Comments (2)
Cite path sampling (Lartillot and Philippe, 2006) to beast.inference.PathSamplingStep
and beast.inference.PairedPathSamplingStep
.
Cite generalized stepping-stone sampling (Fan et al., 2011) to beast.gss.GeneralisedSteppingStoneStep
.
The fix will be available after a new release.
from model-selection.
After the new release, it will show:
====== Package 24 : MODEL_SELECTION ======
Load classes from : ~/Library/Application Support/BEAST/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar
beast.gss.GeneralisedSteppingStoneStep
Xie, W., Lewis, P. O., Fan, Y., Kuo, L., & Chen, M. H. (2011).
Improving marginal likelihood estimation for Bayesian phylogenetic model selection.
Systematic biology, 60(2), 150-160.
10.1093/sysbio/syq085
Description : Calculate marginal likelihood through generalised path sampling for a single step
beast.inference.PairedPathSamplingStep
Lartillot, N., & Philippe, H. (2006).
Computing Bayes factors using thermodynamic integration.
Systematic biology, 55(2), 195-207.
10.1080/10635150500433722
Description : Calculate marginal likelihood through path sampling for a single step when comparing two models
beast.inference.PathSamplingStep
Lartillot, N., & Philippe, H. (2006).
Computing Bayes factors using thermodynamic integration.
Systematic biology, 55(2), 195-207.
10.1080/10635150500433722
Description : Calculate marginal likelihood through path sampling for a single step
Find total 3 cited BEAST classes.
from model-selection.
Related Issues (9)
- robustify for empty compound distributions
- PathSampleAnalyser with 14 steps and -alpha 0 fails
- Using the beast 2.6 path sampler xml on beast 2.7 gives unhelpful error messages that are hard to debug HOT 3
- Path sampling multi threading duplicates taxon sets
- Would be nice if run0.{sh,bat} could use variables.
- nullCannot instantiate class. Please check the spec attribute.
- Include complete path to beast.jar HOT 1
- Rename PathSampler to SteppingStoneSampler
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