Hill-number evenness

Evenness expressed through Hill numbers as the ratio of diversity of order q to richness (qD / 0D), which ranges from 0 to 1.

Usage

hilleven(
  data,
  q = c(1, 2),
  tree = NULL,
  dist = NULL,
  tau = NULL,
  type = c("auto", "neutral", "phylogenetic", "functional"),
  out = c("tibble", "matrix")
)

Arguments

data

Counts: a numeric vector (one sample), a matrix/data.frame (taxa x samples), a phyloseq object or a TreeSummarizedExperiment.

q

Numeric vector of diversity orders (> 0 are meaningful for evenness). Defaults to c(1, 2).

tree

A phylogenetic tree of class phylo whose tip labels match the taxa in data.

dist

A functional distance matrix (or dist) over the taxa.

tau

Optional functional distance threshold. Defaults to max(dist).

type

Diversity type: "auto" (default) infers it from the inputs (counts only -> neutral, +tree -> phylogenetic, +dist -> functional); an explicit "neutral", "phylogenetic" or "functional" asserts the type and is validated against the inputs (e.g. "phylogenetic" requires a tree; "neutral" ignores any tree/dist carried by the object).

out

Output shape: "tibble" (default) returns a long-format data.frame with columns q, sample, value; "matrix" returns a matrix with samples in rows and orders in columns.

Value

A long-format data.frame of class hill_evenness (default) with a plot() method, or a matrix of evenness values (samples in rows, orders in columns) when out = "matrix".

See also

hilldiv()

Examples

counts <- matrix(c(10, 0, 5, 2, 8, 1), nrow = 3,
                 dimnames = list(c("t1", "t2", "t3"), c("s1", "s2")))
hilleven(counts)
#> Computing neutral evenness of "q1" and "q2".
#> <hilldiv3 result: neutral>
#> 4 rows x 3 cols
#> 
#>   q sample     value
#> 1 1     s1 0.9449408
#> 2 2     s1 0.9000000
#> 3 1     s2 0.7124362
#> 4 2     s2 0.5845411
plot(hilleven(counts, q = c(1, 1.5, 2)))
#> Computing neutral evenness of "q1", "q1.5", and "q2".