Operator for supporting negative values

[walterxie]

From Alexei:

While looking at the LPhyBEAST code with Sebastian Hoehna we noticed that there is a bug for RealParameters in the DefaultOperatorSchedule. If the parameter comes from a Normal or Laplace distribution (or any distribution with support in negative values) the it should have a RandomWalkOperator instead of a ScaleOperator.

[walterxie]

LinguaPhylo/linguaPhylo#526

[walterxie]

I think it is solved :

Θ ~ Normal(mean=3.0, sd=1.0); now produces:

<distribution id="Theta.prior" spec="distribution.Prior" x="@Theta">
     <distr id="Normal" spec="distribution.Normal">
            <parameter id="RealParameter1" spec="parameter.RealParameter" name="mean">3.0</parameter>
            <parameter id="RealParameter2" spec="parameter.RealParameter" name="sigma">1.0</parameter>
     </distr>
</distribution>

...

<operator id="Theta.randomWalk" spec="operator.kernel.BactrianRandomWalkOperator" parameter="@Theta" scaleFactor="0.75" weight="1.0"/>

[alexeid]

Should there be a scale factor for a random walk? I thought it should be window size?

[walterxie]

BactrianRandomWalkOperator uses scale factor https://github.com/CompEvol/beast2/blob/master/src/beast/base/inference/operator/kernel/BactrianRandomWalkOperator.java . I have emailed Remco, and will let you know after he replies.

[walterxie]

CompEvol/beast2#1169

[walterxie]

close this for new release. create #165 to remind updating after beast2 new release.