a few notes on various projects

warning-signals

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:

methods(class="gfit")

Returns:

[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.

knitcitations

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…

Reading

The debates continue: Szuwalski (2013) , and the reply Vert-pre et. al. (2013) , reflecting confusion over the article earlier this year, Vert-pre et. al. (2013b) .
Disupting the claim of Ditlevsen & Johnsen (2010) and others, Cimatoribus et. al. (2013) argue that DO events do show warning signals. But are they chance transitions then?
Looking over Lenton (2011) , which has a review of some of the evidence against warning signals for noise-induced transitions.
An even earlier result from Ludwig, in Ludwig (1975) .

References

A. A. Cimatoribus, S. S. Drijfhout, V. Livina, G. van der Schrier, (2013) Dansgaard-Oeschger Events: Bifurcation Points in The Climate System. Climate of The Past 9 323-333 10.5194/cp-9-323-2013
Peter D. Ditlevsen, Sigfus J. Johnsen, (2010) Tipping Points: Early Warning And Wishful Thinking. Geophysical Research Letters 37 n/a-n/a 10.1029/2010GL044486
Timothy M. Lenton, (2011) Early Warning of Climate Tipping Points. Nature Climate Change 1 201-209 10.1038/nclimate1143
Donald Ludwig, (1975) Persistence of Dynamical Systems Under Random Perturbations. Siam Review 17 605-640 10.1137/1017070
C. Szuwalski, (2013) Production is A Poor Metric For Identifying Regime-Like Behavior in Marine Stocks. Proceedings of The National Academy of Sciences 110 E1436-E1436 10.1073/pnas.1301759110
K. A. Vert-pre, R. O. Amoroso, O. P. Jensen, R. Hilborn, (2013) Reply to Szuwalski: Policies Robust to Uncertainty in Causes of Productivity Changes Are Needed. Proceedings of The National Academy of Sciences 110 E1437-E1437 10.1073/pnas.1302181110
K. A. Vert-pre, R. O. Amoroso, O. P. Jensen, R. Hilborn, (2013) Frequency And Intensity of Productivity Regime Shifts in Marine Fish Stocks. Proceedings of The National Academy of Sciences 110 1779-1784 10.1073/pnas.1214879110