Tip dating tutorial on beast2.org and in beast2 release

[alexeid]

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.

[alexeid]

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.

[rbouckaert]

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.

[alexeid]

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 notifications@github.com 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.

[rbouckaert]

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.

[walterxie]

related to #208