Bayesian Integrative Models of Trait Evolution
Write xml file with model
Control tuning parameters of the jive algorithm
Format traits matrix to parse into make_jive function
Hyper-prior function
Create a list that can be used as an input to mcmc_bite
Calculate marginal likelihood by thermodynamic integration (LTI)
MCMC algorithm
Plots summary of Bayes Factors calculations
plot Hyper-prior function
plot input data from a jive object
Plot trace and density from a log file
Plot posterior probabilities from beast
Plots estimates of species traits distribution
Simulate JIVE process
Simulate MTE process
Contains the JIVE (joint inter and intra-specific model of variance evolution) model and other Bayesian models aimed at understanding trait evolution. The goal of the package is to join phylogenetic comparative models (PCM) that tend to integrate various type of data (individual observations, environmental data, fossil data) into a hierarchical Bayesian framework. It contains various PCMs as well as functions to join those models into a hierarchical Bayesian framework in a flexible and user friendly way. It contains various Markov chain Monte-Carlo (MCMC) algorithms, methods for model comparison and many plotting function for pre- and post-processing data visualization. Finally, this package integrates functions allowing bridges between 'R' and the 'BEAST2' implementations of PCMs. Kostikova A, Silvestro D, Pearman PB, Salamin N (2016) <doi:10.1093/sysbio/syw010>. Gaboriau T, Mendes FK, Joly S, Silvestro D, Salamin N (in prep).