fastBM {phytools} | R Documentation |
(Reasonably) fast quantitative trait simulation on phylogenies
Description
Simulates one or multiple continuous traits on the tree under various evolutionary models.
Usage
fastBM(tree, a=0, mu=0, sig2=1, bounds=c(-Inf,Inf), internal=FALSE, nsim=1,
...)
Arguments
tree |
is a phylogenetic tree in |
a |
a value for ancestral state at the root node. |
mu |
an optional value for the mean of random normal changes along branches of the tree - can be used to simulate a trend if |
sig2 |
instantaneous variance of the BM process, |
bounds |
a vector with the lower and upper bounds (respectively) for bounded Brownian simulation - by default simulation is unbounded. |
internal |
logical value indicating whether or not to return states for internal nodes. |
nsim |
number of simulations. |
... |
optional arguments |
Details
This function conducts (reasonably) fast quantitative trait simulation on a phylogeny under several different models: Brownian motion (default), BM with a trend (for mu!=0
), bounds (for bounds!=c(-Inf,
Inf)
), and OU.
Value
A vector (for nsim=1
) or matrix containing the tip states for the n
species in the tree, and (optionally) the ancestral states for internal nodes.
Author(s)
Liam Revell liam.revell@umb.edu
References
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
See Also
Examples
## simulate 10 characters on the Anolis tree
## under Brownian motion
data(anoletree)
X<-fastBM(anoletree,nsim=10)
head(X)