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 the
hypothesized selective regimes (there are four alternatives in this
example). Explanations of the data are given below. Mean species
lengths.
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 <mabutler at utk 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, in press.
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) attach(bimac) tree.plot(node,ancestor,time,names=species,regimes=OU.LP) brown.fit(log(size),node,ancestor,time/max(time)) hansen.fit(log(size),node,ancestor,time/max(time),OU.1) hansen.fit(log(size),node,ancestor,time/max(time),OU.3) hansen.fit(log(size),node,ancestor,time/max(time),OU.4) hansen.fit(log(size),node,ancestor,time/max(time),OU.LP)