Estimate the quadratic entropy Rao1982divent of species from abundance or probability data. An estimator Lande1996divent is available to deal with incomplete sampling.
ent_rao(x, ...)
# S3 method for class 'numeric'
ent_rao(
x,
distances = NULL,
tree = NULL,
normalize = TRUE,
estimator = c("Lande", "naive"),
as_numeric = FALSE,
...,
check_arguments = TRUE
)
# S3 method for class 'species_distribution'
ent_rao(
x,
distances = NULL,
tree = NULL,
normalize = TRUE,
estimator = c("Lande", "naive"),
gamma = FALSE,
...,
check_arguments = TRUE
)
An object, that may be a numeric vector containing abundances or probabilities, or an object of class abundances or probabilities.
Unused.
A distance matrix or an object of class stats::dist
An ultrametric, phylogenetic tree. May be an object of class phylo_divent, ape::phylo, ade4::phylog or stats::hclust.
If TRUE
, phylogenetic is normalized: the height of the tree is set to 1.
An estimator of entropy.
If TRUE
, a number or a numeric vector is returned rather than a tibble.
If TRUE
, the function arguments are verified.
Should be set to FALSE
to save time when the arguments have been checked elsewhere.
If TRUE
, \(\gamma\) diversity, i.e. diversity of the metacommunity, is computed.
A tibble with the site names, the estimators used and the estimated entropy.
Rao's entropy is phylogenetic or similarity-based entropy of order 2.
ent_phylo and ent_similarity with argument q = 2
provide more estimators
and allow estimating entropy at a chosen level.
All species of the species_distribution
must be found in the matrix of
distances
if it is named.
If it is not or if x
is numeric, its size must equal the number of species.
Then, the order of species is assumed to be the same as that of the
species_distribution
or its numeric equivalent.
# Entropy of each community
ent_rao(paracou_6_abd, tree = paracou_6_taxo)
#> # A tibble: 4 × 5
#> site weight estimator order entropy
#> <chr> <dbl> <chr> <dbl> <dbl>
#> 1 subplot_1 1.56 Lande 2 0.970
#> 2 subplot_2 1.56 Lande 2 0.977
#> 3 subplot_3 1.56 Lande 2 0.973
#> 4 subplot_4 1.56 Lande 2 0.973
# Similar to (but estimators are not the same)
ent_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2)
#> # A tibble: 4 × 5
#> site weight estimator q entropy
#> <chr> <dbl> <chr> <dbl> <dbl>
#> 1 subplot_1 1.56 UnveilJ 2 0.943
#> 2 subplot_2 1.56 UnveilJ 2 0.953
#> 3 subplot_3 1.56 UnveilJ 2 0.951
#> 4 subplot_4 1.56 UnveilJ 2 0.939
# Functional entropy
ent_rao(paracou_6_abd, distances = paracou_6_fundist)
#> # A tibble: 4 × 5
#> site weight estimator order entropy
#> <chr> <dbl> <chr> <dbl> <dbl>
#> 1 subplot_1 1.56 Lande 2 0.365
#> 2 subplot_2 1.56 Lande 2 0.393
#> 3 subplot_3 1.56 Lande 2 0.383
#> 4 subplot_4 1.56 Lande 2 0.365
# gamma entropy
ent_rao(paracou_6_abd, tree = paracou_6_taxo, gamma = TRUE)
#> # A tibble: 1 × 4
#> site estimator order entropy
#> <chr> <chr> <dbl> <dbl>
#> 1 Metacommunity Lande 2 0.976