dist.species: Calculate pairwise distances among species

In lliu1871/phybase: Basic functions for phylogenetic analysis

Calculate pairwise distances among species

Description

If some species have multiple taxa, the pairwise distance between two species is equal to the average of the distances between all pairs of taxa in the two species. This functions returns the pairwise distances among species (average over all taxa in the species).

Usage

dist.species(dist, species.structure)

Arguments

dist	the distance matrix of taxa
species.structure	a matrix with rows representing species and columns representing taxa. 1: the species (row) has the taxon at the corresponding column. see the example.

Value

This functions returns the distance matrix of species.

Author(s)

Liang Liu

See Also

See Also as dist.taxa

Examples

treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00705):0.00929,O:0.01635):0.1,W:0.11635);"
nodematrix<-read.tree.nodes(treestr)$nodes
dist<-dist.taxa(nodematrix,5)
species.structure<-matrix(0,nrow=2,ncol=5) #2 species and 5 taxa
species.structure[1,]<-c(1,1,1,0,0)        #taxa 1,2,3 belong to the first species
species.structure[2,]<-c(0,0,0,1,1)        #taxa 4,5 belong to the second species
dist.species(dist,species.structure)

lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.