geospiza | R Documentation |
Morphological measurements of Darwin's finches, together with a phylogeny.
The object geospiza
is a list containing:
phy
, a phylogenetic tree of class 'phylo' (see read.tree
)
dat
, a data frame containing data on various morphological measurements.
Aaron A. King, Emmanuel Paradis, Daniel Lawson
Data obtained from the geiger package, version 2.0.7.1. It is attributed there to D. Schluter, with no other details given.
Other examples:
anolis.ssd
,
bimac
,
ouch-package
### Darwin's finches.
## Save time for CRAN
### The data were taken from package 'geiger' due to the latter being orphaned.
if (requireNamespace("ape")) {
data(geospiza)
plot(geospiza$phy)
print(geospiza$dat)
### make an ouchtree out of the phy-format tree
ot <- ape2ouch(geospiza$phy)
### merge data with tree info
otd <- as(ot,"data.frame")
otd <- merge(otd,geospiza$dat,by.x="labels",by.y="row.names",all=TRUE)
### row-names are used by 'hansen'
rownames(otd) <- otd$nodes
print(otd)
### this data-frame now contains the data as well as the tree geometry
### now remake the ouch tree
ot <- with(otd,ouchtree(nodes=nodes,ancestors=ancestors,times=times,labels=labels))
plot(ot)
b1 <- brown(tree=ot,data=otd[c("tarsusL","beakD")])
summary(b1)
### evaluate an OU model with a single, global selective regime
otd$regimes <- as.factor("global")
h1 <- hansen(
tree=ot,
data=otd[c("tarsusL","beakD")],
regimes=otd["regimes"],
sqrt.alpha=c(1,0,1),
sigma=c(1,0,1),
maxit=10000
)
summary(h1)
plot(h1)
}
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