phytools (version 0.4-45)

sim.history: Simulate stochastic character history under some model

Description

This function simulates a stochastic character history for a discretely valued character trait on the tree. The resultant tree is stored as a modified "phylo" object in stochastic character map (e.g., make.simmap) format.

Usage

sim.history(tree, Q, anc=NULL, nsim=1, ...)

Arguments

tree

a phylogenetic tree as an object of class "phylo".

Q

a matrix containing the instantaneous transition rates between states. Note that normally this is the transpose of the matrix produced by fitDiscrete in the geiger package or make.simmap<

anc

an optional value for the state at the root node; if NULL, a random state will be assigned.

nsim

number of simulations.

...

other optional arguments. Currently only message, a logical value indicating whether or not to turn on informational messages (defaults to message=TRUE).

Value

• A modified phylogenetic tree of class "phylo" (or a modified "multiPhylo" object, for nsim > 1) with the following additional elements:
• maps
  a list of named vectors containing the times spent in each state on each branch, in the order in which they occur.
• mapped.edge
  a matrix containing the total time spent in each state along each edge of the tree.
• states
  a vector containing the tip states.
• node.states
  a matrix containing the states at internal & terminal nodes (according to the dimensions of edge).

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

See Also

make.simmap, read.simmap, plotSimmap, sim.rates