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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

Reproduce:

    bbt_run(
      fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
      site_models = create_hky_site_model(),
      mcmc = beautier::create_mcmc(chain_length = 2000)
    )

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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024
Error 124 parsing the xml input file

Failed to set the string value to 'Inf' for beastobject id=RealParameter.2

Error detected about here:
  <beast>
      <run id='mcmc' spec='MCMC'>
          <distribution id='posterior' spec='util.CompoundDistribution'>
              <distribution id='prior' spec='util.CompoundDistribution'>
                  <prior id='KappaPrior.s:anthus_aco' name='distribution'>
                      <LogNormal id='LogNormalDistributionModel.1' name='distr'>
                          <parameter id='RealParameter.2' name='S'>

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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

I think the line after gives the problems:

<parameter id="RealParameter.2" estimate="false" lower="0" name="S" upper="Inf">1.25</parameter>

Solution: replace Inf by Infinity

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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

I think this is fixed!

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