FD_Clark: Dendrogram-Based Functional Diversity weighted Indices used...

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

Description

Dendrogram-Based Functional Diversity weighted Indices used in Clarck et al 2012 (plos One) Calculate functional trait diversity for a set of communities using Petchey and Gaston 2002 index weighted version used in Clarck et al 2012

Usage

FD_Clark(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 the best 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'.
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

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

FDabund See Clark description.

FDjointabund See Clark description.

Note

This indexes are highly correlated with FDw and FDwcomm, but 1) the use of recalculated dendograms for each community is not advised 2) can not be applied to categorical traits (ignored in this function)

Examples

ex1 <- FD_Clark(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.