a few notes on various projects


  • Working on revisions for ews-review
  • Grr, the challenges of open science – can’t stick confidential reviews in ews-review repo where they belong, or track them on the issues tracker, without disclosing their contents. What are the terms of use for these things anyhow>

phylogentics / pmc

  • Apparently pmc does have users – at least one recognized that my Vignette is broken following the latest Gieger update. Need to add simulate and update methods for the new fitContinuous, and then integrate these. pmc/#3
  • Another pmc request. Sounds like I should also add support for OUwie fits. See if I can get Jeremy to add simulate and update methods. pmc/#4

Dear phylogeneticists: please define a methods API for your functions. Accessing coefficients using something like output[[1]][[2]]$somevar$name[4] is not only cumbersome, but bound to break when you modify your function, so provide a coef method. Likewise provide simulate and update methods so we can all raise the bar on our statistics a little bit.

Alternatively put the code on Github, where sensible folks can fork it, add some common-sense classes and give you a pull request.

Code tricks

Because I’m always wondering how to do this one: let’s see what methods are defined for Geiger’s new gfit class:



[1] coef.gfit*   logLik.gfit*

   Non-visible functions are asterisked

ht Michael Hannon for that one, and a good way to confuse some folks on SO.


  • Fixed a minor issue in tooltip formatting, knitcitations/#37. Unfortunately not updated in earlier notebook entires, but should be fixed from here on).
  • Interesting ideas from some folks about adding CSL support, and thinking about being able to pull data into knitcitations from personal zotero libraries, knitcitations/#38. Zotero API seems to have some nice features for listing entries of a collection in a variety of file formats, including CSL styling for the returns.
  • Nearly a month since last push (0.4-4). Should update CRAN to current development version (0.4-6) sometime this week…



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