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
- 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
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)
#> [1] 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)
#> removing the unnecessary option fig=TRUE:
#> * image,fig=TRUE, fig.cap="matrix package's image"
#> removing the unnecessary option fig=TRUE:
#> * keep.source=TRUE, fig=TRUE
#> changing keep.source=TRUE to tidy=FALSE:
#> * keep.source=TRUE,
#> changing \SweaveOpts{} to opts_chunk$set():
#> * \SweaveOpts{keep.source=TRUE, fig=TRUE}
#> /usr/local/bin/pandoc +RTS -K512m -RTS /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/example-knitr.Rnw --to markdown-simple_tables-pipe_tables-fenced_code_attributes --from latex --output /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/example-knitr-part1.md --resource-path /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article -f /Users/runner/work/_temp/Library/texor/sweave_code_reader.lua --lua-filter /Users/runner/work/_temp/Library/texor/r_code_chunk_patcher.lua
#> /usr/local/bin/pandoc +RTS -K512m -RTS /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/example-knitr.Rnw --to latex --from latex --output /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/example-generated.tex --resource-path /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article -f /Users/runner/work/_temp/Library/texor/sweave_code_remove.lua
#> /usr/local/bin/pandoc +RTS -K512m -RTS /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/example-generated.tex --to markdown-simple_tables-pipe_tables-fenced_code_attributes --from latex --output /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/example-knitr-part2.md --resource-path /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article -f /Users/runner/work/_temp/Library/texor/algorithm_reader.lua
#> /usr/local/bin/pandoc +RTS -K512m -RTS /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/example-generated.tex --to latex --from latex --output /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/example-generated.tex --resource-path /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article -f /Users/runner/work/_temp/Library/texor/algorithm_remove.lua
#> Found Bib file example.bib
#> Cannot aggregate bibliography as there is no embedded bibliography
#> Found 0 Matches for target : example
#> Found 0 Matches for target : example
#> Found 0 Matches for target : example\*
#> Found 0 Matches for target : example\*
#> Found 0 Matches for target : Sin
#> Found 0 Matches for target : Sin
#> Found 0 Matches for target : Sout
#> Found 0 Matches for target : Sout
#> Found 0 Matches for target : Scode
#> Found 0 Matches for target : Scode
#> Found 0 Matches for target : Sinput
#> Found 0 Matches for target : Sinput
#> Found 0 Matches for target : Soutput
#> Found 0 Matches for target : Soutput
#> Found 0 Matches for target : smallverbatim
#> Found 0 Matches for target : smallverbatim
#> Found 0 Matches for target : boxedverbatim
#> Found 0 Matches for target : boxedverbatim
#> Found 0 Matches for target : smallexample
#> Found 0 Matches for target : smallexample
#> Found 0 Matches for target : table\*
#> Changed \begin{table\*} to \begin{table}
#> Found 0 Matches for target : table\*
#> Changed \end{table*} to \end{table}
#> Found 0 Matches for target : multicolumn
#> changed \multicolumn to \multicolumnx
#> Found 0 Matches for target : widetable
#> Changed \begin{widetable} to \begin{table}
#> Found 0 Matches for target : widetable
#> Changed \end{widetable} to \end{table}
#> Auto add label for table env
#> Found 0 Matches for target : figure\*
#> Changed \begin{figure\*} to \begin{figure}
#> Found 0 Matches for target : figure\*
#> Changed \end{figure\*} to \end{figure}
#> Found 0 Matches for target : widefigure
#> Changed \begin{widefigure} to \begin{figure}
#> Found 0 Matches for target : widefigure
#> Changed \end{widefigure} to \end{figure}
#> Found 0 Matches for target : widefigure\*
#> Changed \begin{widefigure\*} to \begin{figure}
#> Found 0 Matches for target : widefigure\*
#> Changed \end{widefigure\*} to \end{figure}
#> /usr/local/bin/pandoc +RTS -K512m -RTS /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/RJwrapper.tex --to native --from latex --output /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/temp-native.txt -s --resource-path /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/RJwrapper.tex --lua-filter /Users/runner/work/_temp/Library/texor/find_pdf_files.lua
#> Found 0 Matches for target : figure\*
#> Changed \begin{figure\*} to \begin{figure}
#> Found 0 Matches for target : figure\*
#> Changed \end{figure\*} to \end{figure}
#> Found 0 Matches for target : widefigure
#> Changed \begin{widefigure} to \begin{figure}
#> Found 0 Matches for target : widefigure
#> Changed \end{widefigure} to \end{figure}
#> Found 0 Matches for target : widefigure\*
#> Changed \begin{widefigure\*} to \begin{figure}
#> Found 0 Matches for target : widefigure\*
#> Changed \end{widefigure\*} to \end{figure}
#> Found 0 Matches for target : algorithm
#> Changed \begin{algorithm} to \begin{figure}
#> Found 0 Matches for target : algorithm
#> Changed \end{algorithm} to \end{figure}
#> /usr/local/bin/pandoc +RTS -K512m -RTS /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/RJwrapper.tex --to markdown-simple_tables-pipe_tables-fenced_code_attributes --from latex --output /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article/RJwrapper.md -s --resource-path /private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article --lua-filter /Users/runner/work/_temp/Library/texor/issue_checker.lua --lua-filter /Users/runner/work/_temp/Library/texor/abs_filter.lua --lua-filter /Users/runner/work/_temp/Library/texor/bib_filter.lua --lua-filter /Users/runner/work/_temp/Library/texor/equation_filter.lua --lua-filter /Users/runner/work/_temp/Library/texor/image_filter.lua --lua-filter /Users/runner/work/_temp/Library/texor/sec_depth.lua --lua-filter /Users/runner/work/_temp/Library/texor/fig_code_chunk.lua --lua-filter /Users/runner/work/_temp/Library/texor/widetable_patcher.lua --lua-filter /Users/runner/work/_temp/Library/texor/R_code.lua --lua-filter /Users/runner/work/_temp/Library/texor/table_caption.lua --lua-filter /Users/runner/work/_temp/Library/texor/auto_number_equations.lua --lua-filter /Users/runner/work/_temp/Library/texor/table_code_chunk.lua --lua-filter /Users/runner/work/_temp/Library/texor/conversion_compat_check.lua --lua-filter /Users/runner/work/_temp/Library/texor/bookdown_ref.lua --citeproc
#> Detected the following packages from article:
#> CRAN:
#> Bioconductor:
#> ! `package.dir` (/private/var/folders/t_/mmhnh941511_hp2lwh383bp00000gn/T/RtmpQhQvJb/sweave_article) does not contain a DESCRIPTION, hence not updated
#> [1] TRUE
# 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)