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Accumulation curve analysis

accumulation_test.Rd

This function generates accumulation (rarefaction) curves for each sample in a given phyloseq object.

Usage

accumulation_test(input, step = 5)

Arguments

input

A phyloseq object.

step

A numeric value. The step size for drawing the accumulation curve. Default = 5.

Value

A list containing:

  • accumulation_plot: A ggplot object with all sites faceted.

  • threshold_density: A ggplot density/histogram plot of the 75% ACE thresholds.

  • individual_plots: A list of ggplot objects, one per site.

Details

It fits a general accumulation model using the Abundance Coverage Estimator (ACE) as an asymptote, and identifies the sequencing depth at which 75% of the ACE value is reached. It also produces a density plot showing the distribution of these 75% completion thresholds.

Examples

library(Sibyl)
# Creating a smaller subset of the data
adults_sub <- phyloseq::subset_samples(adults, location=="VK3")
# Running accumulation tests on a phyloseq object, higher step size reduces 
# execution time.
accumulation_test(adults_sub, step=50)