prevalence {microbiome} | R Documentation

## OTU Prevalence

### Description

Simple prevalence measure.

### Usage

    prevalence(
      x,
      detection = 0,
      sort = FALSE,
      count = FALSE,
      include.lowest = FALSE
    )

### Arguments

`x` | A vector, data matrix or `phyloseq` object
`detection` | Detection threshold for absence/presence (strictly greater by default).
`sort` | Sort the groups by prevalence
`count` | Logical. Indicate prevalence as fraction of samples (in percentage [0, 1]; default); or in absolute counts indicating the number of samples where the OTU is detected (strictly) above the given abundance threshold.
`include.lowest` | Include the lower boundary of the detection and prevalence cutoffs. FALSE by default.

### Details

For vectors, calculates the fraction (count=FALSE) or number (count=TRUE) of samples that exceed the detection. For matrices, calculates this for each matrix column. For phyloseq objects, calculates this for each OTU. The relative prevalence (count=FALSE) is simply the absolute prevalence (count=TRUE) divided by the number of samples.

### Value

For each OTU, the fraction of samples where a given OTU is detected. The output is readily given as a percentage.

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

A Salonen et al. 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')

### Examples

    data(peerj32)
    pr <- prevalence(peerj32$phyloseq, detection=0, sort=TRUE, count=TRUE)

[Package microbiome version 1.12.0 Index]