ancThresh {phytools} | R Documentation |
This function uses Bayesian MCMC to estimate ancestral states and thresholds for a discrete character under the threshold model from quantitative genetics (Felsenstein 2012).
ancThresh(tree, x, ngen=1000, sequence=NULL, method="mcmc", model=c("BM","OU","lambda"), control=list(), ...)
tree |
phylogenetic tree. |
x |
a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns. |
ngen |
number of generations to run the MCMC. |
sequence |
assumed ordering of the discrete character state. If not supplied and |
method |
only method currently available is |
model |
model for the evolution of the liability. Options are |
control |
list containing the following elements: |
... |
additional arguments to be passed to |
This function returns as list with four elements:
ace |
posterior probabilities for each character state at each internal node, with the burn-in excluded. |
mcmc |
full posterior sample for the states. |
par |
full posterior sample for the thresholds, the |
liab |
full posterior sample of the liabilities at internal and tip nodes. |
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. (2014) Ancestral character estimation under the threshold model from quantitative genetics. Evolution, bold68, 743-759.