Comments (3)
I would suggest a longer run with a larger burn-in, and increase the thinning parameter (2nd MCMC in particular looks to have a lot of autocorrelation)
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That was fast !!
Thank you very much, I will give it a try and let you know how it goes :)
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Hello again,
I have been trying a lot of things since the last message... Now my runs converge. When I included all the populations of the hybrid zone, BGC identified only one population as hybrid (hybrid index of 0.5), and all the other populations as P1 (average 0.98 HI). So I ran it again with only the hybrid pop and I get the result attached.
FWH_FINAL_all_hiXphi_alphaAndBeta-2.pdf
I am not sure if everything ran normally. Do you have any idea what is happening here ?
Thanks
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Related Issues (17)
- Hybrid Index HOT 1
- Error with parsing alleles depth HOT 7
- Error HOT 9
- get_bgc_outliers error HOT 15
- Rename snps$crazy.a and snps$crazy.b to something more intuitive
- Rebuild docker image with updates to vcf2bgc.py HOT 1
- Fix run_bgc.sh estpost LnL file naming HOT 1
- run bgc error in docker HOT 3
- ClineHelpR R package conda install? HOT 1
- jinja2 HOT 2
- R function: combine_bgc_output HOT 2
- GSL error. HOT 2
- phiPlot visualization issue HOT 1
- Add vcf2bgc script
- vcf2bgc.py file HOT 6
- pafscaff HOT 6
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