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add correct citations #9

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walterxie opened this issue May 22, 2018 · 2 comments
Closed

add correct citations #9

walterxie opened this issue May 22, 2018 · 2 comments
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@walterxie
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The current @Citation is automatically inherited. If beast.gss.GeneralisedSteppingStoneStep, beast.inference.PairedPathSamplingStep, beast.inference.PathSamplingStep do not have citations, then they will use BEAST 2 paper as the citation because they are inherited from MCMC.

@walterxie walterxie added the bug label May 22, 2018
@walterxie
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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.

@walterxie
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walterxie commented May 22, 2018

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.

walterxie added a commit that referenced this issue May 22, 2018
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