dbFD_w: Distance-Based Functional Diversity Indices from FD package...

In ibartomeus/fundiv: tools to calculate several functional trait diversity indexes

Description

dbFD implements a flexible distance-based framework to compute multidimensional functional diversity (FD) indices. dbFD returns the three FD indices of Villéger et al. (2008): functional richness (FRic), functional evenness (FEve), and functional divergence (FDiv), as well functional dispersion (FDis; Laliberté and Legendre 2010), Rao's quadratic entropy (Q) (Botta-Dukát 2005), a posteriori functional group richness (FGR) (Petchey and Gaston 2006), and the community-level weighted means of trait values (CWM; e.g. Lavorel et al. 2008). Some of these FD indices consider species abundances. dbFD includes several options for flexibility. dbFD_w also allows to weight all metrics by biomass

Usage

dbFD_w(x, a, w, w.abun = TRUE, stand.x = TRUE, ord = c("podani",
  "metric"), asym.bin = NULL, corr = c("sqrt", "cailliez", "lingoes",
  "none"), calc.FRic = TRUE, m = "max", stand.FRic = FALSE,
  scale.RaoQ = FALSE, calc.FGR = FALSE, clust.type = "ward",
  km.inf.gr = 2, km.sup.gr = nrow(x) - 1, km.iter = 100,
  km.crit = c("calinski", "ssi"), calc.CWM = TRUE, CWM.type = c("dom",
  "all"), calc.FDiv = TRUE, dist.bin = 2, print.pco = FALSE,
  messages = TRUE, Weigthedby = c("abundance", "biomasCarabids",
  "biomasBees", "biomassValue"), biomassValue = NA, op_qhull = "FA")

Arguments

Weigthedby	character string indicating if should be weighted by 'abundance' or 'biomassValue'. When biomassValue is in "length" units for Carabids or Bees, use options 'bi09:43:19omasCarabids' or 'biomasBees' to automatically convert it to mass.
biomassValue	numerical vector with body weigh (or length) values for each species in the same order as species are provided. It can also be a matrix or data frame with one mass value for each community and species (both communities and species arranged like in a.
op_qhull	access the options for calculating the volume of the convex hull. If a long scary warning appears mentioning qhull read convhullngeometry help page. default in FD is= "FA", but sometimes is needed to add stuff.
same	as dbFD

Value

same as dbFD

FDis vector listing the FDis of each community weighted by abundance or biomass

RaoQ vector listing the RaoQ of each community weighted by abundance or biomass

FEve vector listing the FEve of each community weighted by abundance or biomass

FDiv vector listing the FDiv of each community weighted by abundance or biomass

Examples

library(FD)
ex1 <- dbFD_w(x = dummy$trait, a = dummy$abun, Weigthedby = "biomassValue",
biomassValue = c(1.2, 2.3, 0.6, 1.0, 3.4, 0.2, 1.6, 2.2))
ex1

ibartomeus/fundiv documentation built on May 18, 2019, 1:29 a.m.