lmaurits / BEASTling

A linguistics-focussed command line tool for generating BEAST XML files.
BSD 2-Clause "Simplified" License
20 stars 6 forks source link

log_params duplicates log entries. #236

Closed SimonGreenhill closed 5 years ago

SimonGreenhill commented 5 years ago
[admin]
basename = pano2
log_params = True

[MCMC]
chainlength = 500000

[languages]
monophyletic = True
exclusions = Nawa

[model pano]
data = pano-cldf/Wordlist-metadata.json
model = binaryctmc
gamma_categories = 10

Generates this logfile:

    <logger fileName="pano2.log" id="tracelog" logEvery="50" sort="smart">
      <log idref="prior" />
      <log idref="likelihood" />
      <log idref="posterior" />
      <log idref="birthRate.t:beastlingTree" />
      <log idref="birthRate.t:beastlingTree" />
      <log id="treeStats" spec="beast.evolution.tree.TreeStatLogger" tree="@Tree.t:beastlingTree" />
      <log idref="clockRate.c:default" />
      <log idref="gammaShape.s:pano" />
    </logger>

(note duplicate birthRate.t:beastlingTree)

lmaurits commented 5 years ago

Thanks for the report! This probably crept in with the switch to a more flexible tree prior system.