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processValues[] in DiscreteTraitBranchRateModel should be size of the number of states NOT the number of rates #325

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
processValues[] in DiscreteTraitBranchRateModel should be size of the number of 
states NOT the number of rates

double[] getProcessValues(final Tree tree, final NodeRef node)

Original issue reported on code.google.com by dong.w.xie@gmail.com on 7 Jul 2010 at 10:47

GoogleCodeExporter commented 9 years ago 
solution:

add  <dataType idref="???" />  in the xml to get data type and then 
getStateCount().

example xml H5N1_HA_discrete_traits.xml available in 
trunk\examples\Phylogeography 

    <discreteTraitRateModel id="branchRates">
        <treeModel idref="treeModel"/>

        <ancestralTreeLikelihood idref="geoTreeLikelihood"/>
        <dataType idref="geography"/>

        <!--<attributePatterns idref="geoPatterns"/>-->
        <rate>
            <parameter id="trait.rates" value="1 1 1 1 1 1 1"/>
        </rate>
    </discreteTraitRateModel>

Original comment by dong.w.xie@gmail.com on 7 Jul 2010 at 11:06

GoogleCodeExporter commented 9 years ago

Original comment by dong.w.xie@gmail.com on 7 Jul 2010 at 11:08