pair.dist.mulseq {phybase} | R Documentation |
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).
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)