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 |
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. doi:10.1086/426002.
See Also
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)