bimac {ouch} | R Documentation |
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.
data(bimac)
A data frame with 45 observations on the following 8 variables.
ns
small
medium
large
small
medium
large
anc
small
medium
large
ancestor
and time
.
Each node of the phylogenetic tree has a corresponding row in the data frame, numbered from 1 to 45.
The columns ancestor
and time
specify the phylogeny.
The ancestor
variable specifies the topology: it is a list indicating the ancestor of each node.
The root node has ancestor 0.
The variable time
specifies the temporal location of each node, with the root node being at time 0.
OU.1
, OU.3
, OU.4
, OU.LP
).
These columns are factors, the levels of which correspond to the ``paintings'' of the respective adaptive regime hypotheses onto the phylogeny.
Each selective regime is named (small, medium, large, etc.).
Put the corresponding name on each branch segment to indicate which selective regime it belongs to.
Each column corresponds to a different painting of the selective regimes, and thus to a different hypothesis.
In this example, there are 3 alternative models (see Butler & King 2004):
OU.4
is 4-regime model,
OU.3
is 3-regime model (all ancestors are medium),
OU.LP
is linear parsimony model.
Marguerite A. Butler <mbutler at hawaii dot edu> and Aaron A. King <kingaa at umich dot edu>
Butler, M.A. and A.A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683-695.
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.
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'],alpha=1,sigma=1)) plot(h2) print(h3 <- hansen(log(bimac['size']),tree,bimac['OU.3'],alpha=1,sigma=1)) plot(h3) print(h4 <- hansen(log(bimac['size']),tree,bimac['OU.4'],alpha=1,sigma=1)) plot(h4) h5 <- hansen(log(bimac['size']),tree,bimac['OU.LP'],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))