BAT (version 2.5.1)

hull.alpha: Alpha diversity using convex hulls.

Description

Estimation of functional richness of one or multiple sites, based on convex hull.

Usage

hull.alpha(comm, trait, return.hull = FALSE)

Arguments

comm

A "convhulln" object or a sites x species matrix, with incidence data about the species in the community.

trait

A matrix of traits for each species in comm (a species for each row and traits as columns). Must be provided only if 'comm' is a sites x species matrix.

return.hull

Boolean indicating whether the generated 'convhulln' objects used to calculate alpha diversity should be returned (default is FALSE).

Value

A vector of alpha diversity values for each site. If return.hull is set to TRUE, the function also returns the list of convex hulls used to compute alpha diversity.

Details

Estimates the functional richness (alpha FD) of one or more communities using convex hull. Note that a minimum of 4 observations for each community are needed to generate the convex hull. Functional richness is expressed as the total volume of the convex hull.

Examples

# NOT RUN {
comm <- rbind(c(1,1,1,1,1), c(1,1,1,1,1), c(0,0,1,1,1),c(0,0,1,1,1))
rownames(comm) = c("Community_1","Community_2","Community_3","Community_4")
colnames(comm) = c("Sp_1","Sp_2","Sp_3","Sp_4", "Sp_5")

trait <- cbind(c(2.2,4.4,6.1,8.3,3),c(0.5,1,0.5,0.4,4),c(0.7,1.2,0.5,0.4,5),c(0.7,2.2,0.5,0.3,6))
rownames(trait) = c("Sp_1","Sp_2","Sp_3","Sp_4","Sp_5")
colnames(trait) = c("Trait_1","Trait_2","Trait_3","Trait_4")

#example with convex hull as imput
hull.alpha(geometry::convhulln(trait,options = "FA"))

#example with comm and trait as imput
hull.alpha(comm = comm, trait = trait, return.hull = FALSE)

alpha_hull <- hull.alpha(comm = comm, trait = trait, return.hull = TRUE)
alpha_hull[[1]] #alpha diversity
alpha_hull[[2]] #list of convex hulls
# }