core_members: Core Taxa
In microbiome: Microbiome Analytics

Description Usage Arguments Details Value Author(s) References Examples

Determine members of the core microbiota with given abundance and prevalences

1	core_members(x, detection = 1/100, prevalence = 50/100, include.lowest = FALSE)

`x`	`phyloseq-class` object
`detection`	Detection threshold for absence/presence (strictly greater by default).
`prevalence`	Prevalence threshold (in [0, 1]). The required prevalence is strictly greater by default. To include the limit, set include.lowest to TRUE.
`include.lowest`	Include the lower boundary of the detection and prevalence cutoffs. FALSE by default.

For phyloseq object, lists taxa that are more prevalent with the given detection threshold. For matrix, lists columns that satisfy these criteria.

Vector of core members

Contact: Leo Lahti microbiome-admin@googlegroups.com

A Salonen et al. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16 20, 2012. To cite the microbiome R package, see citation('microbiome')

data(dietswap)
# Detection threshold 1 (strictly greater by default);
# Note that the data (dietswap) is here in absolute counts
# (and not compositional, relative abundances)
# Prevalence threshold 50 percent (strictly greater by default)
a <- core_members(dietswap, 1, 50/100)