core_matrix {microbiome} | R Documentation

## Core Matrix

### Description

Creates the core matrix.

### Usage

    core_matrix(x, prevalences = seq(0.1, 1, , 1), detections = NULL)

### Arguments

`x` | `phyloseq` object or a taxa x samples abundance matrix
`prevalences` | a vector of prevalence percentages in [0,1]
`detections` | a vector of intensities around the data range

### Value

Estimated core microbiota

### Author(s)

Contact: Jarkko Salojarvi 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

    ## Not run:
        # Not exported
        data(peerj32)
        core <- core_matrix(peerj32$phyloseq)

    ## End(Not run)

[Package microbiome version 1.2.1 Index]