rare_members {microbiome} | R Documentation

## Rare Taxa

### Description

Determine members of the rare microbiota with given abundance and prevalence threshold.

### Usage

    rare_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 less prevalent than the given prevalence threshold. Optionally, never exceeds the given abundance threshold (by default, all abundanecs accepted). For matrix, lists columns that satisfy these criteria.

### Value

Vector of rare taxa

### Author(s)

Leo Lahti microbiome-admin@googlegroups.com

### References

To cite the microbiome R package, see citation('microbiome')

### See Also

core_members

### Examples

    data(dietswap)
    # Detection threshold: the taxa never exceed the given detection threshold
    # Prevalence threshold 20 percent (strictly greater by default)
    a <- rare_members(dietswap, detection=100/100, prevalence=20/100)

[Package microbiome version 1.12.0 Index]