aggregate_rare {microbiome} | R Documentation

## Aggregate Rare Groups

### Description

Combining rare taxa.

### Usage

    aggregate_rare(x, level, detection, prevalence, include.lowest = FALSE, ...)

### Arguments

`x` | `phyloseq-class` object
`level` | Summarization level (from `rank_names(pseq)`)
`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

`phyloseq-class` object

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

See citation('microbiome')

### Examples

    data(dietswap)
    s <- aggregate_rare(dietswap, level = 'Phylum',
        detection = 0.1/100, prevalence = 5/100)

[Package microbiome version 1.12.0 Index]