bimac {ouch}R Documentation

Anolis bimaculatus lizard size data

Description

This is the Anolis bimaculatus dataset used in Butler & King (2004). It is used to test a hypothesis of character displacement using an interspecific dataset of body sizes and current data on sympatry/allopatry.

Format

A data frame with 45 observations on the following 11 variables.

Details

Explanations of the data follow:

Author(s)

Marguerite A. Butler and Aaron A. King

Source

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

References

Lazell, J. D. 1972. The anoles (Sauria: Iguanidae) of the Lesser Antilles. Bull. Mus. Comp. Zool., 143:1–115.

Losos, J. B. 1990. A phylogenetic analysis of character displacement in Caribbean Anolis lizards. Evolution, 44:558–569.

See Also

Other examples: anolis.ssd, ouch-package

Examples

## 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)

[Package ouch version 2.17-1 Index]