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rambaut / beast-mcmc

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Fixed rate relaxed molecular clock still generating upDownOperator on rate/ heights #452

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
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.

Original issue reported on code.google.com by ramb...@gmail.com on 20 Apr 2011 at 11:26

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 27 Jul 2011 at 11:55

GoogleCodeExporter 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;

Original comment by dong.w.xie@gmail.com on 22 Nov 2011 at 2:40