phyloseq_randomize: Randomize abundance table and phylogeny in phyloseq objects...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Randomize abundance table and phylogeny in phyloseq objects (for null model testing and simulation).

Description

Randomize abundance table and phylogeny in phyloseq objects (for null model testing and simulation).

Usage

phyloseq_randomize(physeq, null_model = "phylogeny.pool", verbose = T, ...)

Arguments

physeq	A phyloseq-class object
null_model	Character string defining the null model (for the description of supported models see randomizeMatrix)
verbose	Logical; if TRUE, additional information messages will be displayed
...	Additional arguments may be passed to randomizeMatrix

Details

Currently only null models from picante package are implemented.

Value

A phyloseq-class object with randomized abundance table and/or phylogeny.

See Also

randomizeMatrix, commsim

Examples

# Load data
data("esophagus")

## Randomize phyloseq object
# Shuffle tips of the phylogenetic tree
phyloseq_randomize(esophagus, null_model = "phylogeny.pool")
# Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness
phyloseq_randomize(esophagus, null_model = "independentswap")

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.