Type:	Package
Title:	Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Version:	1.5.6
Description:	Articles in the 'R Journal' were first authored in 'LaTeX', which performs admirably for 'PDF' files but is less than ideal for modern online interfaces. The 'texor' package does all the transitional chores and conversions necessary to move to the online versions.
License:	MIT + file LICENSE
URL:	https://github.com/Abhi-1U/texor
BugReports:	https://github.com/Abhi-1U/texor/issues
Encoding:	UTF-8
RoxygenNote:	7.3.2
Imports:	rmarkdown, pdftools, tools, tinytex, yaml, stringr, xfun, logger, rjtools, rebib, cli, whisker, desc
Suggests:	bookdown, knitr, spelling, rstudioapi, testthat (≥ 3.0.0)
VignetteBuilder:	knitr
Config/testthat/edition:	3
Language:	en-US
SystemRequirements:	pandoc (>= 3.1) - https://pandoc.org
NeedsCompilation:	no
Packaged:	2025-04-01 18:46:44 UTC; abhi
Author:	Abhishek Ulayil [aut, cre, cph], Heather Turner [ctb], Christophe Dervieux [ctb], Mitchell O'Hara-Wild [ctb], Dianne Cook [ctb], Yinxiang Huang [ctb]
Maintainer:	Abhishek Ulayil <perricoq@outlook.com>
Repository:	CRAN
Date/Publication:	2025-04-01 19:00:02 UTC

Check if article has tikz images or not

Description

This simple utiliy function will check for tikzpicture environment

Usage

article_has_tikz(article_dir)

Arguments

Value

TRUE if tikz image is present else FALSE

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::article_has_tikz(your_article_path)
unlink(your_article_folder,recursive = TRUE)

check markdown file

Description

Checks if the markdown file generated is empty or not due to some pandoc related error during conversion to markdown.

Usage

check_markdown_file(article_dir)

Arguments

Value

FALSE if markdown file is corrupted/empty else TRUE

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
rmarkdown::pandoc_version()
texor::include_style_file(your_article_path)
rebib::aggregate_bibliography(your_article_path)
texor::convert_to_markdown(your_article_path)
texor::check_markdown_file(your_article_path)
unlink(your_article_folder, recursive = TRUE)

convert LaTeX wrapper to markdown

Description

Uses pandoc along with several lua filters found at inst/extdata/filters in texor package

Usage

convert_to_markdown(
  article_dir,
  kable_tab = TRUE,
  autonumber_eq = FALSE,
  fig_in_r = TRUE
)

Arguments

Details

convert latex(wrapper) file to markdown

Value

creates a converted markdown file, as well as a pkg_meta.yaml file

Note

pandoc (along with lua interpreter) is already installed with R-studio, hence if not using R-studio you will need to install pandoc. https://pandoc.org/installing.html

Use pandoc version greater than or equal to 3.1

Kable tables will work for simple static data, any math / code / image within any table will send the package into fallback mode (normal markdown tables) for the rest of tables in the article.

Examples

# Note This is a minimal example to execute this function
article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
rmarkdown::pandoc_version()
texor::include_style_file(your_article_path)
rebib::aggregate_bibliography(your_article_path)
texor::convert_to_markdown(your_article_path)
unlink(your_article_folder,recursive = TRUE)

convert LaTeX wrapper to native pandoc AST

Description

Uses pandoc along with several lua filters found at inst/extdata/filters in texor package

Usage

convert_to_native(article_dir, autonumber_eq = FALSE)

Arguments

Details

convert latex(wrapper) file to pandoc AST

Value

creates a converted native AST file, as well as a pkg_meta.yaml file

Note

pandoc (along with lua interpreter) is already installed with R-studio, hence if not using R-studio you will need to install pandoc. https://pandoc.org/installing.html

Use pandoc version greater than or equal to 3.1

Examples

# Note This is a minimal example to execute this function
article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
rmarkdown::pandoc_version()
texor::include_style_file(your_article_path)
rebib::aggregate_bibliography(your_article_path)
texor::convert_to_native(your_article_path)
unlink(your_article_folder,recursive = TRUE)

convert one single pdf file to png

Description

function to invoke 'pdftools:pdf_convert()'

This function is designed to be used internally and is called by 'texor::pdf_to_png(file_dir)' function for converting individual of pdf image.

