prevalence: Simple prevalence measure

In microbiome/microbiomeold: Tools for microbiome analysis

Description

Simple prevalence measure

Usage

prevalence(x, detection.threshold, sort = FALSE)

Arguments

x	Abundance data matrix: samples x features (microbes)
detection.threshold	Detection threshold for absence/presence.
sort	Sort the groups by prevalence

Details

Calculates for each sample the fraction of samples that exceed the detection threshold

Value

Number of OTUs.

Author(s)

Contact: Leo Lahti [e-mail]

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)
  prevalence(peerj32$microbes, detection.threshold = 1.8, sort = TRUE)

microbiome/microbiomeold documentation built on May 22, 2019, 9:57 p.m.