Catching up

Catching up on notebook entries for last week and the beginning of this week in one go here. In the process of wrapping up a variety of older projects, so this is kinda all over the place.


  • Create function table,
  • finalize functions
  • Add support for references. Done, see getRefs. (And isn’t it awesome that you can link to a specific linenumber (i.e. line 280) in github by adding #L280 to the end of the url?)
  • Picked up some great grep tools in the process thanks to stackoverflow: handling empty matches and multiple matches
  • No luck in setting templates for pandoc’s conversion to word. Should be possible with --reference.docx but no luck. (meanwhile, who knew .docx and .odt were just zip archives you could unzip and poke around the xml? Unfortunately styles.xml is a bit opaque to me).


  • Replace all sapply calls with dedicated functions
  • Table of functions
  • Simplify presentation
  • markdownify the Sweave file.

Prosecutor’s fallacy

  • Running examples


  • Collecting, organizing and selecting examples into knitr format from demo files.


  • Duncan is running a brown bag seminar on big data computing. We’re coordinating all material over on github.


  • Write ievobio proposals
  • prsb review – Done.
  • Experimenting with a Jekyll based site using CSS from twitter-bootstrap.
  • Coordinating Academic Publishing panel discussion

Misc code tricks

ruby versions can drive you nuts sometimes.