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richelbilderbeek / Cer2016

Community Ecology Research course 2016
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Tuning operators #122

Closed richelbilderbeek closed 7 years ago

richelbilderbeek commented 8 years ago

This is part of the testthat.log file after a Peregrine cluster run. One can see that BEAST2 suggests to tune parameters itself.

Operator                                                     Tuning    #accept    #reject      Pr(m)  Pr(acc|m)
ScaleOperator(treeScaler.t:article_1_3_2_1_1_2_2_2)          0.5000         21        452     0.0385     0.0444 Try setting scaleFactor to about 0.707
ScaleOperator(treeRootScaler.t:article_1_3_2_1_1_2_2_2)      0.5000         25        443     0.0385     0.0534 Try setting scaleFactor to about 0.707
Uniform(UniformOperator.t:article_1_3_2_1_1_2_2_2)                -       1271       3223     0.3846     0.2828 
SubtreeSlide(SubtreeSlide.t:article_1_3_2_1_1_2_2_2)         1.0000         28       2278     0.1923     0.0121 Try decreasing size to about 0.5
Exchange(narrow.t:article_1_3_2_1_1_2_2_2)                        -        498       1842     0.1923     0.2128 
Exchange(wide.t:article_1_3_2_1_1_2_2_2)                          -         17        442     0.0385     0.0370 
WilsonBalding(WilsonBalding.t:article_1_3_2_1_1_2_2_2)            -         34        472     0.0385     0.0672 
ScaleOperator(BirthRateScaler.t:article_1_3_2_1_1_2_2_2)     0.7500        270        195     0.0385     0.5806 Try setting scaleFactor to about 0.562
ScaleOperator(DeathRateScaler.t:article_1_3_2_1_1_2_2_2)     0.7500        337        153     0.0385     0.6878 Try setting scaleFactor to about 0.562

     Tuning: The value of the operator's tuning parameter, or '-' if the operator can't be optimized.
    #accept: The total number of times a proposal by this operator has been accepted.
    #reject: The total number of times a proposal by this operator has been rejected.
      Pr(m): The probability this operator is chosen in a step of the MCMC (i.e. the normalized weight).
  Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator).

Total calculation time: 8.136 seconds
End likelihood: -144444.49417535294

Steps are:

richelbilderbeek commented 7 years ago

This issue was moved to richelbilderbeek/wiritttes#1