nonparametric-bayes: framing the issues for the manuscript

Marc meeting: nonparametric-bayes manuscript

Very good meeting today going over some big picture considerations in the presentation of the nonparametric-bayes manuscript with Marc. (Also see new entries in issues log on nonparametric-bayes.) Make it clear that we are making a point rather than providing a tool. Focus on the tipping point context rather than the general management context.

  • Comparison against a parametric Bayesian model (40)
  • Comparison against an active learning parametric model facing a tipping point (41)

Parametric Bayesian model

Drafting parametric Bayesian case for comparison, following Marc’s suggestion. So far, code as implemented in BUGS

More on the exit time problem

Warning signals Reading

  • Alan pointed out Boerlijst et. al. (2013) on warning signals in PLoS ONE today. A very nice piece! It’s quite useful how it show that the early warning signal can appear in unmonitored variables (e.g. juvenile dynamics) or in variables without adequate noise to provide a signal. Kind of funny that they pitch it as a counterexample to the conjecture that early warning signals are universal, since even Scheffer has avoided that word, and it’s not really a counterexample given the caveat of some process noise and complete observability of the system people have so far assumed (while your work with Derin is a more conclusive counter-example by going beyond fold bifurcations)… Anyway, good examples. We need a better understanding of warning signals in this multi-dimensional context at large.

  • Recently Noam pointed out Streeter & Dugmore (2013) , which looks like a nice spatial warning signal example (with the classic patterns, rather than the Bel et. al. (2012) pattern), but haven’t had time for a closer read yet.

Other reading

  • Trying to get a hold of Ludwig & Walters (1981) as well. A tough day for reading with the UCSC subscription access down due to “power outages”

  • Interesting preprint on advice for data reuse, White et. al. (2013)

Misc and code-tricks

  • My knitr scripts are not executing in parallel with snow/snowfall packages(?) Parallelizes fine when run chunk by chunk. (e.g. example with snowfall). Knitr runs parallel fine with multicore. Weird.

  • An interesting puzzle on knitr list today: wrangling crazy ascii tables in Hmisc::summary.function. A good solution would just rewrite the class’s print method to be a table object (e.g. compatible with xtable and pander::pandoc_table), but instead we can hack the ascii, adjusting the options that are passed to print.char.matrix:

  • Created a PURL persistent identifier for the notebook Existing public top level domain. Waiting for approval for my own top-level domain (cboettig).

df = data.frame(Age = round(rnorm(100, 50,15)), Sex = rep(c("M", "W")))
out <- summary.formula( ~ Age + Sex, data = df, method = "reverse")
print(out, hsep= '|', csep='|', vsep='-', left.border=FALSE, top.border=FALSE)


  • Golan Bel, Aric Hagberg, Ehud Meron, (2012) Gradual Regime Shifts in Spatially Extended Ecosystems. Theoretical Ecology 5 591-604 10.1007/s12080-011-0149-6
  • Maarten C. Boerlijst, Thomas Oudman, André M. de Roos, Ricard V. Solé, (2013) Catastrophic Collapse Can Occur Without Early Warning: Examples of Silent Catastrophes in Structured Ecological Models. Plos One 8 e62033-NA 10.1371/journal.pone.0062033
  • Donald Ludwig, Carl J. Walters, (1981) Measurement Errors And Uncertainty in Parameter Estimates For Stock And Recruitment. Canadian Journal of Fisheries And Aquatic Sciences 38 711-720 10.1139/f81-094
  • Zeev Schuss, Bernard J. Matkowsky, (1979) The Exit Problem: A New Approach to Diffusion Across Potential Barriers. Siam Journal on Applied Mathematics 36 604-623 10.1137/0136043
  • R. Streeter, A. J. Dugmore, (2013) Anticipating Land Surface Change. Proceedings of The National Academy of Sciences 110 5779-5784 10.1073/pnas.1220161110
  • Ethan White, Elita Baldridge, Zachary Brym, Kenneth Locey, Daniel McGlinn, Sarah Supp, (2013) Nine simple ways to make it easier to (re)use your data. PeerJ PrePrints
  • Donald Ludwig, (1981). Escape from Domains of Attraction for Systems Perturbed by Noise, Nonlinear Phenomena in Physics and Biology.