library(Rnw2Rmd)The Rnw2Rmd package automates parts of the process of converting
Sweave vignettes to R Markdown (or Quarto). It is employed by the
conversion template for Bioconductor packages at
https://github.com/waldronlab/sweave2rmd_conversiontemplate.
Output Rmd documents will still have to be tested and corrected manually, but this should be a lot less work than starting from scratch. Please report issues at https://github.com/Bioconductor/sweave2rmd/issues.
We demonstrate usage on demo Rnw2Rmd-test.Rnw vignette included in the
inst/example directory of this package:
fpath <- system.file("example/Rnw2Rmd-test.Rnw", package="Rnw2Rmd")Perform the conversion:
dir.create(tempdir <- tempfile())
test_rmd <- file.path(tempdir, "Rnw2Rmd-test.Rmd")
Rnw2Rmd(from = fpath, to = test_rmd, validate = TRUE)Note, some validation errors are not actually much of a problem and you
can use validate=FALSE to skip validation and still get a useful draft
conversion.
Compare the source document:
#> [1] \\section{First level}
#> [2]
#> [3] \\subsection{Second level}
#> [4]
#> [5] \\subsubsection{Thrid level}
#> [6]
#> [7] Nothing to see here, folks!
#> [8]
#> [9] The \\R{} programming language
#> [10]
#> [11] \\R\\ is a programming language.
#> [12]
#> [13] The name of one programming language is simply \\R.
#> [14]
#> [15] \\Biocpkg{BiocStyle} is a \\Bioconductor{} package.
#> [16]
#> [17] The \\CRANpkg{knitr} is used to create \\textbf{markdown} vignettes.
#> [18]
#> [19] Sometimes packages, like \\Githubpkg{AnVILAz}, are only found on Github.
#> [20]
#> [21] The \\R{} package \\Rpackage{foo} is not found in any common repository
#> [22]
#> [23] \\software{samtools} is pretty \\textit{important} in Bioinformatics...
#> [24]
#> [25] \\Robject{mtcars} is a \\Rcode{data.frame}.
#> [26]
#> [27] \\Rfunction{data.frame} is a function used to create a \\Rcode{data.frame}.
#> [28]
#> [29] \\Rfunction{data.frame()} is a function used to create a \\Rcode{data.frame}.
#> [30]
#> [31] Sometimes inline \\R{} code \\Rcode{x <-
#> [32] 1 + 1} can span two lines.
#> [33]
#> [34] Here's some \\emph{italic} text
#> [35]
#> [36] Here's an Sexpr that should be evaluated \\Sexpr{1 + 1}
#> [37]
#> [38] \\begin{itemize}
#> [39] \\item One item
#> [40] \\item Another item
#> [41] \\end{itemize}
#> [42]
#> [43] \\begin{description}
#> [44] \\item[foo] bar
#> [45] \\end{description}
#> [46]
#> [47] <<>>=
#> [48] 1 + 1
#> [49] @
#> [50]
#> [51] <<named, echo = FALSE>>=
#> [52] 1 + 1
#> [53] @
and the generated document:
#> [1] ---
#> [2] title: ""
#> [3] author: ""
#> [4] date: "`r format(Sys.time(), '%B %d, %Y')`"
#> [5] output:
#> [6] BiocStyle::html_document
#> [7] vignette: >
#> [8] %\\VignetteIndexEntry{ }
#> [9] %\\VignetteEngine{knitr::rmarkdown}
#> [10] %\\VignetteEncoding{UTF-8}
#> [11] ---
#> [12]
#> [13] # First level
#> [14]
#> [15] ## Second level
#> [16]
#> [17] ### Thrid level
#> [18]
#> [19] Nothing to see here, folks!
#> [20]
#> [21] The *R* programming language
#> [22]
#> [23] *R* is a programming language.
#> [24]
#> [25] The name of one programming language is simply *R*.
#> [26]
#> [27] `r Biocpkg(BiocStyle)` is a *Bioconductor* package.
#> [28]
#> [29] The `r CRANpkg(knitr)` is used to create **markdown** vignettes.
#> [30]
#> [31] Sometimes packages, like `r Githubpkg(AnVILAz)`, are only found on
#> [32] Github.
#> [33]
#> [34] The *R* package `foo` is not found in any common repository
#> [35]
#> [36] `samtools` is pretty *important* in Bioinformatics\\...
#> [37]
#> [38] `mtcars` is a `data.frame`.
#> [39]
#> [40] `data.frame` is a function used to create a `data.frame`.
#> [41]
#> [42] `data.frame()` is a function used to create a `data.frame`.
#> [43]
#> [44] Sometimes inline *R* code `x <-
#> [45] 1 + 1` can span two lines.
#> [46]
#> [47] Here's some *italic* text
#> [48]
#> [49] Here's an Sexpr that should be evaluated `r 1 + 1`
#> [50]
#> [51] ```{=latex}
#> [52] \\begin{itemize}
#> [53] - One item
#> [54] - Another item
#> [55] \\end{itemize}
#> [56] ```
#> [57] ```{=latex}
#> [58] \\begin{description}
#> [59] - [foo] bar
#> [60] \\end{description}
#> [61] ```
#> [62] ```{r}
#> [63] 1 + 1
#> [64] ```
#> [65]
#> [66] ```{r named, echo = FALSE}
#> [67] 1 + 1
#> [68] ```