prepare_breakaway: Prepare frequency counts for breakaway package

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Prepare frequency counts for breakaway package

Description

This function prepares input data for breakaway package (Willis, Bunge, 2015).

Usage

prepare_breakaway(OTUs, remove_singletons = FALSE)

Arguments

OTUs	Data frame with OTU abundances (rows = species, cols = samples) or phyloseq/otu_table object
remove_singletons	Logical; if TRUE, singleton counts will be removed

Details

In case of sequencing errors singletons can be excluded from the data ('remove_singletons = TRUE') and species richness estimation can be performed with breakaway_nof1 function.

Value

List of the sample frequency count tables for each sample.

References

Willis A., Bunge J. (2015) Estimating diversity via frequency ratios // Biometrics 71(4), P. 1042–1049. DOI: 10.1111/biom.12332

Examples

data("esophagus")
eso <- prepare_breakaway(esophagus)
eso_nof1 <- prepare_breakaway(esophagus, remove_singletons = TRUE)

# Estimate species richness (observed + unobserved) for the second sample in esophagus data
library(breakaway)
breakaway(eso[[2]], plot = T)
breakaway_nof1(eso_nof1[[2]], plot = T)

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