core {microbiome} | R Documentation

## Core Microbiota

### Description

Filter the phyloseq object to include only prevalent taxa.

### Usage

    core(x, detection, prevalence, 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.
`...` | Arguments to pass.

### Value

Filtered phyloseq object including only prevalent taxa

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

Salonen A, Salojarvi J, Lahti L, de Vos WM. 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')

### See Also

core_members, rare_members

### Examples

    data(dietswap)
    # Detection threshold 0 (strictly greater by default);
    # Prevalence threshold 50 percent (strictly greater by default)
    pseq <- core(dietswap, 0, 50/100)
    # Detection threshold 0 (strictly greater by default);
    # Prevalence threshold exactly 100 percent; for this set
    # include.lowest=TRUE, otherwise the required prevalence is
    # strictly greater than 100
    pseq <- core(dietswap, 0, 100/100, include.lowest = TRUE)

[Package microbiome version 1.12.0 Index]