Note : The extensions in LaTeX source code will automatically be changed during pandoc conversion by a lua filter (refer : inst/extdata/image_filter.lua)

Usage

convert_to_png(file_path, dpi = 180)

Arguments

Value

png file of the same

Note

If you find inconsistencies in the raster image generated from PDF using this function. Please update poppler utils to newer versions (possibly latest one).

Examples

article_dir <- system.file("examples/pdf_conversion",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"pdf_conversion",sep="/")
rmarkdown::pandoc_version()
texor::convert_to_png(paste0(your_article_path,"/normal.pdf"))
unlink(your_article_folder,recursive = TRUE)

Copy Supporting Documents like images,bib file,etc.

Description

Copies supporting documents like images,pdf,bib files into the output folder for building the HTML version of the R-Markdown file.

Usage

copy_other_files(from_path)

Arguments

Value

copies dependency files into the output folder.

Examples

article_dir <- system.file("examples/article", package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
rmarkdown::pandoc_version()
texor::include_style_file(your_article_path)
rebib::aggregate_bibliography(your_article_path)
texor::copy_other_files(your_article_path)
list.files(paste0(your_article_path,"/web/"))
unlink(your_article_folder,recursive = TRUE)

count latex environments

Description

count common environments like table,figure,verbatim etc..

Usage

count_env(article_dir, env_name)

Arguments

Value

count of the environment, FALSE otherwise

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
figures <- texor::count_env(article_dir, "figure")
print(paste("figure count : ", figures))

count inline elements

Description

counts inline elements embedded within the latex file currently supported inlines : math (based on $$), code (based on \code) and Citations (based on \cite,\citealp, \citep, \citet)

Usage

count_inline(article_dir, inline)

Arguments

Value

count of the inline element, FALSE otherwise

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
math <- texor::count_inline(article_dir, "math")
code <- texor::count_inline(article_dir, "inlinecode")
cite <- texor::count_inline(article_dir, "cite")
print(paste("math inlines : ", math, "\n",
            "code inlines : ", code, "\n",
            "citations    : ", cite))

Create an R Journal article with a modified template for texor.

Description

Create an R Journal article with a modified template for texor.

Usage

create_article(name = "test", edit = TRUE)

Arguments

Details

Outputs an LaTeX R Journal paper template set of files in the project directory.

find wrapper file

Description

Finds a different named wrapper file for RJournal article

Usage

find_wrapper(article_dir)

Arguments

Value

wrapper file name or empty string if none

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::find_wrapper(your_article_path)
unlink(your_article_folder,recursive = TRUE)

Modify Markdown to R-markdown

Description

generate rmarkdown file in output folder

Usage

generate_rmd(article_dir, web_dir = TRUE, interactive_mode = FALSE)

Arguments

Value

R-markdown file in the web folder

Note

Use pandoc version greater than or equal to 3.1

Examples

# Note This is a minimal example to execute this function
article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir2"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <-  xfun::normalize_path(paste(your_article_folder,"article",sep="/"))
texor::include_style_file(your_article_path)
rebib::aggregate_bibliography(your_article_path)
data <- texor::handle_figures(your_article_path,
                    texor::get_texfile_name(your_article_path))
texor::patch_code_env(your_article_path) # Step 4
texor::patch_table_env(your_article_path) # Step 5
texor::patch_equations(your_article_path) # Step 5.5
texor::patch_figure_env(your_article_path)
rmarkdown::pandoc_version()
texor::convert_to_markdown(your_article_path)
texor::generate_rmd(your_article_path)
unlink(your_article_folder,recursive = TRUE)

get Journal details

Description

get Journal details

Usage

get_journal_details(article_dir)

Arguments

Value

journal details in an object

Examples

article_dir <- "/home/user/documents/2022-1/2020-36/"
texor::get_journal_details(article_dir)

get markdown file name

Description

get markdown file name

Usage

get_md_file_name(article_dir)

Arguments

Value

markdown file name

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::get_md_file_name(your_article_path)
unlink(your_article_folder,recursive = TRUE)

Get the name of the tex file included within wrapper file

Description

The wrapper file refers to an external tex file which contains the actual document content.

Usage

get_texfile_name(article_dir)

Arguments

Value

String name of the tex-file name

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::get_texfile_name(your_article_path)
unlink(your_article_folder,recursive = TRUE)

Get the name of the wrapper file in the article dir

Description

This function gets the wrapper file name from the commonly named R-Journal wrapper files.

