Get beta diversity table — betas • tidytacos

betas() returns a tidy table with the beta diversity for each combination of samples.

Usage

betas(ta, unique = T, method = "bray", binary = F, ...)

Arguments

ta

A tidytacos object.

unique

A logical scalar. Avoid redundancy by removing all self sample comparisons and keep only one of two pairwise comparisons? Default is TRUE.

method

The dissimilarity index. See vegan::vegdist() for all options. Default is "bray".

binary

A logical scalar. Perform presence/absence standardization before analysis. See vegan::vegdist(). Default is FALSE.

...

Arguments passed on to vegan::vegdist

x: Community data matrix.
diag: Compute diagonals.
upper: Return only the upper diagonal.
na.rm: Pairwise deletion of missing observations when computing dissimilarities (but some dissimilarities may still be NA, although calculation is handled).

Details

This function calculates the beta diversity using the vegan::vegdist() function of Vegan. It will report one diversity estimate for each combination of samples.

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)

# Report numbers
numbers <- data %>% betas()