add_alphas: Add alpha diversity measures

In SWittouck/tidyamplicons: Functions to Manipulate and Visualize Amplicon Abundance Data

Add alpha diversity measures

Description

add_diversity_measures adds two alpha diversity measures to the samples tibble of a tidyamplicons object.

Usage

add_alphas(ta)

Arguments

ta	Tidyamplicons object.

Details

This function adds two alpha diversity measures (observed and inverse Simpson) to the samples tibble of a tidyamplicons object under the variable names observed and inverse_simpson, respectively. This function will also add relative abundances if not present using add_rel_abundance.

Examples

# Initiate abundance matrix
x <- matrix(
 c(1500, 1300, 280, 356),
 ncol = 2
)
rownames(x) <- c("taxon1", "taxon2")
colnames(x) <- c("sample1", "sample2")

# Convert to tidyamplicons object
data <- create_tidyamplicons(x,
                     taxa_are_columns = FALSE
                     )

# Add total abundance
data <- data %>%
 add_diversity_measures()

SWittouck/tidyamplicons documentation built on Aug. 15, 2023, 3:14 a.m.