microbial (version 0.0.21)

betadiv: calcaute beta diversity

Description

calcaute beta diversity

Usage

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

Value

list with beta diversity data.frame and PCs

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.

Author

Kai Guo

Examples

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