Monday

Power in Phylogenies  Paper (PMC)

  • Working through / incorporated Graham’s edits
  • Added confidence intervals discussion
  • tweaks to associated pmc package
  • Exploring confidence intervals (and lack thereof) in literature on comparative methods.  Pagel (1999) (Pagel, 1999) includes them, but few other papers do.  He does not include any discussion about how these are calculated.
  • Seems Sweave makes sense for the recreate-figures code from the cached data-files, but perhaps not for the entire analysis code-base (in demos/).  A pity it isn’t easy to get syntax-highlighting output.

Also working on clean-up and reorganization of directory structure.

Aside: installed jetpack plugin, breaks flickr-gallery plugin unless video inclusion short-codes are disabled.  Removing jetpack brakes the API key for wp-stats, cannot seem to fix this, (says wrong API key, doesn’t match the install of wp-stats), so have gone back to jetpack.

References