FDtree: Cretae a dendrogram for use in FD analysis

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

Description

Calculate dendrogram and extract branch lengths for use in FD analysis.

Usage

FDtree(S, 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"))

Arguments

S	matrix or data frame of functional traits. Traits can be numeric, ordered, or factor. NAs are tolerated.
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)

Value

an xtree object

The queality of the tree is printed. The quality of the dendogram representation. clustering performance is assessed by the correlation with the cophenetic distance

Examples

ex1 <- FDtree(S = dummy$trait, w = NA,
                   Distance.method = "gower", ord = "podani", Cluster.method = "average")
ex1

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