Usage

get_wrapper_type(article_dir, auto_wrapper = FALSE, interactive_mode = FALSE)

Arguments

Details

Usually the R journal wrapper files are named either 1. RJwrapper.tex 2. RJwrap.tex 3. wrapper.tex

Value

String with name of wrapper file or empty

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::get_wrapper_type(your_article_path)
unlink(your_article_folder,recursive = TRUE)

handle figures

Description

handle figures

Usage

handle_figures(article_dir, file_name)

Arguments

Value

A block of figure data for better conversion.

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::handle_figures(your_article_path,texor::get_texfile_name(your_article_path))
unlink(your_article_folder,recursive = TRUE)

Include Style file

Description

Includes the Metafix.sty style file

Usage

include_style_file(article_dir)

Arguments

Details

This style file helps texor and pandoc to retain metadata and ease the conversion process.

Value

adds Metafix.sty file in the article_dir also includes it in RJwrapper file.

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::include_style_file(your_article_path)
unlink(your_article_folder,recursive = TRUE)

latex to web

Description

automated function for converting a single RJarticle to web

Usage

latex_to_web(
  dir,
  log_steps = TRUE,
  example = FALSE,
  auto_wrapper = TRUE,
  temp_mode = TRUE,
  web_dir = FALSE,
  interactive_mode = FALSE,
  autonumber_eq = FALSE,
  compile_rmd_in_temp = !temp_mode,
  kable_tab = FALSE,
  fig_in_r = FALSE
)

Arguments

Value

RJweb article document in /web folder

Note

Use pandoc version greater than or equal to 3.1

Do not set example = TRUE param when working with conversions.

example param is set TRUE in example, to conform with CRAN check restrictions.

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::latex_to_web(your_article_path,log_steps = FALSE, example = TRUE, temp_mode =FALSE)
unlink(your_article_folder, recursive = TRUE)

texor log setup

Description

a wrapper function for logger package to set up log file for logging

Usage

log_setup(article_dir, file_name, namespace, idx)

Arguments

Value

NULL but also creates a log file in the article_dir

Examples

dir.create(your_article_folder <- file.path(tempdir(), "exampledir"))
example_files <-  system.file("examples/article", package = "texor")
x <- file.copy(from = example_files,to=your_article_folder,recursive = TRUE)
your_article_path <- paste(your_article_folder,"article",sep="/")
 texor::log_setup(your_article_path, "log-file.log", "texor", 2)
unlink(your_article_folder,recursive = TRUE)

check texor pandoc compatibility

Description

texor package requires minimum pandoc version above or equal to 3.1, hence this utility will check for the installation and version status.

Usage

pandoc_version_check()

Value

TRUE if v >= 3.1, else FALSE

Examples

rmarkdown::pandoc_version()

texor::pandoc_version_check()

patch all code environments

Description

This function calls the 'filter_code_env()' function over the following code environments described in Rjournal.sty

1. example 2. example* 3. Sin 4. Sout 5. Sinput 6. Soutput 7. smallverbatim

Usage

patch_code_env(article_dir)

Arguments

Value

patches code environments in LaTeX file and also backs up the old file before modification , FALSE otherwise

Examples

# Note This is a minimal example to execute this function
article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir2"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <-  xfun::normalize_path(paste(your_article_folder,"article",sep="/"))
texor::patch_code_env(your_article_path)
unlink(your_article_folder,recursive = TRUE)

patch equations

Description

this function patches equations (particularly eqnarray)

Usage

patch_equations(article_dir)

Arguments

Value

patches equations environments in LaTeX file and also backs up the old file before modification

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::patch_equations(your_article_path)
unlink(your_article_folder,recursive = TRUE)

patch figure environments

Description

This function calls the stream editor to change figure* to figure 1. figure*

Usage

patch_figure_env(article_dir, with_alg = TRUE)

Arguments

Value

patches figure environments in LaTeX file and also backs up the old file before modification

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::patch_figure_env(your_article_path)
unlink(your_article_folder,recursive = TRUE)

patch table environment

Description

function to modify env and commands in TeX using GNU sed

These are due to the pandoc's limitations and ease in conversion.

Usage

patch_table_env(article_dir)

Arguments

Details

changes are made to : 1. table* environment to table environment 2. \multicolumn to \multicolumnx \multicolumnx is redefined in Metafix.sty as \renewcommand{\multicolumnx}[3]{\multicolumn{#1}{c}{#3}}

Value

patches table environments in LaTeX file and also backs up the old file before modification

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::patch_table_env(your_article_path)
unlink(your_article_folder,recursive = TRUE)

pre conversion statistics

Description

count common environments,inlines for debugging purposes

Usage

pre_conversion_statistics(article_dir, write_yaml = TRUE)

Arguments

Value

conversion stat block with details also a yaml file if param enabled.

