pair.dist.mulseq: Calculate pairwise distances among species
In bomeara/phybase: Basic functions for phylogenetic analysis

Description Usage Arguments Value Author(s) See Also Examples

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).

1	pair.dist.mulseq(dist, species.structure)

`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.

This functions returns the distance matrix of species.

Liang Liu

See Also as pair.dist

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<-pair.dist(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
pair.dist.mulseq(dist,species.structure)