ";")[[1]],
 regex.sw = TRUE,
 ignore.case.sw = FALSE)
}

## Running an advanced analysis with filter and search words to
## extract tables and obtain documentation files
if(PDE_check_Xpdf_install() == TRUE){
 outputtables <- PDE_pdfs2table_searchandfilter(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,
 filter.words = strsplit("cohort;case-control;group;study population;study participants", ";")[[1]],
 regex.fw = FALSE,
 ignore.case.fw = TRUE,
 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]],
 regex.sw = TRUE,
 ignore.case.sw = FALSE,
 eval.abbrevs = TRUE,
 out.table.format = ".csv (WINDOWS-1252)",
 write.table.locations = TRUE,
 write.tab.doc.file = TRUE,
 exp.nondetc.tabs = TRUE,
 cpy_mv = "nocpymv",
 delete = TRUE)
}

Extracting sentences from a PDF (Portable Document Format) file

Description

PDE_pdfs2txt_searchandfilter extracts sentences from a single PDF file according to search and filter words and writes output in the corresponding folder.

Usage

PDE_pdfs2txt_searchandfilter(
  pdfs,
  out = ".",
  filter.words = "",
  regex.fw = TRUE,
  ignore.case.fw = FALSE,
  filter.word.times = "0.2%",
  search.words,
  search.word.categories = NULL,
  regex.sw = TRUE,
  ignore.case.sw = FALSE,
  eval.abbrevs = TRUE,
  out.table.format = ".csv (WINDOWS-1252)",
  context = 0,
  write.txt.doc.file = TRUE,
  delete = TRUE,
  cpy_mv = "nocpymv",
  verbose = TRUE
)

Arguments

pdfs

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

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%.

search.words

List of strings. List of 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.

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.

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.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.

See Also

PDE_extr_data_from_pdfs

Examples

## Running a simple analysis with filter and search words to extract sentences
if(PDE_check_Xpdf_install() == TRUE){
 outputtables <- PDE_pdfs2txt_searchandfilter(pdf = paste0(system.file(package = "PDE"),
                                      "/examples/Methotrexate/29973177_!.pdf"),
 out = paste0(system.file(package = "PDE"),"/examples/MTX_txt+-0/"),
 filter.words = strsplit("cohort;case-control;group;study population;study participants", ";")[[1]],
 regex.fw = FALSE,
 ignore.case.fw = TRUE,
 search.words = strsplit("(M|m)ethotrexate;(T|t)rexal;(R|r)heumatrex;(O|o)trexup", ";")[[1]],
 regex.sw = TRUE,
 ignore.case.sw = FALSE)
}

## Running an advanced analysis with filter and search words to
## extract sentences and obtain documentation files
if(PDE_check_Xpdf_install() == TRUE){
 outputtables <- PDE_pdfs2txt_searchandfilter(pdf = paste0(system.file(package = "PDE"),
                                       "/examples/Methotrexate/29973177_!.pdf"),
 out = paste0(system.file(package = "PDE"),"/examples/MTX_txt+-1/"),
 context = 1,
 filter.words = strsplit("cohort;case-control;group;study population;study participants", ";")[[1]],
 regex.fw = FALSE,
 ignore.case.fw = TRUE,
 filter.word.times = "0.2%",
 search.words = strsplit("(M|m)ethotrexate;(T|t)rexal;(R|r)heumatrex;(O|o)trexup", ";")[[1]],
 regex.sw = TRUE,
 ignore.case.sw = FALSE,
 eval.abbrevs = TRUE,
 out.table.format = ".csv (WINDOWS-1252)",
 write.txt.doc.file = TRUE,
 cpy_mv = "nocpymv",
 delete = TRUE)
}

Browsing the PDE (PDF Data Extractor) analyzer results.

Description

The PDE_reader_i allows the user-friendly visualization and quick-processing of the obtained results.

Usage

PDE_reader_i(verbose = TRUE)

Arguments

verbose

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

Note

A detailed description of the elements in the user interface can be found in the markdown file (README_PDE.md)

Examples


 PDE_reader_i()