Examples

article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::patch_code_env(your_article_path)
texor::patch_table_env(your_article_path)
texor::patch_equations(your_article_path)
texor::patch_figure_env(your_article_path)
texor::pre_conversion_statistics(your_article_path,write_yaml = FALSE)
unlink(your_article_folder,recursive = TRUE)

call rmarkdown::render to generate html file

Description

call rmarkdown::render to generate html file

Usage

produce_html(
  article_dir,
  example = FALSE,
  web_dir = TRUE,
  interactive_mode = FALSE
)

Arguments

Value

Renders a RJwrapper.html file in the /web folder, in example it will return TRUE

Note

Use pandoc version greater than or equal to 3.1

Do not set example = TRUE param when working with conversions.

example param is set TRUE in example, to conform with CRAN check restrictions.

Examples

# Note This is a minimal example to execute this function
article_dir <- system.file("examples/article",
                 package = "texor")
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::include_style_file(your_article_path)
rmarkdown::pandoc_version()
texor::convert_to_markdown(your_article_path)
texor::generate_rmd(your_article_path)
texor::copy_other_files(your_article_path)
texor::produce_html(your_article_path,example = TRUE)
unlink(your_article_folder,recursive = TRUE)

Modify Markdown from Sweave to R-markdown

Description

generate rmarkdown file in output folder

Usage

rnw_generate_rmd(
  article_dir,
  web_dir = TRUE,
  interactive_mode = FALSE,
  output_format,
  autonumber_eq = FALSE,
  autonumber_sec = TRUE,
  algorithm_render = FALSE
)

Arguments

Value

R-markdown file in the web folder

Note

Use pandoc version greater than or equal to 3.1

Examples

# Note This is a minimal example to execute this function
# Please refer to texor::rnw_to_rmd for a detailed example

Sweave to RMarkdown

Description

automated function for converting a single Sweave file to R Markdown file

Usage

rnw_to_rmd(
  input_file,
  output_format,
  clean_up = TRUE,
  autonumber_eq = FALSE,
  autonumber_sec = TRUE,
  suppress_package_startup_message = FALSE,
  kable_tab = TRUE,
  fig_in_r = TRUE,
  algorithm_render = FALSE
)

Arguments

Value

True if R Markdown file successfully generated in the same folder

Note

Use pandoc version greater than or equal to 3.1

Examples

# move example Sweave article and associated files to a temporary directory
example_dir <- system.file("examples", "sweave_article", package = "texor")
file.copy(from = example_dir, to = tempdir(), recursive = TRUE)
article_dir <- file.path(tempdir(), "sweave_article")

# convert example Sweave article to Rmd
rnw_to_rmd(file.path(article_dir, "example.Rnw"),
           output_format = "bookdown",
           clean_up = TRUE,
           autonumber_eq = TRUE,
           autonumber_sec = FALSE)

# convert Rmd to HTML (comment this step to avoid failure on R CMD Check)
# rmarkdown::render(file.path(article_dir, "example.Rmd"))
# browseURL(file.path(article_dir, "example.html"))

# remove temporary files
unlink(article_dir, recursive = TRUE)

stream editor

Description

R equivalent of GNU-sed

Usage

stream_editor(raw_lines, pattern, target, replacement)

Arguments

Value

raw_lines : modified vector of lines

Examples

example_string <- "\\target{} \\not_a_target{}"
texor::stream_editor(example_string,"\\s*\\\\target\\{\\}", "\\\\target", "\\\\hit")

log messages for various categories

Description

a wrapper function for logging different types of log entries

Usage

texor_log(message, category, idx)

Arguments

Value

NUll, but also appends message to the log file in article_dir

Examples

dir.create(your_article_folder <- file.path(tempdir(), "exampledir"))
example_files <- system.file("examples/article", package = "texor")
x <- file.copy(from = example_files,to=your_article_folder,recursive = TRUE)
your_article_path <- paste(your_article_folder,"article",sep="/")
texor::log_setup(your_article_path, "log-file.log", "texor" , 2)
texor::texor_log("Hello", "INFO", 2)
cat(readLines(paste(your_article_path,"/log-file.log",sep="")),sep="\n")
unlink(your_article_folder,recursive = TRUE)