brown {ouch}

R Documentation

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, M.A. and A.A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683–695.

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)

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