I want to use BEAST to do EBSP analyses with two loci. I open two "input.nex" files in BEAUti to generate a "output.xml" file (In the Trees panel select Extended Bayesian skyline plot for the tree prior), and then run BEAST. I do not know if this is right and I do not know what to do next. I can not construct the trend of demographic history in Tracer just like BSP. I got one log file but two trees files (for each locus), and I do not know how to import both tree files into Tracer.
Dear Jingjing,
If you want to look over your trees you need to open then in TreeAnnotator, to perform the burning and then you can open the treefiles using Figtree. Tracer will show yoou the performance of MCMC only.
Hope it helps,
M
This problem has been solved.
http://scholar.google.co.nz/scholar?oi=bibs&hl=en&cluster=9003460531033052764
Hi, Jingjing,
I have the same problem. But I can not open the Hyperlink. Can you tell me how to do it ? Thanks.
Hi Aslı Şalcıoğlu,
I've attached the R script of plotting EBSP named 'plotEBSP.R'.
1) Save this script file to your analysis folder (i.e. test). This folder should also contain the EBSP.log file along with the rest of the output files from the mcmc run).
2) In R, set your working directory to the folder contained 'plotEBSP.R'
3) Use the source command to read plotEBSP.R file:
> source ("plotEBSP.R")
4) Plot the results of EBSP analysis:
> plotEBSP("EBSP.log", useHPD=FALSE, log="y")
Hope this is helpful.
All the best,
Fangluan
But this script is used for EBSP plot in BEAST 2.4.8. I want to make EBSP plot for BEAST 1.8.3. with csv files?
Fangluan Gao I have made BSP analysis through tracer using beast2.6.1, and exported the plot data, now i want to make BSP figure in R studio. if you have script kindly provide me. Also i want to make multiple BSP results in a single plot.
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