brown: Phylogenetic Brownian motion models

Description Usage Arguments Value Author(s) References See Also Examples

Description

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

Usage

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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

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## Analysis of Anolis bimaculatus data
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 May 17, 2021, 1:09 a.m.

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