calibration file

[Alejandro Zuluaga]

Hi everyone

Looking at previous posts I saw that in the calibration file each calibration was assigned to a uniform (-U) or exponential (-E) distribution. However, in the most recent example file for the DPPPdiv software there is a -t for each one of the calibrations. There is also the options -exhp and -dphp that could be apply to the calibrated nodes, which is confusing for me.

What is the meaning of the -t? Can I still use -U and -E in the last version?

Thanks

Alejandro

[Tracy Heath]

Hi Alejandro,

The -t flag indicates that the time provided represents a fossil occurrence time and the referenced node is calibrated using the FBD model from Heath et al. 2014 (PNAS). The other options are for the hyperprior on exponential calibration densities described in Heath 2012 (Syst. Biol.). Actually -exhp and -dphp are slightly redundant. In that case, you should use -dphp. And the -E flag for the calibrations. 

Please let me know if any of this needs clarification.

Cheers!

Tracy

--
You received this message because you are subscribed to the Google Groups "dppdiv-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dppdiv-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.