getTipdata.Rd: Add species richness data to tips of phylogenetic tree

Description

Adds species richness (taxonomic) data to phylogenetic tree

Usage

getTipdata(tipdata, phy)

Arguments

tipdata

either of the following: a vector of species diversities, where the name of each element corresponds to the name of a terminal in a phylogenetic tree, or a data frame with a single column, where the row names are the names of the terminals

phy

a class 'phylo' phylogenetic tree, perhaps obtained by read.tree

Value

a phylogenetic tree with the standard components of class 'phylo' plus the following component:
phenotypeSpecies diversities associated with each terminal taxon

Details

getTipdata takes species richness data and adds a new component phenotype to your phylogenetic tree. The phenotype data could in principle be anything, but the function is designed to add species richness data to the tree to facilitate analysis by fitLambda_1rate and fitNDR_2rate. This function requires that the names in tipdata exactly match phy$tip.label; if they don't, you will (probably) receive an error message. If you fail to supply a vector with names or a dataframe with row.names, the input vector will be matched exactly to the to tips in the order in which they are stored in your tree (e.g., tipdata[1] will correspond to phy$tip.label[1]). This is not recommended.

References

Rabosky, D. L., S. C. Donnellan, A. L. Talaba, and I. J. Lovette. 2007. Exceptional among-lineage variation in diversification rates during the radiation of Australia's largest vertebrate clade. Proc. Roy. Soc. Lond. Ser. B 274:2915-2923.