phylobeta_core computes efficiently for large community matrices and
trees the necessary quantities used by the betapart package to compute
pairwise and multiple-site phylogenetic dissimilarities.
phylobeta_core(x, phy)
phylobeta(x, phy, index.family = "sorensen")an object of class Matrix, matrix or phyloseq
a phylogenetic tree (object of class phylo)
family of dissimilarity indices, partial match of "sorensen" or "jaccard".
phylobeta_core returns an object of class "phylo.betapart",
see phylo.betapart.core for details. This object can be called
by phylo.beta.pair or phylo.beta.multi.
phylobeta returns a list with three phylogenetic dissimilarity
matrices. See phylo.beta.pair for details.
read.community, phylo.betapart.core,
beta_core
library(ape)
tree <- read.tree(text = "((t1:1,t2:1)N2:1,(t3:1,t4:1)N3:1)N1;")
com <- sparseMatrix(c(1,3,4,1,4,5,1,2,3,4,5,6,3,4,6),
c(1,1,1,2,2,2,3,3,3,3,3,3,4,4,4),x=1,
dimnames = list(paste0("g", 1:6), tree$tip.label))
com
#> 6 x 4 sparse Matrix of class "dgCMatrix"
#> t1 t2 t3 t4
#> g1 1 1 1 .
#> g2 . . 1 .
#> g3 1 . 1 1
#> g4 1 1 1 1
#> g5 . 1 1 .
#> g6 . . 1 1
pbc <- phylobeta_core(com, tree)
pb <- phylobeta(com, tree)