pakillo / template Goto Github PK

• https://github.com/stephlocke/pRojects
• https://rstudio.github.io/rstudio-extensions/rstudio_project_templates.html
• https://github.com/benmarwick/researchcompendium
• https://github.com/lwjohnst86/prodigenr
• https://github.com/jdblischak/workflowr

makefile.R by now, just rendering Rmarkdown documents in appropriate order, or running R scripts, or calling functions (e.g. read data, make_figures, etc)

Hello,

This is a really good idea (i.e. using R packages to facilitate reproducibility) and I have been doing this for sometime. I would like to suggest an additional step and that is being able to replicate R version and package versions since, obviously, changes in package code/functions overtime can break your analysis code. Ideally we would be able to set a R and package version in the DESCRIPTION file, and I can remember some rather recent discussion concerning this on the Bioconductor Developer mailing list, but, as far as I understood, this is not possible at the moment (probably stemming from the fact that, even though they are a practical solution, R packages were not thought to serve the purpose we want to use them for). I have recently resolved this using the liftr package and docker. I made a 'quick and dirty' example at reproducibleAnalysis for you to have a look at if you would like. I don't know if this is the best solution but it may be a starting point to work from. Id also be glad to hear any comments you might have!

Kind Regards,
Jason

I really like this template and have learned a lot by studying its organisation.

Do you have an example of this template being used for a real-world report or publication?

From the README:

Write a makefile or master script to organise and execute all parts of the analysis.

The drake R package is like Make, but for R-focused data science projects. It is not in the reproducibility guide you mentioned, but it is part of rOpenSci.

My blog posts moved:

http://rmflight.github.io/post/analyses-as-packages/

Thanks!

-Robert

https://github.com/RMHogervorst/badgecreatr