make.simmap: Simulate stochastic character maps on a phylogenetic tree or trees

Description

This function performs stochastic mapping using several methods. For Q="empirical", it first fits a continuous-time reversible Markov model for the evolution of x and then simulates stochastic character histories using that model and the tip states on the tree. This is the same procedure that is described in Bollback (2006), except that simulation is performed using a fixed value of the transition matrix, Q, instead of by sampling Q from its posterior distribution. For Q="mcmc", it first samples Q nsim times from the posterior probability distribution of Q using MCMC, then it simulates nsim stochastic maps conditioned on each sampled value of Q. For Q set to a matrix, it samples stochastic mappings conditioned on the fixed input matrix.

Usage

make.simmap(tree, x, model="SYM", nsim=1, ...)

Arguments

tree

a phylogenetic tree as an object of class "phylo", or a list of trees as an object of class "multiPhylo".

a vector containing the tip states for a discretely valued character, or a matrix containing the prior probabilities of tip states in rows.

model

a character string containing the model - options as in ace.

nsim

number of simulations. If tree is an object of class "multiPhylo", then nsim simulations will be conducted per tree.

...

optional arguments. So far, pi gives the prior distribution on the root node of the tree - options are "equal", "estimated", or a vector with the frequencies. If pi="estimated" then the stationary distri

Value

A modified phylogenetic tree of class "phylo" (or a modified "multiPhylo" object, for nsim > 1) with the following additional elements:
mapsa list of named vectors containing the times spent in each state on each branch, in the order in which they occur.
mapped.edgea matrix containing the total time spent in each state along each edge of the tree.
Qthe assumed or sampled value of Q.
logLthe log-likelihood of the assumed or sampled Q.

Details

Uses code modified from ace (by Paradis et al.) to perform Felsenstein's pruning algorithm & compute the likelihood. As of phytools>=0.2-33 x can be a vector of states or a matrix containing the prior probabilities of tip states in rows. In this case the column names of x should contain the states, and the row names should contain the tip names. Note that there was a small (but potentially significant) bug in how node states were simulated by make.simmap in versions of phytools<=0.2-26. between="" phytools="" 0.2-26="" and="" 0.2-36="" there="" was="" also="" a="" bug="" for="" asymmetric="" models="" of="" character="" change="" (e.g.,="" model="ARD"). Finally, between phytools 0.2-33 and phytools 0.2-47 there was an error in use of the conditional likelihoods for the root node, which caused the root node of the tree to be sampled incorrectly. All of these issues should be fixed in the present version. Q="mcmc" and Q set to a fixed value were introduced to phytools >= 0.2-53. As of the present version of phytools, this method is still somewhat experimental & should be used with caution. If tree is an object of class "multiPhylo" then nsim stochastic maps are generated for each input tree.

References

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289--290. Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback (2003) Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138. Bollback, J. P. (2006) Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.