rarefy_even_coverage2: 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 using vegan

Description

rarefy_even_coverage2 performs coverage-based rarefaction for a phyloseq object using vegan package

Usage

rarefy_even_coverage2(
  ps_obj,
  coverage = 0.97,
  remove_not_rarefied = FALSE,
  include_rarecurve_results = FALSE,
  knots = 1000,
  n_rarefy_iter = 10,
  rareplot_step_size = 100,
  rarefy_average_method = "round",
  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_rarecurve_results	Logical. If TURE, rarecurve results will also be included for visualization. The first object is a rarefied phyloseq object, and the second object is rarecurve results. If FALSE, it returns a rarefied phyloseq object only.
knots	Numeric. Specify knots of rareslope function.
n_rarefy_iter	Numeric. The number of iterations of rarefactions (default = 1).
rareplot_step_size	Numeric. Step size for rarecurve function. Only affect the resolution of a rarefaction plot.
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().
ran_seed	Numeric. Random seed.

Value

Rarefied phyloseq object (ps_rare). If include_rarecurve_results = TRUE, rarecurve 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.