BayesTraits V3.0.5 Aug 2021

Description

BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.

Version 3.0.5 of BayesTraits

Bug Fix - Geo Model with Distribution of data – updating ancestral sates could use old tip values.

Bug Fix - Geo Model - an incorrect likelihood could be accepted when the RNG produces a zero value.

Change - Zero RJ rates was relaxed from 1E-21 to 1E-07.

Add - Prior for CV switching rates.

Version 3.0.2 of BayesTraits

Bug Fix - Maximum likelihood values of kappa and gamma were incorrect.

Change – Geo model can now use variable rates.

Version 3.0.1 of BayesTraits

Bug Fix - Fossilising state 1,0 was set to the fossil value of state 0,1 with discrete models.

Version 3.0.0 of BayesTraits

Automatically detect shifts in rates of evolution (Variable Rates model) for MultiState / discrete data, as well as continuous.

Kappa, lambda, delta and rate scalars can be applied to nodes within a tree

Allow patterns of evolution to vary within a tree for MultiState / discrete data

Improved parallelism

Integration of a fast / high precision likelihood calculation for multi-state and discrete models

Reverse Jump MCMC (RJ-MCMC) methods to detect changes in evolutionary patterns (kappa, lambda, and delta)

Improved Maximum Likelihood searching

Geographical models

Distributions of trait data instead of single values

More control over priors

Downloads

BayesTraits V3.0.5 Manual (PDF)

Standard Builds
BayesTraits V3.0.5 - Windows 64
BayesTraits V3.0.5 - Linux 64
BayesTraits V3.0.5 - OS X

Windows 64 Alternative Builds
BayesTraits V3.0.5 - Threaded / Multi Core

Linux 64 Alternative Builds
BayesTraits V3.0.5 - Threaded / Multi Core

OS X Alternative Builds
BayesTraits V3.0.5 - Threaded / Multi Core

Source Code
BayesTraits V3.0.5 - Source Code

Variable Rates Post Processor
Variable Rates Post Processor

Harmonic Mean Marginal Likelihood Calculator
Marginal Likelihood Harmonic Mean Calculator

Older versions
BayesTraits V3.0.2
BayesTraits V3.0.1
BayesTraits V3.0
BayesTraits V2.0.2
BayesTraits V2
BayesTraits V2 Beta
BayesTraitsV1

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