Birth Death Skyline Serial tutorial different from BEAUTi 2.1.3

[Nick Matzke]

Hi,

I'm working through the BDSKY tutorial here:

http://bdssm-beast2.googlecode.com/files/bdsky_tutorial.pdf

On page  4, the figure indicates that "Interval Number" should be an option once "Birth Death Skyline Serial" is selected as the tree prior in the priors panel.

However, I'm looking at BEAUTi 2.1.3, which I downloaded and installed today.  I loaded some DNA and tip dates, and then selected "Birth Death Skyline Serial" -- but no "Interval Number" line appears.  The other parameters appear just fine, as in the figure.

Any insight would be appreciated!  

Cheers!

Nick

[Denise]

Dear Nick,

You are right, we've removed the intervalNumber input in the newest version. You now specify the number of intervals simply by setting the dimension of the BDSKY parameters. The reason for this is that you can have different numbers of changes for the different parameters. For example R0 can have dimension 10, and the sampling proportion dimension 2. This is the setup we used in the PNAS paper to set the sampling rate to 0 before the time of the first sample. (However, if you want to fix the time of a rate change you'll need to do some XML file hacking. I'm happy to help if you'd like to do that.)

Thank you for pointing this out, I'm afraid I forgot to change it in the tutorial. I'll change it asap. Please note that we've moved to Github, so you'll find the new version there: https://github.com/BEAST2-Dev/bdsky.

Best

Denise

[Nick Matzke]

Thanks for this Denise!!!

Nick

[Denise]

Dear Nick,

Here's the updated tutorial: https://github.com/BEAST2-Dev/bdsky/blob/d6c528aa5beed1badcb3d0607efd153ab6086c6d/doc/bdsky_tutorial_2.1.1.pdf?raw=true

Best,

Denise