pctax (version 0.1.3)

z_diversity: Calculate Zeta Diversity

Description

This function calculates Zeta diversity for each group in the provided otutab.

This function plots the Zeta diversity results obtained from the z_diversity function.

Usage

z_diversity(otutab, group_df = NULL, zetadiv_params = list())
# S3 method for zeta_res
plot(x, lm_model = c("exp", "pl")[1], ribbon = FALSE, text = TRUE, ...)

Value

zeta_res

A ggplot object.

Arguments

otutab

A matrix or data frame containing OTU (Operational Taxonomic Unit) counts.

group_df

A data frame containing group information.

zetadiv_params

Additional parameters to be passed to the Zeta.decline.mc function from the zetadiv package.

x

Zeta diversity results obtained from z_diversity function.

lm_model

The linear model to be used for fitting ('exp' or 'pl').

ribbon

Logical, whether to add a ribbon to the plot for standard deviation.

text

Logical, whether to add R-squared and p-value text annotations.

...

Additional arguments to be passed to ggplot2 functions.

Examples

# \donttest{
if (requireNamespace("zetadiv")) {
  data(otutab, package = "pcutils")
  zeta_result <- z_diversity(otutab, metadata["Group"], zetadiv_params = list(sam = 10))
  plot(zeta_result, lm_model = "exp", text = TRUE)
}
# }