plot.mvegclust: Plots clustering results

Description Usage Arguments Value Author(s) Examples

View source: R/plot.mvegclust.R

Description

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

Usage

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## 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

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## 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")

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
PROCESSING 2 MOBILE CLUSTERS
PROCESSING 3 MOBILE CLUSTERS
PROCESSING 4 MOBILE CLUSTERS
PROCESSING 5 MOBILE CLUSTERS

vegclust documentation built on May 29, 2018, 9:04 a.m.