Bayesian Integrative Models of Trait Evolution

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Documentation for package ‘bite’ version 0.3

Help Pages

Anolis_map Anolis map of regimes
Anolis_traits Anolis snout to vent length
Anolis_tree Anolis phylogenetic tree
control_jive Control tuning parameters of the jive algorithm
format_jive_traits Format traits matrix to parse into 'make_jive' function
hpfun Hyper-prior function
make_jive Create a list that can be used as an input to mcmc_bite
marginal_lik Calculate marginal likelihood by thermodynamic integration (LTI)
mcmc_bite MCMC algorithm
plot_bf Plots summary of Bayes Factors calculations
plot_hp plot Hyper-prior function
plot_jive plot input data from a jive object
plot_mcmc_bite Plot trace and density from a log file
plot_post_beast Plot posterior probabilities from beast
plot_pvo Plots estimates of species traits distribution
sim_jive Simulate JIVE process
sim_mte Simulate MTE process
xml_bite Write xml file with model