variable_members {microbiome} | R Documentation

## Variable Microbiota

### Description

Filter the phyloseq object to include only variable taxa.

### Usage

    variable_members(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. FALSE by default.

### Details

Variable taxa are members of the microbiota that are not rare, and not members of the core microbiota. Such taxa reach notable abundance in a notable fraction of the population. The variable members are calculated by using the indicated prevalence threshold to define rare taxa; and its complement 1-prevalence to define core taxa. The remaining taxa are considered variable. The same detection threshold is used in all cases.

### Value

Filtered phyloseq object including only variable taxa.

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

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

### See Also

core_members, core, rare

### Examples

    data(dietswap)
    # Detection threshold 0 (strictly greater by default);
    # Prevalence threshold 50 percent (strictly greater by default)
    pseq.rel <- transform(dietswap, 'compositional')
    pseq <- variable_members(pseq.rel, 0.5/100, 20/100)

[Package microbiome version 1.2.1 Index]