CompEvol
Tip dating tutorial on beast2.org and in beast2 release
There was quite a demand at #TamingTheBEAST workshop for estimating tip dates. We should provide a tutorial dedicated to this task. Currently there is only this page (http://beast2.org/2015/06/09/sampling-tip-dates/) and while the explanation for XML editing is correct, the BEAUti solution described on that page doesn't work.
The tip dating tutorial could use the Dengue data set or the RSVA data set and just pretend that one tip has an unknown date.
After 6bc01816182d9a54ae58c34fc42b978a901fedc8 it should now be simply a matter of
- specifying a MRCAPrior on the tip (with a 'clade' containing the tip) .
- check the tipsonly checkbox in BEAUti.
- specify a prior distribution on the tip.
It would be nice if there was some way to read information in from text file or nexus. I have data sets with hundreds of tips to be estimated.
On 25/07/2016, at 8:34 AM, Remco Bouckaert [email protected] wrote:
After 6bc0181 it should now be simply a matter of
specifying a MRCAPrior on the tip (with a 'clade' containing the tip) . check the tipsonly checkbox in BEAUti. specify a prior distribution on the tip. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or mute the thread.
The NexusParser already supports this: if you add a block
begin assumptions; calibrate taxon1 = lognormal(1,2) calibrate taxon2 = uniform(2,3) end;
two MRACPriors will be created, one for taxon1 and one for taxon2, and both will be accompanied by a TipDatesRandomWalker for sampling these tips. Just realised that the tipsOnly flag is not set when this happens, so will fix that.
