Calculate alpha diversity indices

This function calculates several alpha diversity indices (Shannon, Simpson, Observed Species, Chao1, ACE, Pielou, and Faith's PD) using the vegan and picante packages. The function takes a feature table (x) as input and returns a list containing the requested alpha diversity indices.

Usage

mStat_calculate_alpha_diversity(x, alpha.name, tree = NULL)

Arguments

x

Feature table (e.g., OTU/ASV table) with taxa in rows and samples in columns.

alpha.name

character vector containing the names of alpha diversity indices to calculate. Possible values are: "shannon", "simpson", "observed_species", "chao1", "ace", "pielou", and "faith_pd".

tree

Phylogenetic tree object of class "phylo". Required for Faith's phylogenetic diversity ("faith_pd") calculation.

Value

A list containing the requested alpha diversity indices.

Examples

if (FALSE) { # \dontrun{
# Create example feature table
otu.tab <- matrix(data = rpois(100, 5), nrow = 10, ncol = 10)
rownames(otu.tab) <- paste0("Taxon_", 1:10)
colnames(otu.tab) <- paste0("Sample_", 1:10)

# Calculate non-phylogenetic alpha diversity indices
alpha.obj <- mStat_calculate_alpha_diversity(
  x = otu.tab,
  alpha.name = c("shannon", "simpson", "observed_species", "chao1", "ace", "pielou")
)

# Calculate Faith's PD when picante is available
if (requireNamespace("picante", quietly = TRUE)) {
  tree <- ape::rtree(n = nrow(otu.tab), tip.label = rownames(otu.tab))
  faith_pd <- mStat_calculate_alpha_diversity(
    x = otu.tab,
    alpha.name = "faith_pd",
    tree = tree
  )
}
} # }