Hi Krzysztof, It certainly can be true that the most credible shift configuration is one where there are no inferred rate shifts, but also prefer a model with one rate shift. The issue is mentioned in the BAMM documentation <http://bamm-project.org/rateshifts.html>
BAMM looks like it found evidence of a rate shift on your phylogeny. However, the exact location of that rate shift is not certain. In your plots, shift configuration #2 shows a rate increase on the upper clade, whereas #3 shows a rate decrease in the lower clade. #4 and #5 tell similar stories. Note that the configurations with 1 rate shift (#2-#5) combined are seen more often than configurations with 0 rate shifts (#1). Personally I'm unclear on how useful the most credible shift configuration actually is. To me that throws away a lot of the power of BAMM by reducing its inference down to a point estimate. Jonathan On Thu, Aug 14, 2014 at 5:08 PM, Krzysztof Kozak <kk...@cam.ac.uk> wrote: > Dear All, > > I have been asked to analyse my chronogram using BAMM, and I like the idea. > Sadly, I am puzzled by the output. I worked through the example and read the > entire documentation, but still don't grasp why different analyses suggest > different answers. > > 1. On one hand, several functions suggest that there are 1-2 rate shifts in > my data. > - Plotting netdiv rate shows it changing somewhat at two times. > - plot.bammdata(edata) shows increased rate on the branch leading to a > disproportionately large clade > - rescaling the branch lengths by the Bayes Factor of a rate shift > (bayesFactorBranches) also shows that branches leading to more speciose > clades are very long > - computeBayesFactors gives this output: > 0 1.0000000 0.2860509 0.2273844 0.3127353 0.3841264 1.091439 0.3605840 > 1 3.4958818 1.0000000 0.7949089 1.0932856 1.3428605 3.815542 1.2605592 > 2 4.3978396 1.2580058 1.0000000 1.3753596 1.6893262 4.799974 1.5857908 > 3 3.1975924 0.9146741 0.7270825 1.0000000 1.2282796 3.489977 1.1530008 > 4 2.6033098 0.7446790 0.5919520 0.8141469 1.0000000 2.841354 0.9387120 > 5 0.9162216 0.2620860 0.2083345 0.2865348 0.3519449 1.000000 0.3303749 > 7 2.7732786 0.7932987 0.6306002 0.8673021 1.0652895 3.026865 1.0000000 > > - simple summary of the posterior summary(edata) also favours models with > shifts > Shift posterior distribution: > 0 0.1800 > 1 0.4300 > 2 0.2800 > 3 0.0840 > 4 0.0240 > 5 0.0025 > 7 0.0005 > > 2. On the other hand, the plot of Credible Shift Sets always shows the model > with no shifts as most frequent (??? - an example is attached). > - ...and the best shift configuration is indeed without shifts, as checked > with > priorshifts <- getBranchShiftPriors(tree, prior) > best <- getBestShiftConfiguration(edata, prior, BFcriterion = 5) > > To summarise: I do not understand how it is possible to find substantial > Bayes Factors in support of a model with two rate shifts, and yet have the > model without shifts as the "best configuration". > I hope this is not too naive and I will appreciate any feedback. > > Best, > __ > Krzysztof "Chris" Kozak > PhD Candidate, Department of Zoology > University of Cambridge, CB2 3EJ > http://heliconius.zoo.cam.ac.uk/people/krzysztof-kozak/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
