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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
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Fixed rate relaxed molecular clock still generating upDownOperator on rate/ heights #461

Closed msuchard closed 9 years ago

msuchard commented 9 years ago

Originally reported on Google Code with ID 452

Create a relaxed clock in BEAUti without estimating the rate (i.e., fixed to 1.0). BEAUti
will generate:

<upDownOperator scaleFactor="0.75" weight="3">
  <up>
    <parameter idref="ucld.mean"/>
  </up>
  <down>
   <parameter idref="treeModel.allInternalNodeHeights"/>
  </down>
</upDownOperator>

So the rate will not remain constant.

Reported by rambaut on 2011-04-20 11:26:38

msuchard commented 9 years ago

Reported by rambaut on 2011-07-27 11:55:50

msuchard commented 9 years ago 
remove isEstimated variable from PartitionClockModel, and use rateParam.isFixed only.
But setEstimatedRate(boolean isEstimatedRate) has to set all clock rate parameters
create in PartitionClockModel, in order to keep isEstimatedRate() correct when changing
clock type. This is important for adding a new clock type in future;

Reported by dong.w.xie on 2011-11-22 02:40:03