Hi Elisa, 

The problem you're having with the EBSP may be due to the incorrectly indicated path to the plotEBSP.R script file. You should check if you actually have this file on your computer as it doesn't come with a standard BEAST2.x.x package when you download it from beast2.org (you can find this file on GitHub though). In case you can't find this script file on your computer, I've attached it here (see the plotEBSP.R file below). 

1) Save this script file to your analysis folder ("mystery-run" in the tutorial). This folder should also contain your EBSP.log file along with the rest of the output files from the mcmc run).

2) In R, set your working directory to "mystery-run" by either typing

>setwd ("indicate a path to the folder on your computer"), e.g.

> setwd ("C:/Users/OksanaV/BEAST.v2.4.1.Windows/BEAST/mystery-run")

or, in RStudio, you can just go to Session -> Set Working Directory -> Choose directory...and then navigate to the "mystery-run" folder on your computer.

3) Now you can use the source command to read plotEBSP.R file:

> source ("plotEBSP.R")

4) Plot your results:

> plotEBSP("EBSP.log", useHPD=FALSE, log="y")

Hope this helps.

Cheers,

Oksana

Hi Elisa, 

The problem you're having with the EBSP may be due to the incorrectly indicated path to the plotEBSP.R script file. You should check if you actually have this file on your computer as it doesn't come with a standard BEAST2.x.x package when you download it from beast2.org (you can find this file on GitHub though). In case you can't find this script file on your computer, I've attached it here (see the plotEBSP.R file below). 

1) Save this script file to your analysis folder ("mystery-run" in the tutorial). This folder should also contain your EBSP.log file along with the rest of the output files from the mcmc run).

2) In R, set your working directory to "mystery-run" by either typing

>setwd ("indicate a path to the folder on your computer"), e.g.

> setwd ("C:/Users/OksanaV/BEAST.v2.4.1.Windows/BEAST/mystery-run")

or, in RStudio, you can just go to Session -> Set Working Directory -> Choose directory...and then navigate to the "mystery-run" folder on your computer.

3) Now you can use the source command to read plotEBSP.R file:

> source ("plotEBSP.R")

4) Plot your results:

> plotEBSP("EBSP.log", useHPD=FALSE, log="y")

Hope this helps.

Cheers,

Oksana

What does "is not working" mean? There are lots of ways something can fail to work---it gives you a different plot than what you wanted, it makes an empty plot, it does nothing, it returns an error, etc. For any kind of programming question like this, it's hard for anyone to give advice unless you explain exactly what problem you experienced.