hull.beta: Beta diversity partitioning using convex hull hypervolumes.

In BAT: Biodiversity Assessment Tools

Beta diversity partitioning using convex hull hypervolumes.

Description

Pairwise beta diversity partitioning into replacement and net difference in amplitude components of convex hulls.

Usage

hull.beta(comm, func = "jaccard", comp = FALSE)

Arguments

comm	A list of 'convhulln' objects, preferably built with function hull.build.
func	Partial match indicating whether the Jaccard (default) or Soerensen family of beta diversity measures should be used.
comp	Boolean indicating whether beta diversity components (shared and unique fractions) should be returned.

Details

Computes a pairwise decomposition of the overall differentiation among convex hull hypervolumes. The beta diversity measures used here follow the partitioning frameworks developed by Podani & Schmera (2011), Carvalho et al. (2012) and Legendre (2019) and later expanded to PD and FD by Cardoso et al. (2014), where Btotal = Brepl + Brich or Btotal = Bgain + Bloss. Btotal = total beta diversity, reflecting both species replacement and loss/gain; Brepl = beta diversity explained by replacement of species alone; Brich = beta diversity explained by species loss/gain (richness differences) alone; Bgain = beta diversity explained by species gain from T1 to T2; Bloss = beta diversity explained by species lost from T1 to T2.

Value

Five pairwise distance matrices, one per each of the five beta diversity metrics. If comp = TRUE also three distance matrices with beta diversity components.

References

Cardoso, P., Rigal, F., Carvalho, J.C., Fortelius, M., Borges, P.A.V., Podani, J. & Schmera, D. (2014) Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference components. Journal of Biogeography, 41, 749-761.

Carvalho, J.C., Cardoso, P. & Gomes, P. (2012) Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. Global Ecology and Biogeography, 21, 760-771.

Legendre, P. (2019) A temporal beta-diversity index to identify sites that have changed in exceptional ways in space–time surveys. Ecology and Evolution, 9: 3500-3514.

Podani, J. & Schmera, D. (2011) A new conceptual and methodological framework for exploring and explaining pattern in presence-absence data. Oikos, 120, 1625-1638.

Examples

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))
colnames(comm) = c("SpA","SpB","SpC","SpD", "SpE")
rownames(comm) = c("Site 1","Site 2","Site 3","Site 4")

trait <- cbind(c(2.2,4.4,6.1,8.3,3),c(0.5,1,0.5,0.4,4))
colnames(trait) = c("Trait 1","Trait 2")
rownames(trait) = colnames(comm)

hvlist = hull.build(comm, trait)
hull.beta(hvlist)
hull.beta(hvlist, comp = TRUE)

BAT documentation built on Aug. 8, 2025, 6:35 p.m.