Example dataset for the CAIC package
This is a comparative dataset on Perissodactyla taken from the examples include with the original CAIC program.
data(shorebird)
The datafile contains a phylogeny (perissodactyla.tree) of 18 perissodactyl species as a 'phylo' object from the ape library. The tip names are the binomial names of the species. The file also contains a data frame (perissodactyla.data) of variables 5 variables for 13 of those species:
The species binomial name.
Log female weight
Log gestation length
Log neonatal weight
A factor indicating whether or not the species displays territorial behaviour.
The dataset is incomplete - it does not include data for each species in the phylogeny and contains missing values. See the examples for the behaviour of the 'comparative.data' function in handling missing data.
Purvis, A. and Rambaut, A. (1995). Comparative Analysis by Independent Contrasts (CAIC) User's Guide.
caic, pgls
data(perissodactyla) # default behaviour is to omit incomplete data rows (perisso <- comparative.data(perissodactyla.tree, perissodactyla.data, Binomial)) # but this can be turned off (perisso <- comparative.data(perissodactyla.tree, perissodactyla.data, Binomial, na.omit=FALSE)) na.omit(perisso)
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