BayesTraits V4.1.1 Oct 2023

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 4.1.1 of BayesTraits

Bug Fix - proposal mechanism issue with the fabric betas x branch (VR_LS_BL) parameters.

Removed the default prior on fabric betas x branch lengths (VR_LS_BL) as the prior is data specific.

Ancestral states can now be reconstructed for fabric and global trend models.

The default prior on the node scalars (fabric / variable rates) has been changes to its earlier distribution.

Downloads

BayesTraits V4.1.1 Manual (PDF)

Standard Builds
BayesTraits V4.1.1 - Windows 64
BayesTraits V4.1.1 - Linux 64
BayesTraits V4.1.1 - OS X Intel
BayesTraits V4.1.1 - OS X ARM

Alternative Builds
The threaded versions are no longer being supplied as binaries but can be built via the source code. New threaded methods are under development.

Source Code
BayesTraits V4.1.1 - Source Code

Variable Rates Post Processor
Variable Rates Post Processor

Fabric Model Post Processor
Fabric Model Post Processor

Harmonic Mean Marginal Likelihood Calculator
Marginal Likelihood Harmonic Mean Calculator

Version 4.0.1 of BayesTraits

Bug Fix - Geo Model - proposal mechanism was biased around the Antimeridian.

Version 4.0.0 of BayesTraits

Automatically detects and models directional changes, as well as evolvability changes. See Pagel etal, General statistical model shows that macroevolutionary patterns and processes are consistent with Darwinian gradualism, Nature Communications, 2022

A global trend model to test if trait change shows a general pattern of increase or decrease along paths through the tree that differ in their total evolvability.

Variable Rates models and other Reverse Jump tree transformation methods can be used on samples of trees, incorporating uncertainty in topology and branch length estimates into the analysis.

Threshold costs can be applied to Reverse Jump tree transformations

Draw random values from prior distributions, which can be used to visualise priors

Speed improvements when using distributions of data, for large trees this can improve performance by two orders of magnitude.

Threaded version of the Geo model and non-threaded are consistent with each other for a given random seed.

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

Older versions
BayesTraits V4.0.1
BayesTraits V4.0.0
BayesTraits V3.0.5
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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