optimize {vegsoup}R Documentation

Optimize Partitioning

Description

Modify the partitioning of an object as to optimize silhouette widths (distance based method) or Dufrene and Legendre's indicator value (original data).

Usage

## S4 method for signature 'VegsoupPartition'
optsil(x, maxitr = 100, verbose = FALSE, ...)

## S4 method for signature 'VegsoupPartition'
optindval(x, maxitr = 100, minsiz = 5, verbose = FALSE, ...) 

Arguments

x

'VegsoupPartition' object.

maxitr

integer. The maximum number of iterations to perform.

verbose

logical. Print elapsed CPU time.

minsiz

integer. The minimum size of the partition to consider reassigning a sample out of.

...

arguments passed to as.dist (optsil) or link{as.matrix} (optindval).

Details

optsil is a simple wrapper for function optsil in package optpart to polish an existing clustering.

optindval interfaces function optindval in package optpart. This method maximizes the Dufrene and Legendre's indicator value (Indval).

Value

Returns a modified object of class 'VegsoupPartition' with possibly changed partitioning vector.

Note

Both methods can be very slow when applied to big data sets! optsil is usually faster.

Author(s)

Roland Kaiser, implemented for vegsoup using Dave W. Roberts optsil and optindval procedures of package optpart.

References

Dufrene, M. and Legendre, P. 1997 Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecological Monographs, 67,345–366.

Rousseeuw, P. 1987 Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. Journal of Computational and Applied Mathematics, 53,53–65.

Roberts, D. 2015 Vegetation classification by two new iterative reallocation optimization algorithms. Plant Ecology, 216,741–758.

See Also

indval, silhouette

Examples

require(vegsoup)
data(windsfeld)

x <- VegsoupPartition(windsfeld, k = 5)

## Not run: 
## wait until optpart registers S3methods
xs <- optsil(x, verbose = TRUE)
xi <- optindval(x, verbose = TRUE)
confusion(xs, xi)

## End(Not run)

[Package vegsoup version 0.2-7 Index]