plot.mvegclust: Plots clustering results

In miquelcaceres/vegclust: Fuzzy Clustering of Vegetation Data

Description

Create plots used to study vegclust clustering results for an increasing number of clusters

Usage

## S3 method for class 'mvegclust'
plot(x, type="hnc", excludeFixed=TRUE, verbose=FALSE, ylim=NULL, 
                         xlab=NULL, ylab=NULL, maxvar=0.6, minsize=20,...)

Arguments

x	An object returned from functions hier.vegclust or random.vegclust.
type	A string indicating the type of plot desired. Current accepted values are "hnc","hmemb","var","hcs" and "valid".
excludeFixed	A flag to indicate whether clusters with fixed centroids should be excluded from plots.
verbose	A flag to print extra information.
ylim	A vector with the limits for the y axis.
xlab	String label for the x axis.
ylab	String label for the y axis.
maxvar	Maximum cluster variance allowed for the type="valid" plot.
minsize	Minimum cluster size allowed for the type="valid" plot.
...	Additional plotting parameters.

Value

Different information is returned depending on the type of plot chosen.

Author(s)

Miquel De Cáceres, Forest Science Center of Catalonia

Examples

## Loads data  
data(wetland)
  
## This equals the chord transformation 
## (see also \code{\link{decostand}} in package 'vegan')
wetland.chord = as.data.frame(sweep(as.matrix(wetland), 1, 
                              sqrt(rowSums(as.matrix(wetland)^2)), "/"))

## Create noise clustering from hierarchical clustering at different number of clusters
wetland.hc = hclust(dist(wetland.chord),method="ward") 
wetland.nc = hier.vegclust(wetland.chord, wetland.hc, cmin=2, cmax=5, m = 1.2, 
                           dnoise=0.75, method="NC")

## Plot changes in the number of objects falling into the noise cluster
plot(wetland.nc, type="hnc")

## Plots the number of objects falling into "true" clusters, 
## the number of objects considered intermediate, 
## and the number of objects falling into the noise
plot(wetland.nc, type="hmemb")

## Plot minimum, maximum and average cluster size
plot(wetland.nc, type="hcs")

## Plot minimum, maximum and average cluster variance
plot(wetland.nc, type="var")

## Plot number of groups with high variance, low membership or both
plot(wetland.nc, type="valid")

miquelcaceres/vegclust documentation built on May 29, 2019, 2:57 p.m.