Package 'texor' reference manual

Title:	Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
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.
Authors:	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 <[email protected]>
License:	MIT + file LICENSE
Version:	1.5.0
Built:	2024-11-17 06:11:40 UTC
Source:	https://github.com/abhi-1u/texor

Check if article has tikz images or not

Description

This simple utiliy function will check for tikzpicture environment

Usage

article_has_tikz(article_dir)
article_has_tikz(article_dir)

Arguments

article_dir

path to the directory which contains tex article

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)
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)
check_markdown_file(article_dir)

Arguments

article_dir

path to the directory which contains tex article

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

Arguments

`article_dir`	path to the directory which contains tex article
`kable_tab`	converts to kable table instead of markdown tables
`autonumber_eq`	whether to autonumber the equations, default is FALSE
`fig_in_r`	whether to include figures in R code chunks, default is TRUE

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)
# 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)
convert_to_native(article_dir, autonumber_eq = FALSE)

Arguments

`article_dir`	path to the directory which contains tex article
`autonumber_eq`	whether to autonumber the equations, default is FALSE

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)
# 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)
convert_to_png(file_path, dpi = 180)

Arguments

`file_path`	path to the pdf file
`dpi`	Set DPI for converting PDF files. default: 180

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)
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)
copy_other_files(from_path)

Arguments

from_path

String indicating base path for the working directory

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)
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)
count_env(article_dir, env_name)

Arguments

`article_dir`	path to the directory which contains RJ article
`env_name`	name of the environment

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))
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)
count_inline(article_dir, inline)

Arguments

`article_dir`	path to the directory which contains RJ article
`inline`	name of the inline element

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

Arguments

`name`	the name of the tex file, will default to "test"
`edit`	Opens the file for editing in RStudio/R GUI.

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)
find_wrapper(article_dir)

Arguments

article_dir

path to the directory which contains tex article

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

Arguments

`article_dir`	path to the directory which contains tex article
`web_dir`	option to create a new web directory, default TRUE
`interactive_mode`	interactive mode for converting articles with options. default FALSE

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)
# 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)
get_journal_details(article_dir)

Arguments

article_dir

path to the directory which contains tex article

Value

journal details in an object

Examples

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

Arguments

article_dir

path to the directory which contains tex article

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)
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)
get_texfile_name(article_dir)

Arguments

article_dir

path to the directory which contains tex article

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

Arguments

`article_dir`	path to the directory which contains tex article
`auto_wrapper`	automatically creates a wrapper if TRUE, else asks user. default value FALSE
`interactive_mode`	interactive mode for converting articles with options.

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)
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)
handle_figures(article_dir, file_name)

Arguments

`article_dir`	path to the directory which contains tex article
`file_name`	name of the LaTeX file

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)
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)
include_style_file(article_dir)

Arguments

article_dir

path to the directory which contains tex article

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)
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 = TRUE,
  fig_in_r = TRUE
)
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 = TRUE,
  fig_in_r = TRUE
)

Arguments

`dir`	directory path
`log_steps`	Enable/Disable Logging of conversion steps
`example`	for examples only by default keep it FALSE.
`auto_wrapper`	automatically creates a wrapper if TRUE, else asks user. default value TRUE
`temp_mode`	temp mode will convert the document in a temporary folder and keep the original article untouched. default value = TRUE
`web_dir`	option to create a new web directory, default FALSE
`interactive_mode`	interactive mode for converting articles with options. default FALSE
`autonumber_eq`	whether to autonumber the equations, default is FALSE
`compile_rmd_in_temp`	This works only with a forked version of rjtools.
`kable_tab`	converts to kable table instead of markdown tables
`fig_in_r`	whether to include figures in R code chunks, default is TRUE Not recommended to use with CRAN or github version of the rjtools package. (default FALSE)

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)
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)
log_setup(article_dir, file_name, namespace, idx)

Arguments

`article_dir`	path to the directory which contains tex article
`file_name`	name of the log file
`namespace`	namespace of log file
`idx`	index of log level

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)
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()
pandoc_version_check()

Value

TRUE if v >= 3.1, else FALSE

Examples

rmarkdown::pandoc_version()

texor::pandoc_version_check()
rmarkdown::pandoc_version()

texor::pandoc_version_check()

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)
patch_figure_env(article_dir, with_alg = TRUE)

Arguments

`article_dir`	path to the directory which contains tex article
`with_alg`	to include algorihtm environment or not

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)
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)
patch_table_env(article_dir)

Arguments

article_dir

path to the directory which contains tex article

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)
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)
pre_conversion_statistics(article_dir, write_yaml = TRUE)

Arguments

`article_dir`	path to the directory which contains RJ article
`write_yaml`	write to a yaml file (default = TRUE)

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

Arguments

`article_dir`	path to the directory which contains tex article
`example`	only enabled for running examples for documentation and to enable export of this function.
`web_dir`	option to create a new web directory, default TRUE
`interactive_mode`	interactive mode for converting articles with options. default FALSE

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

Arguments

`article_dir`	path to the directory which contains tex article
`web_dir`	option to create a new web directory, default TRUE
`interactive_mode`	interactive mode for converting articles with options. default FALSE
`output_format`	knit output type for the RMarkdown file, options for "bookdown", "biocstyle", "litedown"
`autonumber_eq`	whether to autonumber the equations, default is FALSE
`autonumber_sec`	whether to autonumber the sections, default is TRUE
`algorithm_render`	Enable to include algorithms with pseudocode.js, default is FALSE optional is TRUE

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
# 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
)
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

`input_file`	input Sweave file path
`output_format`	knit output type for the RMarkdown file options for "bookdown", "biocstyle", "litedown"
`clean_up`	whether to clean up the intermediate files, default is TRUE
`autonumber_eq`	whether to autonumber the equations, default is FALSE
`autonumber_sec`	whether to autonumber the sections, default is TRUE
`suppress_package_startup_message`	whether to suppress the package startup message, default is FALSE
`kable_tab`	converts to kable table instead of markdown tables
`fig_in_r`	whether to include figures in R code chunks, default is TRUE
`algorithm_render`	Enable to include algorithms with pseudocode.js, default is FALSE optional is TRUE

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)
# 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)
stream_editor(raw_lines, pattern, target, replacement)

Arguments

`raw_lines`	a vector of readLines from the file
`pattern`	a regex pattern to match
`target`	target string to be replaced
`replacement`	replacement string to be substituted

Value

raw_lines : modified vector of lines

Examples

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

Arguments

`message`	message to be sent
`category`	category of the log message
`idx`	index of log level

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)
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)

Package 'texor'

Help Index

Check if article has tikz images or not

Description

Usage

Arguments

Value

Examples

check markdown file

Description

Usage

Arguments

Value

Examples

convert LaTeX wrapper to markdown

Description

Usage

Arguments

Details

Value

Note

Examples

convert LaTeX wrapper to native pandoc AST

Description

Usage

Arguments

Details

Value

Note

Examples

convert one single pdf file to png

Description

Usage

Arguments

Value

Note

Examples

Copy Supporting Documents like images,bib file,etc.

Description

Usage

Arguments

Value

Examples

count latex environments

Description

Usage

Arguments

Value

Examples

count inline elements

Description

Usage

Arguments

Value

Examples

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

Description

Usage

Arguments

Details

find wrapper file

Description

Usage

Arguments

Value

Examples

Modify Markdown to R-markdown

Description

Usage

Arguments

Value

Note

Examples

get Journal details

Description

Usage

Arguments

Value

Examples

get markdown file name