On 18/01/2024, at 1:38 AM, Victor Lundström <lundstr...@gmail.com> wrote:
Hi everyone,I'm working my way through the steps found in this book chapter to produce a time-calibrated treeso that I can compare divergence events to palaeoclimatic events recorded in my study area (western norway):The data for the study can be found here: GitHub - erikgjes/Bayes_Phylogenies: Data and code associated with book chapter on Bayesian Phylogenies in ArchaeologyOn page 171, the authors present the results from 6 (out of 16) different models by assessingthe marginal likelihood score. Wanting to try something similar for my analysis, I decidedto replicate their top 6 models. However, since I can't get the path sampler app to work for some reason, I decided to simply rely on the likelihood score that is printed in the trace file (mean likelihood).Also, I produced a total of eight models: Model 1-4: Coalescent bayesian skyline with a strict clock and where the gamma category count starts with 1 model#1, 2 for model#2 and so forth.Model 5-8: Coalescent bayesian skyline with a relaxed exponential clock. The procedure forgamma category count was done in the same way as for models 1 to 4.From this procedure, and according to the author's reasoning (the highest likelihood score = best fit), my best model should be:Gamma category counts: 2Clock: Relaxed ExponentialPrior: Coalescent bayesian Skyline
<image.png>
Would this be a viable way weeding out the best fit model? I should also mentionthat this way of testing is biased to some extent since I haven't yet figured out what otherpriors I should try that allows me to use tip dates. CBS is the only one so far that works for me.
Best,
Victor
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On 19/01/2024, at 9:05 AM, Victor Lundström <lundstr...@gmail.com> wrote:
Hi Remco,
Oh no! Ah well, I was afraid my results had been achieved a little too easy.So how do I go about doing this in path sampler then.
Whenever I try to follow this tutorial: BEAST 2
I get this message, and nothing happens.
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Even if the prompt says ”path sampler finished in 0 seconds”?Thanks again for responding!/Victor
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