rare {microbiome} | R Documentation

## Rare Microbiota

### Description

Filter the phyloseq object to include only rare (non-core) taxa.

### Usage

    rare(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]; strictly greater by default)
`include.lowest` | Include the lower boundary of the detection and prevalence cutoffs in core calculation. FALSE by default.
`...` | Arguments to pass.

### Value

Filtered phyloseq object including only rare 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

### Examples

    data(dietswap)
    # Detection threshold 0 (strictly greater by default);
    # Prevalence threshold 50 percent (strictly greater by default)
    pseq <- rare(dietswap, 0, 50/100)

[Package microbiome version 1.12.0 Index]