Introduction

r 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.

Usage

We demonstrate usage on demo Rnw2Rmd-test.Rnw vignette included in the inst/example directory of this package:

r fpath <- system.file("example/Rnw2Rmd-test.Rnw", package="Rnw2Rmd")

Perform the conversion:

r 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.

The product

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] ```