threshBayes {phytools} | R Documentation |
This function uses Bayesian MCMC to fit the quantitative genetics threshold model (Felsenstein 2012) to data for two discrete characters or one discrete and one continuous character.
threshBayes(tree, X, types=NULL, ngen=1000, control=list())
tree |
an object of class |
X |
a numeric matrix containing values for a numerically coded discrete character and a continuous character; or two discrete characters. The row names of |
types |
a vector of length |
ngen |
a integer indicating the number of generations for the MCMC. |
control |
a list of control parameters for the MCMC. Control parameters include: |
This function returns a list with two elements: par
a matrix containing the posterior sample for the model parameters (evolutionary rates, ancestral states, and correlation); liab
a matrix containing the posterior sample of the liabilities. For continuous characters, the liabilities are treated as known and so the posterior samples are just the observed values.
Liam Revell liam.revell@umb.edu
Felsenstein, J. (2012) A comparative method for both discrete and continuous characters using the threshold model. American Naturalist, 179, 145-156.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
Revell, L. J. (2014) Ancestral character estimation under the threshold model from quantitative genetics. Evolution, bold68, 743-759.
anc.Bayes
, bmPlot
, evol.rate.mcmc