Hi, 

I found that BiocWorkflowTools package can convert R markdown file to LaTex and PDF files, which is F1000Reseach-formatted.

http://bioconductor.org/packages/release/bioc/html/BiocWorkflowTools.html

I think the idea is amazing because the package will increase the value of Bioconductor's documents (vignette) as peer review papers.

However, I still do not clearly understand some parts, that is, the appearance of F1000-PDF and Bioconductor-PDF are different.

Is this F1000-PDF also can be used as Bioconductor's vignette, or this R markdown file can be converted to both F1000-PDF and Bioconductor-PDF/HTML for vignette, by some adjustment of the Rmd file such as change of header lines?

In my opinion, R-studio's knit botton that seamlessly switching F1000Research-pdf/Bioconductor-pdf or Bioconductor's acceptance of F1000Research-type vignette will reduce the burden of R-developers.

Off course, little rewriting the R markdown file is not so hard.

Thanks,

Koki Tsuyuzaki

The original aim of the F1000 template was primarily to make writing and submitting workflow documents easier (https://www.bioconductor.org/developers/how-to/workflows/), where the intention is to send an F1000 style document to the journal, and have a BioC style HTML available via the Bioconductor website.  However there's no reason you can't use the F1000 styling for any R Markdown document, and as Lori says it acceptable, if not encourage, for package vignettes.

From a practical point of view, you can use both styles if by putting the following in the head of your R Markdown document:

output: 
    BiocStyle::html_document: default
    BiocWorkflowTools::f1000_article: default

If you're using the the 'knit' button in R Studio then I think it's only possible to produce the first entry, it doesn't let you select between the two. However, producing the output programmatically you can do any of the following:

## Output just Bioconductor style HTML
rmarkdown::render(input = "Document.Rmd", output_format = 'BiocStyle::html_document')
## Output just F1000Research style PDF
rmarkdown::render(input = "Document.Rmd", output_format = 'BiocWorkflowTools::f1000_article')
## Out both of the above
rmarkdown::render(input = "Document.Rmd", output_format = 'all')

That way you don't have to edit your document at all to produce the two formats, just change the argument to render()

Based on this, I guess there's no reason why both versions can't be made available on the BioC website, it might even be preferable for a reader to find a document that looks very similar to the published paper. This is probably something we need to think about.

Thanks, Lori and Mike!

I'll try the package.