Add alpha diversity measure

add_alpha() adds an alpha diversity measures to the sample table of a tidytacos object.

Usage

add_alpha(
  ta,
  method = "invsimpson",
  keep_empty_samples = FALSE,
  subsample = FALSE,
  ...
)

Arguments

ta

A tidytacos object.

method

The diversity measure to use, see vegan::diversity() for further information on these.

keep_empty_samples

Whether to keep empty samples or not.

subsample

Wether to use subsampling to be able to compare samples of varying sequencing depths. Schloss et al., 2023

...

Arguments passed on to add_subsampled_alpha

min_lib_size

the minimum lib size samples need to have. Samples with lower lib sizes will be discarded and samples with a higher readcount will be itteratively subsampled to this readcount to allow for a fair comparison across read_depths.

itterations

the amount of itterations for subsampling. Please report this number in your research.

Value

A tidytacos object with the alpha diversity measure added.

Details

This function can add different alpha diversity measures to the sample table, specified by the method argument. The following methods are available:

• invsimpson: Inverse Simpson index

• shannon: Shannon index

• simpson: Simpson index

• pielou: Pielou's evenness index

• obs: Observed richness

• s.chao1: Chao1 richness estimator

• s.ace: ACE richness estimator

See also

Other sample-modifiers: add_alphas(), add_dominant_taxa(), add_metadata(), add_ord(), add_sample_clustered(), add_spike_ratio(), add_subsampled_alpha(), add_total_absolute_abundance(), add_total_count(), add_total_density(), cluster_samples()

Other diversity-metrics: add_alphas(), add_ord(), add_subsampled_alpha()

Examples

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

# Convert to tidytacos object
data <- create_tidytacos(x,
  taxa_are_columns = FALSE
)

# Add alpha diversity measures
data <- data %>%
  add_alpha()

data <- data %>%
  add_alpha(method = "shannon")