reproducible-science-curriculum/rr-init

Research project initialization and organization following reproducible research guidelines

rr-init's Issues

references folder

This looks great! I think it might be good to add a references or refs folder. For genomics/microbial ecology project we often use references to map our data against or for classifying sequences. We find it is helpful to have all of those references in a single place.

Output directory for knitr can only be set as function argument

If we want the top-level .Rmd file to be rendered to the doc/paper directory, then this output directory needs to be configurable as an option. However, apparently it isn't; only the directory for figure output can be set. This means that rendering the Markdown, HTML, LaTeX, and PDF versions need to be executed as rmarkdown::render() so that the output path can be passed as an argument. That the "Knit HTML" button is not to be used is likely rather undesirable for practical use and teaching purposes.