geospiza: Data on Darwin's finches

In kingaa/ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Data on Darwin's finches

Description

Morphological measurements of Darwin's finches, together with a phylogeny.

Format

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.

Author(s)

Aaron A. King, Emmanuel Paradis, Daniel Lawson

Source

Data obtained from the geiger package, version 2.0.7.1. It is attributed there to D. Schluter, with no other details given.

See Also

Other examples: anolis.ssd, bimac, ouch-package

Examples

### 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)

}

kingaa/ouch documentation built on April 24, 2024, 11:24 a.m.