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[Bioc-devel] project templating tools

3 messages · Vincent Carey, Nima Hejazi, Michael Lawrence

Original
Nima Hejazi
# 
Hello ---

I have quite a bit of experience with using the ProjectTemplate package, as
I rely on it for most of my applied work in R -- that is, nearly everything
not related to package development (e.g., applied data analysis for
collaborators, simulation studies, etc.). I've found that it provides a
user-friendly layout and robust system for managing how I structure
projects in a way that is accessible to my collaborators (before
discovering ProjectTemplate, I used a handcrafted layout that was obviously
less portable and less well-maintained). I've always heard good things
after recommending it to collaborators.

While I've developed a handful of packages on Bioconductor and CRAN, I'm
not sure I'm able to comment on workflow construction/authoring practices
in a manner sufficient to be useful in answering your underlying question.
Please let me know if I can comment further. Hope this helps.

Warm Regards,
? Nima Hejazi

--
Nima Hejazi
Doctoral Student
Group in Biostatistics <https://www.stat.berkeley.edu/biostat/>
University of California, Berkeley
van der Laan Group <https://www.stat.berkeley.edu/~laan/> | nimahejazi.org
stat.berkeley.edu/~nhejazi <https://www.stat.berkeley.edu/~nhejazi> | Nima's
blog <https://blog.nimahejazi.org/>

On Sun, Jan 21, 2018 at 4:27 AM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

  
  


  


      

    

    

      
      

        


  

        

      Michael Lawrence
    

    

      
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I have always just advocated using R packages as a means to organize
analyses, with an "analysis" subdirectory serving as a sort of scratch
space. The DESCRIPTION serves as a readme, there are places for reusable
functions (/R), data (/data), reports (/vignettes), etc. Several groups
here follow that pattern.

Michael

On Sun, Jan 21, 2018 at 4:27 AM, Vincent Carey <stvjc at channing.harvard.edu>
wrote: