phyloseq_mult_raref_div: Average diversity estimates across multiple rarefaction...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Average diversity estimates across multiple rarefaction iterations.

Description

This function performs multiple rarefaction and estimates average diversity (e.g., Simpson or Shannon indices) for each sample.

Usage

phyloseq_mult_raref_div(
  physeq,
  SampSize = min(sample_sums(physeq)),
  iter = 1000,
  divindex = c("Observed", "Shannon"),
  parallel = FALSE,
  verbose = TRUE,
  ...
)

Arguments

physeq	A phyloseq-class object
SampSize	Rarefaction depth (number of reads to sample)
iter	Number of rarefication iterations
divindex	Alpha-diversity measures to estimate (for the supported indices see estimate_richness)
parallel	Logical; if TRUE, attempts to run the function on multiple cores
verbose	Logical; if TRUE, progress messages from the function will be printed
...	Additional argument may be passed to phyloseq_mult_raref

Value

A data.frame of the richness estimates.

vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.