Thursday

Mostly working on manuscript revisions throughout this week.  Haven’t really learned to integrate this workflow into the notebook.  In some ways it makes more sense not to, as it interrupts the flow of the research description.  But then it looks like I’m not doing anything when I have nothing meaningful in the entry.  Perhaps I should just put a heading saying “Writing.”

Morning’s reading:  Reproducible Research

  • Victoria Stodden highlights the Journal of Biostatistics approach to Reproducible Research.  They have an Associate Editor of reproducibility who marks published papers with D, C, and/or R to indicate that they include all the data, all code, or an R if the AER successfully executes the code on the data to reproduce the results.(Peng, 2009).  The system is purely optional, but visible which papers do and do not attempt to comply.  For instance, the image shows an example of a paper making the R stamp(Lee et. al. 2009)

Other work

  • Discussing web platforms for student2student program with Nick & Sarah – a website to help connect K12 teachers and with graduate student outreach efforts.

Writing and Revisions

  • Received Peter’s revisions for phylogenetics manuscript.  Peter was able to grab the manuscript from git, make his edits and send me a git link to his repository, and I could easily merge the changes into my copy.  Would be better if I used more line-breaks, rather than writing each paragraph without a linebreak, since the diff files display line-by-line changes.  But otherwise, a very smooth process.
  • Capturing workflow on the manuscript is better done through the git log then through the notebook, i.e. for this paper:

References