Precision dating for BEAST 2.x

[walterxie]

Hey,

I mean the precision dating present in BEAST 1.8 i.e. lets say I have a tip date labeled only as 2007 - if I set the precision of this date as "1" and the time is in years than precision dating uniformly samples across 2007, thus taking into account a lack of sampled precision. Or, if I have a date of February 2007 than I could set the precision as "0.83" to sample dates uniformly across the month of February.

Before BEAST 1.8 this could be set manually in the XML (see below), and I am curious if the same way would work for BEAST 2.x

https://groups.google.com/forum/#!topic/beast-users/jSh7FfsQd6U

Thanks. Brian Muchmore

On Tue, Aug 26, 2014 at 5:04 PM, Remco Bouckaert wrote: Hi Brian,

I am not quite sure what you mean by "precision dating", but you sure can use BEAST 2.x for dating, for instance by adding calibrations on clades (use the + button in the prior panel in BEAUti to add such a calibration) or by specifying tip dates (in the tip-dates panel in BEAUti).

Hope this helps,

Remco

[walterxie]

@tgvaughan @rbouckaert @alexeid Hi, Tim,

I read the code today, it looks we already have the most ability to do "precision dating", but using a different way to BEAST 1:

http://www.beast2.org/2015/06/09/sampling-tip-dates.html

Just simply use the uniform prior for the taxon set having one tip only, and set its bound according to the uncertainty calculated by a similar method as BEAST 1 Date.getUncertainty(). This only needs to add a new precision attribute in TraitSet (maybe?) for XML. The rest will be same as "tip date sampling".

Cheers, Walter

[walterxie]

@tgvaughan I did not realise the XML had been completed, for example, testTipDates.xml:

<distribution id="tipDates" monophyletic="false" spec="distributions.MRCAPrior" tipsonly="true" tree="@tree">
  <taxonset id="TaxonSet0" spec="TaxonSet">
     <taxon id="D4PRico86" spec="Taxon"/>
  </taxonset>
  <distr id="Uniform0" lower="1985" offset="0.0" spec="distributions.Uniform" upper="1986"/>
</distribution>

if you change D4PRico86=1985.5 in trait, then it will be a "precision dating" case for year 1985. Therefore, it is only matter of BEAUti work.