Bayesian Integrative Models of Trait Evolution

Documentation for package ‘bite’ version 0.3

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