FD_dendro: Dendrogram-Based Functional Diversity Indices

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

Description

Calculate functional trait diversity for a set of communities using Ptchey and Gaston 2002 index and its weighted version used in Gagig et al. In prep.

Usage

FD_dendro(S, A, w = NA, Distance.method = "gower", ord = c("podani",
  "metric"), Cluster.method = c(ward = "ward", single = "single", complete =
  "complete", UPGMA = "average", UPGMC = "centroid", WPGMC = "median", WPGMA =
  "mcquitty"), stand.x = TRUE, stand.FD = FALSE,
  Weigthedby = c("abundance", "biomasCarabids", "biomasBees", "biomassValue"),
  biomassValue = NA)

Arguments

S	matrix or data frame of functional traits. Traits can be numeric, ordered, or factor. NAs are tolerated.
A	matrix containing the abundances of the species in S (or presence-absence, i.e. 0 or 1). Rows are sites and species are columns. NA not tolerated. The number of species (columns) in A must match the number of species (rows) in S. In addition, the species labels in A and S must be identical and in the same order.
w	vector listing the weights for the traits in x. Can be missing, in which case all traits have equal weights.
Distance.method	metric to calculate the species distance matrix. Only Gower is implemented.
ord	character string specifying the method to be used for ordinal traits (i.e. ordered). "podani" refers to Eqs. 2a-b of Podani (1999), while "metric" refers to his Eq. 3. See gowdis for more details.
Cluster.method	Distance method used to produce the tree. UPGMA="average" is usually giving th ebest results (Podani et al. 2011)
stand.x	ogical; if all traits are numeric, should they be standardized to mean 0 and unit variance? If not all traits are numeric, Gower's (1971) standardization by the range is automatically used; see gowdis for more details.
stand.FD	logical; should FD be standardized by the max FD, so that FD is constrained between 0 and 1?
Weigthedby	character string indicating if should be weighted by 'abundance' or 'biomassValue'. If biomassValue is in length units for Carabids or bees, use options 'biomasCarabids' or 'biomasBees' to autmatically convert 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).

Value

comm vector with the name of the community

n_sp vector listing the number of species for each community

n_tr vector listing the number of traits used

FDpg vector listing FDpg (petchey and gaston) for each community

FDw vector listing FD weighthed by species relative abundances/biomass in each community

FDwcomm vector listing FD weighthed by species abundances/biomass across all communities

qual.FD vector repeating the quality of the dendogram representation. clustering performance is assessed by the correlation with the cophenetic distance

Examples

ex1 <- FD_dendro(S = dummy$trait, A = dummy$abun, Cluster.method = "average", ord = "podani",
                    Weigthedby = "abundance")
ex1

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