clustergram.vegclust {EcotoneFinder}

Vegclust function for clustergram

Description

Vegclust function for clustergram

Usage

clustergram.vegclust(Data, k, method = method, ...)

Arguments

Data

Should be a scales matrix. Where each column belongs to a different dimension of the observations.

k

Number of desired groups for the FCM clustering.

method

Clustering method for the vegclust function.

...

Additional parameters to be passed to the vegclust function.

Details

This is an implementation of Fuzzy c-means clustering (with the vegclust function of the vegclust package) for the clustergram function. The return list is internally used by the clustergram to build the clustergram plot.

Value

A list containing the cluster vector and the centers matrix (see vegclust function).

Examples

  ####### Example data:
   SyntheticTrial <- SyntheticData(SpeciesNum = 100,
                                   CommunityNum = 3, SpCo = NULL,
                                   Length = 500,
                                   Parameters = list(a=c(40, 80, 50),
                                                     b=c(100,250,400),
                                                     c=rep(0.03,3)),
                                   dev.c = .015, pal = c("#008585", "#FBF2C4", "#C7522B"))

   ######## clustergram plot
   clustergram(as.matrix(SyntheticTrial[,2:ncol(SyntheticTrial)]),
                              clustering.function = clustergram.vegclust,
                              k.range = 2:10, line.width = .2)