rarefy_even_coverage: Perform coverage-based rarefaction for a phyloseq object

In ong8181/macam: A collection of miscellaneous R functions for ecology

Perform coverage-based rarefaction for a phyloseq object

Description

rarefy_even_coverage performs coverage-based rarefaction for a phyloseq object using iNEXT package

Usage

rarefy_even_coverage(
  ps_obj,
  coverage = 0.97,
  remove_not_rarefied = FALSE,
  include_iNEXT_results = FALSE,
  correct_singletons = FALSE,
  se = FALSE,
  nboot = 40,
  knots = 50,
  n_rarefy_iter = 1,
  rarefy_average_method = "round",
  sample_method = "phyloseq",
  ran_seed = 1234
)

Arguments

ps_obj	Phyloseq object.
coverage	Numeric. Coverage specified by a user (default = 0.97 = 97%).
remove_not_rarefied	Logical. If TRUE, samples of which coverage is lower than the specified coverage will be removed.
include_iNEXT_results	Logical. If TURE, iNEXT results will be included as a element of the output. The first object is a rarefied phyloseq object, and the second object is an iNEXT result. Also, if TRUE, computation time will increase. If FALSE, it returns a rarefied phyloseq object only.
correct_singletons	Logical. If TURE, singleton counts will be corrected according to the method of Chiu & Chao (2016). Corrected coverage and reads will be used for the rarefaction of the original data.
se	Logical. Specify whether SE of the rarefaction curve is calculated.
nboot	Numeric. Specify nboot of iNEXT function (valid only if include_iNEXT_results = TRUE).
knots	Numeric. Specify knots of iNEXT function (valid only if include_iNEXT_results = TRUE).
n_rarefy_iter	Numeric. The number of iterations of rarefactions (default = 1).
rarefy_average_method	Character. If n_rarefy_iter >= 2, this argument determines how the multiple rarefactions are summarized. rarefy_average_method = "round" uses round(). rarefy_average_method = "floor" uses floor(). rarefy_average_method = "ceiling" uses ceiling().
sample_method	Character. Specify which function is used for rarefaction. sample_method = "vegan" uses vegan::rrarefy(), while sample_method = "phyloseq" uses phyloseq:::rarefaction_subsample().
ran_seed	Numeric. Random seed.

Details

• Hsieh et al. (2016) Methods in Ecology and Evolution https://doi.org/10.1111/2041-210X.12613

Value

Rarefied phyloseq object (ps_rare). If include_iNEXT_results = TRUE, iNEXT results are stored in the second element of the list.

Examples

# rarefy_even_coverage(ps_obj, coverage = 0.97)

ong8181/macam documentation built on Oct. 15, 2024, 7:04 a.m.