# 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

## 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.

• 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 purl.org/globalecology/lab-notebook. Existing public top level domain. Waiting for approval for my own top-level domain (cboettig).

library(Hmisc)
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)

## References

• 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 https://peerj.com/preprints/7
• Donald Ludwig, (1981). Escape from Domains of Attraction for Systems Perturbed by Noise, Nonlinear Phenomena in Physics and Biology.