Error: theta=0 for a population.

[thomlmarshall]

Hi,
I'm trying to run a JML analysis using a posterior distribution of species trees from a SNAPP analysis and am receiving the message in the subject line. I'm not sure where to begin trouble shooting this issue and would love some advice. Thanks!

[thomlmarshall]

Looking at the closed issue with the same error, I think the problem is likely with my species tree file, but the issue is not exactly the same as the other poster. I think it might have something to do with the fact that this was produced by SNAPP, so the file doesn't look exactly the same as the example file. However, I know other researchers have successfully run JML with output from SNAPP before.

Here's one line from my SNAPP tree file:
tree STATE_1000 = (((1[&theta=0.9258947026388666]:0.22681223439637357,2[&theta=0.5181684707622859]:0.22681223439637357)[&theta=0.036620503659802926]:0.05450876905468113,4[&theta=0.5316237757479166]:0.2813210034510547)[&theta=6.151864170328203E-4]:0.04290150034532669,3[&theta=0.3282678525915308]:0.3242225037963814)[&theta=0.0076172597914220125]:0.0;

[simjoly]

Looking rapidly, I think it might have to do with the format of your tree. The code for the population size in your tree file is "&theta", whereas it seems that the program recognizes "&dmv" as the code for the population size. Can you do a search and replace and change the "&theta" for "&dmv" in your tree file and see if it solves the problem?

Note that comparing a species tree estimated with SNAPP might be tricky as getting a relative evolutionary rate for the simulation might not be easy.