ouch (version 2.7-2)

bimac: 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. The data frame consists of the following columns: species which are species names, size which is the phenotypic data, and the variables ancestor and time which specify the topology of the phylogeny and the location of the nodes in time, respectively. The columns OU.1, OU.3, OU.4, and OU.LP specify four hypothetical arrangements of selective regimes. Explanations of the data are given below.

Usage

data(bimac)

source

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

Details

[object Object],[object Object],[object Object]

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.

Examples

data(bimac)
tree <- with(bimac,ouchtree(node,ancestor,time/max(time),species))
plot(tree,node.names=TRUE)
print(h1 <- brown(log(bimac['size']),tree))
plot(h1)
print(h2 <- hansen(log(bimac['size']),tree,bimac['OU.1'],sqrt.alpha=1,sigma=1))
plot(h2)
print(h3 <- hansen(log(bimac['size']),tree,bimac['OU.3'],sqrt.alpha=1,sigma=1))
plot(h3)
print(h4 <- hansen(log(bimac['size']),tree,bimac['OU.4'],sqrt.alpha=1,sigma=1))
plot(h4)
h5 <- hansen(log(bimac['size']),tree,bimac['OU.LP'],sqrt.alpha=1,sigma=1,reltol=1e-5)
print(h5 <- update(h5,method='subplex',reltol=1e-11,parscale=c(0.1,0.1),hessian=TRUE))
simdat <- simulate(h5,nsim=10)
hsim <- update(h5,data=simdat[[1]])
print(summary(hsim))
bsim <- update(h1,data=simdat[[1]])
print(summary(bsim))