Paul O. Lewis

How much information is there for inferring species trees?

Analisa Milkey, Jessica Chen, Paul O. Lewis

A bstract As modern phylogenomics datasets become increasingly large, it is useful to develop recommendations for how to subsample datasets for best species tree inference. Here we apply a new measure of phylogenetic information content that estimates the reduction in tree space …

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Estimating Bayesian Phylogenetic Information Content Using Geodesic Distances

Analisa Milkey, Paul O. Lewis

A bstract A new Bayesian measure of phylogenetic information content is introduced based on geodesic distances in treespace. The measure is based on the relative variance of phylogenetic trees sampled from the posterior distribution compared to the prior distribution. This ratio is …

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A Comparison of Monte Carlo Based Marginal Likelihood Estimators

Aolan Li, Pang-Yu Liu, Yu‐Bo Wang, Analisa Milkey et autres

ABSTRACT Marginal likelihood plays a central role in Bayesian model comparison and hypothesis testing, but its computation is often challenging in practice. This article reviews recent Monte Carlo methods that rely on the availability of Markov chain Monte Carlo (MCMC) samples from …

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The Sequential Multispecies Coalescent

Analisa Milkey, Ming‐Hui Chen, Yübo Wang, Aolan Li et autres

Abstract The multispecies coalescent (MSC) model applies coalescent theory to gene evolution within and among reproductively isolated populations (“species”) to estimate a species tree in the face of gene tree conflict resulting from deep coalescence. Sequential Monte Carlo (SMC) uses particle filtering …

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lorad: Lowest Radial Distance Method of Marginal Likelihood Estimation

Analisa Milkey, Elena Korte, Paul O. Lewis

Estimates marginal likelihood from a posterior sample using the method described in Wang et al. (2023) <doi:10.1093/sysbio/syad007>, which does not require evaluation of any additional points and requires only the log of the unnormalized posterior density for each sampled parameter vector.

LoRaD: Marginal likelihood estimation with haste (but no waste)

Yübo Wang, Analisa Milkey, Aolan Li, Ming‐Hui Chen et autres

The Lowest Radial Distance (LoRaD) method is a modification of the recently introduced Partition-Weighted Kernel method for estimating the marginal likelihood of a model, a quantity important for Bayesian model selection. For analyses involving a fixed tree topology, LoRaD improves upon the …

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IBNR Versus EBNER – An Alternative Method of Allowing for Late Reported Claims

Paul O. Lewis, Louis Rossouw

Afrique du Sud (code pays fourni par la source)

Lessons learned from organizing and teaching virtual phylogenetics workshops

Joëlle Barido‐Sottani, Joshua Justison, Rui Borges, Jeremy M. Brown et autres

No abstract available.

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Lessons learned from organizing and teaching virtual phylogenetics workshops - Supplementary materials

Joëlle Barido‐Sottani, Joshua Justison, Rui Borges, Jeremy M. Brown et autres

Supplementary materials for the journal article "Lessons learned from organizing and teaching virtual phylogenetics workshops", published in the Bulletin of the Society of Systematic Biology, 2022.

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An experimental test of Lanchester's models of combat in the neotropical termite Nasutitermes corniger (Blattodea: Termitidae)

Elizabeth M. Clifton, Paul O. Lewis, Elizabeth L. Jockusch, Eldridge S. Adams

Lanchester's models of combat have been invoked to explain the mechanics of group fighting in social animals. Specifically, Lanchester's square law posits that the fighting ability of the group is proportional to the square of the number of combatants. Although used to …

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Lessons learned from organizing and teaching virtual phylogenetics workshops

Joëlle Barido‐Sottani, Joshua Justison, Rui Borges, Jeremy M. Brown et autres

In 2020 and 2021, the COVID-19 pandemic led to an abrupt overhaul of many academic practices, including the transition of scientific events, such as workshops, to a fully virtual format. We describe our experiences organizing and teaching online-only statistical phylogenetics workshops and …

GLMM R code on survival from An experimental test of Lanchester's models of combat in the neotropical termite Nasutitermes corniger (Blattodea: Termitidae)

Elizabeth M. Clifton, Paul O. Lewis, Elizabeth L. Jockusch, Eldridge S. Adams

This is an Rmarkdown document detailing the code used for the binomial GLMM on survival rates.