I have a dataset that I am trying to get published as part of the supplementary information of a study that is in .Rmd format. The .Rmd file is set up to not only provide an easily readable printout of the statistical analyses performed in the study, but it also set up so to be a tool for other researchers working in the same area to use on their data. The intent being all they would have to do is insert their data and re-knit the file and their results would be printed out without having to rework the R code from scratch.
However, the journal will not accept .Rmd scripts as .Rmd files and possibly will not accept knitted .html printouts of an .Rmd file. The journal suggested to me that I save the .Rmd file as a plain R script using purl() and submit that instead. However, this creates a problem in that the script no longer generates an easily navigable printout (i.e., issues with headers and document text) and is more difficult to use. At the same time, I noticed that purl() seems to produce an R script that contains most of the information of the .Rmd file, particularly if one uses the options documentation=1 or documentation=2.
I am trying to figure out if there is any way to convert an .Rmd file back into an .Rmd file after it has been exported as a basic R script using purl? This way I could potentially submit the analysis as a basic R script as per the journal's requirements, but the user could convert it back into the script that produces a knitted html report if that is what they desire.