RAM (version 1.2.0)

shared.Taxa: Summary of Shared Taxa Across ALL Subjects

Description

This function consumes OTU tables or a taxonomy matrices and returns a list summarizing information about the presence of the taxa in that table at a given taxonomic rank.

Usage

shared.Taxa(data, is.OTU=TRUE, rank="g")

Arguments

data

a list of OTU tables or taxonomy abundance matrices to be analyzed.

is.OTU

whether or not the input data are otu tables

rank

the taxonomic rank to be investigated

Value

• shared.Taxa returns a list containing the information calculated. The names associated with the list describe what that number represents; i.e. "#_of_families_in_all_samples" shows how many taxa at the family level were found to be present in all samples. The last item in the list is a character vector, containing the taxon names of which were present in all samples.

See Also

decostand

Examples

data(ITS1)
shared.Taxa(data=list(ITS1=ITS1))
g1 <- tax.abund(ITS1, rank="g", drop.unclassified=TRUE)
shared.Taxa(data=list(genus_ITS1=g1), rank="g", is.OTU=FALSE)