core_members {microbiome} | R Documentation

## Core Taxa

### Description

Determine members of the core microbiota with given abundance and prevalences

### Usage

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

### Arguments

`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.

### Details

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

### Value

Vector of core members

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

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')

### Examples

    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)

[Package microbiome version 1.12.0 Index]