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#' Compute Functional Evenness (FEve)
#'
#' This function computes Functional Evenness (FEve) following Villéger et al.
#' (2008). NB: By definition FEve is equal to `NA` when the number of species
#' per site is strictly lower than 3.
#'
#' @inheritParams fd_raoq
#'
#' @inheritSection fd_fric Parallelization
#'
#' @examples
#' data(traits_birds)
#' fd_feve(traits_birds)
#'
#' @return a data.frame with two columns:
#' * `site` character column that contains site names based on input `sp_com`
#' row names,
#' * `FEve` numeric column that contains FEve values corresponding to each site.
#'
#' NB: By definition FEve is equal to `NA` when the number of species per site
#' is strictly lower than 3.
#'
#' @references
#' Villéger, S., Mason, N.W.H., Mouillot, D., 2008. New Multidimensional
#' Functional Diversity Indices for a Multifaceted Framework in Functional
#' Ecology. Ecology 89, 2290–2301. \doi{10.1890/07-1206.1}
#'
#' @importFrom stats dist
#' @importFrom future.apply future_apply
#'
#' @export
fd_feve <- function(traits = NULL, sp_com, dist_matrix = NULL) {
if ((!is.null(traits) && !is.null(dist_matrix)) ||
(is.null(traits) && is.null(dist_matrix))) {
stop(
"Please provide either a trait dataset or a dissimilarity matrix",
call. = FALSE
)
}
if (is.data.frame(traits) || is.vector(traits)) {
traits <- as.matrix(traits)
}
if (!is.null(traits) && !is.numeric(traits)) {
stop("Non-continuous trait data found in input traits. ",
"Please provide only continuous trait data", call. = FALSE)
}
if (is.null(dist_matrix)) {
traits <- remove_species_without_trait(traits)
dist_matrix <- dist(traits)
}
dist_matrix <- as.matrix(dist_matrix)
if (!missing(sp_com)) {
common_species <- species_in_common(dist_matrix, sp_com)
dist_matrix <- dist_matrix[common_species, common_species, drop = FALSE]
sp_com <- sp_com[, common_species, drop = FALSE]
} else {
sp_com <- matrix(1,
ncol = nrow(dist_matrix),
dimnames = list("s1", rownames(dist_matrix))
)
}
# Standardize abundance per site
site_abundances <- rowSums(sp_com, na.rm = TRUE)
site_abundances[site_abundances == 0] <- 1 # Account for site with no species
sp_com <- sp_com / site_abundances
feve_site <- future_apply(sp_com, 1, function(site_row) {
fd_feve_single(site_row, dist_matrix)
}, future.globals = FALSE)
data.frame(
site = rownames(sp_com),
FEve = feve_site,
row.names = NULL
)
}
# Hide gory details of computing single FEve values
fd_feve_single <- function(site_row, dist_matrix) {
species <- site_row > 0
if (sum(species) < 3) {
return(NA_real_)
}
mst <- vegan::spantree(dist_matrix[species, species])
one_over_s_minus_one <- 1 / (mst$n - 1)
parent_nodes <- mst$labels[seq_along(mst$kid) + 1]
child_nodes <- mst$labels[mst$kid]
ew <- mst$dist / (site_row[parent_nodes] + site_row[child_nodes])
pew <- ew / sum(ew)
FEve <- (sum(pmin(pew, one_over_s_minus_one)) - one_over_s_minus_one) /
(1 - one_over_s_minus_one)
return(FEve)
}
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