Collected notes from past few days

some writing, some exchange on prosecutor's fallacy, some ropensci, etc


  • some ropensci coordination
  • Adapt basic science abstract and broader impacts statement
  • some writing on notebook features draft
  • nonparametric writing!


  • nonparametric-bayes writing. Combining my generic position piece (beyond-mechanistic-models.Rmd) with the technical nonparametric-bayes writeup (nonparametric-bayes.Rmd) to get a more general-audience paper.
  • ropensci reviewing
  • Note: annoying feature of knitr’s purl: appears to generate valid “external” knitr code, but includes all options in comment headers instead of just the chunk names. This prevents “external” inclusion from identifying these chunks currectly. tangle (option in knit) appears not to generate any header at all. Maybe I’m missing something.

Prosecutor’s Fallacy Comments

  • Further exchanges with John over prosecutors fallacy. Some scratch writing for a potential reply piece.

Our discussion highlighted two potential test cases that would further demonstrate (or refute) that the critical slowing down we observed is an artifact – our ability to detect it in cases that do not transition (e.g. population of all cases reaching a certain excursion) in the original dynamics, and our ability to detect it in scenarios that do not involve transition dynamics at all. Running these two cases as

  • comment.Rmd – repeat the analysis using a generic threshold deviation rather than only populations that have crashed.
  • beer.Rmd – repeat analysis in which there is only a single stable point.

ugh, looks like libraries on zero haven’t been kept up. Some delays before production code will be running.


  • More writing
  • Assemble material for applied math club. Going with particle filtering (Ionides et. al. 2006) and the pomp vignette
  • ropensci reviewing


  • Sounds like exciting stuff happening a the #btpdf2 conference