clustergram: Clustergram base function

In EcotoneFinder: Characterising and Locating Ecotones and Communities

Description

Clustergram base function

Usage

clustergram(Data, k.range = 2:10,
  clustering.function = clustergram.kmeans,
  clustergram.plot = clustergram.plot.matlines, line.width = 0.004,
  add.center.points = TRUE, ...)

Arguments

Data	Should be a scales matrix. Where each column belongs to a different dimension of the observations
k.range	A vector with the number of clusters to plot the clustergram for.
clustering.function	Which clustering method to be used. Default is k-means. Can be FCM is set to clustergram.vegclust. See details
clustergram.plot	Type of plot for the output. See details.
line.width	Graphical parameter. Width of the lines.
add.center.points	Logical. Should the cluster means be plotted (as points).
...	Additional arguments to be passed to the clustering function.

Details

This is the clustergram function created by Matthias Schonlau. See: Schonlau M. The clustergram: A graph for visualizing hierarchical and nonhierarchical cluster analyses. The Stata Journal. 2002;2:391–402.

It is reproduced in this package for convenience. This package also provide extensions of the clustergram method for fuzzy-c-means clustering and for the evolution of the main fuzzy indices. These extensions take the form of additional options to be passed in the clustering.function argument and the clustergram.plot argument.

It is also recommended to run the clustergram analysis several times and compare the obtained outputs, as they may vary significantly.

Value

A clustergram plot of the inputed data

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"))

   ######## 6 clustergram plots
   for (i in 1:6) clustergram(as.matrix(SyntheticTrial[,2:ncol(SyntheticTrial)]),
                              k.range = 2:10, line.width = .2)

EcotoneFinder documentation built on Feb. 17, 2021, 1:07 a.m.