geiger (version 2.0.11)

subset.phylo: blending information from taxonomies and trees

Description

working with systematic reference tables and phylogenies

Usage

# S3 method for phylo
subset(x, taxonomy, rank="", ncores=1, ...)

Arguments

x

a phylogenetic tree of class 'phylo'

taxonomy

a ('matrix') linkage table between tips of the phylogeny and clades represented in the tree; rownames of 'taxonomy' should be tips found in the phylogeny

rank

a column name in 'taxonomy' at which to resample the tree (see Examples)

ncores

max number of cores to use

...

arguments to be passed to other functions (has no effect in the present context)

Author

JM Eastman

Examples

if (FALSE) {
sal <- get(data(caudata))
print(head(sal$tax))

nphy <- subset(sal$phy, sal$tax, "genus", ncores=1)
plot(nphy, type="fan", cex=0.15)
}