Plots clustering results
Create plots used to study vegclust clustering results for an increasing number of clusters
## S3 method for class 'mvegclust'
plot(x, type="hnc", excludeFixed=TRUE, verbose=FALSE, ylim=NULL,
xlab=NULL, ylab=NULL, maxvar=0.6, minsize=20,...)x |
An object returned from functions |
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 |
minsize |
Minimum cluster size allowed for the |
... |
Additional plotting parameters. |
Different information is returned depending on the type of plot chosen.
Miquel De Cáceres, Forest Science Center of Catalonia
## 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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.