brown: Phylogenetic Brownian motion models

In ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Phylogenetic Brownian motion models

Description

The function brown creates a browntree object by fitting a Brownian-motion model to data.

Usage

brown(data, tree)

Arguments

data	Phenotypic data for extant species, i.e., at the terminal ends of the phylogenetic tree. This can either be a numeric vector or a list. If it is a numeric vector, there must be one entry for every node. If it is a list, it must consist entirely of numeric vectors, each of which has one entry per node. A data-frame is coerced to a list.
tree	A phylogenetic tree, specified as an ouchtree object.

Value

brown returns an object of class browntree.

Author(s)

Aaron A. King

References

\Butler

2004

See Also

bimac, anolis.ssd, hansen

Other phylogenetic comparative models: hansen(), ouch-package, ouchtree, paint()

Examples

## Analysis of Anolis bimaculatus data
 ## save time for CRAN
tree <- with(bimac,ouchtree(node,ancestor,time/max(time),spcode))
plot(tree,node.names=TRUE)

h1 <- brown(log(bimac['size']),tree)
h1
plot(h1)

h2 <- hansen(log(bimac['size']),tree,bimac['OU.1'],sqrt.alpha=1,sigma=1)
h2
plot(h2)

h3 <- hansen(log(bimac['size']),tree,bimac['OU.3'],sqrt.alpha=1,sigma=1)
h3
plot(h3)

h4 <- hansen(log(bimac['size']),tree,bimac['OU.4'],sqrt.alpha=1,sigma=1)
h4
plot(h4)

h5 <- hansen(log(bimac['size']),tree,bimac['OU.LP'],sqrt.alpha=1,sigma=1,reltol=1e-5)
h5 <- update(h5,method='subplex',reltol=1e-11,parscale=c(0.1,0.1),hessian=TRUE)
h5
plot(h5)

simdat <- simulate(h5,nsim=10)
hsim <- update(h5,data=simdat[[1]])
summary(hsim)
bsim <- update(h1,data=simdat[[1]])
summary(bsim)

ouch documentation built on April 25, 2023, 9:10 a.m.