fun_ordinariness {divent} | R Documentation |
Functional ordinariness of a community
Description
The ordinariness of a species is the average similarity of its individuals with others (Leinster and Cobbold 2012).
Usage
fun_ordinariness(
species_distribution,
similarities = diag(sum(!colnames(species_distribution) %in% non_species_columns)),
as_numeric = FALSE,
check_arguments = TRUE
)
Arguments
species_distribution |
An object of class species_distribution. |
similarities |
A similarity matrix, that can be obtained by fun_similarity. Its default value is the identity matrix. |
as_numeric |
If |
check_arguments |
If |
Details
All species of the species_distribution
must be found in the matrix of
similarities
if it is named.
If it is not, 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
.
Value
A tibble with the ordinariness of each species, or a matrix if
argument as_numeric
is TRUE
.
References
Leinster T, Cobbold C (2012). “Measuring Diversity: The Importance of Species Similarity.” Ecology, 93(3), 477–489. doi:10.1890/10-2402.1.
Examples
fun_ordinariness(paracou_6_abd, fun_similarity(paracou_6_fundist))
# Compare with probabilities
probabilities(paracou_6_abd)
# Decrease similarities so that ordinariness is close to probability
fun_ordinariness(paracou_6_abd, fun_similarity(paracou_6_fundist, rate = 100))