sim.traits: Simulate multivariate trait evolution

In ericgoolsby/phylocurve: Phylogenetic Comparative Methods for High-Dimensional Traits

Description

This function wraps the sim.char in geiger function to simulate evolutionary models under a given evolutionary rate matrix, with the option of simulating multiple within-species observations and missing data.

Usage

sim.traits(ntaxa = 15, ntraits = 4, nreps = 1,
nmissing = 0, tree, v, anc, intraspecific,
model = "BM", parameters, nsim = 1, return.type = "matrix")

Arguments

ntaxa	Number of species to randomly generate on a pure-birth phylogeny (used if tree is not provided).
ntraits	Number of traits to randomly simulate according to a random evolutionary rate matrix (used if v is not provided).
nreps	Number of within-species observations to simulate (default is 1).
nmissing	Number of observations to randomly remove from the simulated data (default is 0).
tree	Optional: an object of class phylo (if none provided, a random pure-birth phylogeny of size ntraxa is generated).
v	The evolutionary covariance matrix. If none provided, a random covariance matrix of size ntraits-by-ntraits is generated.
anc	An optional vector of ancestral values.
intraspecific	An optional vector of within-species variance.
model	The evolutionary model to simulate trait evolution (BM, OUrandomRoot, OUfixedRoot, EB, lambda, kappa, or delta).
parameters	The evolutionary model parameter in a named list. Example: list(lambda = 0.5)
nsim	Number of datasets to simulate.
return.type	"data.frame" or "matrix"

Value

trait_data	Simulated trait data
tree	The phylogenetic tree
sim_tree	The phylogenetic tree with specified branch length transformations

Author(s)

Eric W. Goolsby

References

Harmon Luke J, Jason T Weir, Chad D Brock, Richard E Glor, and Wendell Challenger. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24:129-131.

See Also

sim.char

ericgoolsby/phylocurve documentation built on April 28, 2021, 10:23 p.m.