View source: R/plot.mvegclust.R
plot.mvegclust | R Documentation |
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, CREAF
## 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")
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