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ropensci / babette

babette is an R package to work with BEAST2
https://docs.ropensci.org/babette
GNU General Public License v3.0
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Doubling of clockPrior ID #94

Closed richelbilderbeek closed 3 years ago

richelbilderbeek commented 3 years ago

Follow-up from #93:

Thanks @GaryNapier for this report.

111988076-eb153680-8b07-11eb-8062-46c2ce0a7a7a

richelbilderbeek commented 3 years ago

Here is the problem, from the error issue_94.txt

<distribution id="posterior" spec="util.CompoundDistribution">
    <distribution id="prior" spec="util.CompoundDistribution">
        <distribution id="YuleModel.t:THAILAND_TEST.clust_1.dated" spec="beast.evolution.speciation.YuleModel" birthDiffRate="@birthRate.t:THAILAND_TEST.clust_1.dated" tree="@Tree.t:THAILAND_TEST.clust_1.dated"/>
        # ...
        <prior id="ClockPrior.c:THAILAND_TEST.clust_1.dated" name="distribution" x="@clockRate.c:THAILAND_TEST.clust_1.dated">
            <Uniform id="Uniform.150" name="distr" upper="Infinity"/>
        </prior>
        # ...
        <prior id="ClockPrior.c:THAILAND_TEST.clust_1.dated" name="distribution" x="@clockRate.c:THAILAND_TEST.clust_1.dated">
            <LogNormal id="LogNormalDistributionModel.0" name="distr">
                <parameter id="RealParameter.0" estimate="false" name="M">1</parameter>
                <parameter id="RealParameter.1" estimate="false" lower="0" name="S" upper="Infinity">1.25</parameter>
            </LogNormal>
        </prior>
    </distribution>
</distribution>
richelbilderbeek commented 3 years ago

This Issue appears fixed.

richelbilderbeek commented 3 years ago

I predict due to test at https://github.com/ropensci/beastier/commit/c18fd28a7d618a1aab323bf3ac3b895f5c629f64 that this is fixed.

richelbilderbeek commented 3 years ago

I predict due to test at https://github.com/ropensci/beastier/commit/c18fd28a7d618a1aab323bf3ac3b895f5c629f64 that this is fixed.

GaryNapier commented 3 years ago

Thanks Richel, I will test soon.

GaryNapier commented 3 years ago

Thanks Richel, I think this has worked! No errors when I run my original code from my previous issue.

richelbilderbeek commented 3 years ago

Awesome! Thanks so much for checking my work!

Happily closing this Issue :+1: