alphacone: Alpha Diversity Metric Distributions

In escamero/mirlyn: Multiple Iterations of Rarefying for Library Normalization

Alpha Diversity Metric Distributions

Description

alphacone() will generate a dataframe of the alpha diversity metric for different library sizes. Different rarefied library sizes may have impact on both the measured value of the diversity metric and the perceived variation in the metric values. Generations of the distribution of the alpha diversity metric allows for a comprehensive examination of the alpha diversity metric values to account for variation introduced into the diversity metric as an artifact of rarefied library size.

Usage

alphacone(
  x,
  rep = 1000,
  steps = seq(from = 0.001, to = 1, by = 0.01),
  diversity = "shannon",
  lower.q = 0.025,
  upper.q = 0.975,
  replace = FALSE,
  set.seed = NULL,
  mc.cores = 1L
)

Arguments

x	The phyloseq object.
rep	The number of replications of rarefying to perform.
steps	The library sizes to rarefy to as a function of the library sizes of samples.
diversity	The diversity metric. By default, the Shannon Index will be utilized in the generation of the dataframe. Diversity indexes available in vegan are supported.
lower.q	The lower quantile for the distribution cone. By default it will provide the 2.5th.
upper.q	The upper quantile for the distribution cone. By default, the 97.5th will be applied.
replace	Whether to use replacement during sampling.
set.seed	The seed value for reproducibility.
mc.cores	From parallel::mclapply().

Value

A data.frame of the distribution of the diversity metric.

Examples

library(mirlyn)
data(example)

## Not run: 
alphacone_example <- alphacone(example, rep = 100)

## End(Not run)

escamero/mirlyn documentation built on Aug. 6, 2023, 9:30 p.m.