betadiv {microbial}

calcaute beta diversity

Description

calcaute beta diversity

Usage

betadiv(physeq, distance = "bray", method = "PCoA")

Arguments

physeq

A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.

distance

A string character specifying dissimilarity index to be used in calculating pairwise distances (Default index is "bray".). "unifrac","wunifrac","manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , "binomial", "chao", "cao" or "mahalanobis".

method

A character string specifying ordination method. All methods available to the ordinate function of phyloseq are acceptable here as well.

Value

list with beta diversity data.frame and PCs

Author(s)

Kai Guo

Examples

{
data("Physeq")
phy<-normalize(physeq)
res <- betadiv(phy)
}