(Required). A phyloseq-class or an otu_table-class object. The latter is only appropriate for methods that do not require any additional data (one-table). For example, the “wunifrac” option (UniFrac) requires phyloseq-class that contains both an otu_table and a phylogenetic tree (phylo).

(Required). A character string. Provide one of the currently supported options. See distanceMethodList for a detailed list of the supported options here, and links to accompanying documentation.

Note that for the common definition of Jaccard distance using the vegan-package implementation, an additional argument is needed, with the full call having the form: distance(physeq, method = "jaccard", binary = TRUE)

The following methods are implemented explicitly within the phyloseq-package, and accessed by the following method options:

"unifrac"

Original (unweighted) UniFrac distance, UniFrac

"wunifrac"

weighted-UniFrac distance, UniFrac

"dpcoa"

sample-wise distance used in Double Principle Coordinate Analysis, DPCoA

"jsd"

Jensen-Shannon Divergence, JSD

Alternatively, you can provide a character string that defines a custom distance method, if it has the form described in designdist.

(Optional). A character string. The type of pairwise comparisons being calculated: sample-wise or taxa-wise. The default is c("samples").

Additional arguments passed on to the appropriate distance function, determined by the method argument.