Tree prior:Coalescent :Bayesian Skyline. what does "Number of groups" mean ?
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hy zheng
Jul 28, 2019, 5:50:10 AM7/28/19
to beast-users
I should choose the Tree prior:Coalescent :Bayesian Skyline.But I do not know what does "Number of groups" mean,can anybody tell me? Thanks !!
韦杰鸿
Jul 30, 2019, 2:58:55 AM7/30/19
to beast-users
As far as I know, number of groups represent number of coalescent events you want captured in your analyses. If your studied populations have many coalescent event, increasing number of groups will help you to get more details on demographic dynamics. But more groups sometimes lead to lower ESS and require longer chain length to reach sufficient convergence. https://taming-the-beast.org/tutorials/Skyline-plots/
在 2019年7月28日星期日 UTC+8下午5:50:10，hy zheng写道：
在 2019年7月28日星期日 UTC+8下午5:50:10，hy zheng写道：
hy zheng
Jul 30, 2019, 2:27:37 PM7/30/19
to beast-users
Thank you very very much!
在 2019年7月30日星期二 UTC+8下午2:58:55，韦杰鸿写道：
在 2019年7月30日星期二 UTC+8下午2:58:55，韦杰鸿写道：
Ренат Адельшин
Aug 5, 2019, 2:27:56 AM8/5/19
to beast-users
That is the number of coalescent intervals (intervals between internal nodes on the tree). In each interval Skyline finds an effective population size (as a mean of exp. distribution) and unites them in a single plot. If your tree is not informative enough the trace will have a bad convergence during MCMC (or just doesn't converge at all). You also can find precision number of intervals by Extended Bayesian Skyline.
воскресенье, 28 июля 2019 г., 17:50:10 UTC+8 пользователь hy zheng написал:
воскресенье, 28 июля 2019 г., 17:50:10 UTC+8 пользователь hy zheng написал:
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