VegsoupPartition-class: VegsoupPartition Class
In vegsoup: Classes and Methods for Phytosociology

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

Class "VegsoupPartition" is a class directly extending class Vegsoup and represents a partitioning of an object into clusters.

Objects can be created by calls of the form new("VegsoupPartition", ...) where ... expand to slots 'part', 'method' and 'k'. It is strongly advisable to use the class creator function VegsoupPartition.

part:: Object of class "numeric" giving the partitioning (clustering) vector.
partitioning.method:: Object of class "character" giving the method thta was used to create the object.
k:: Object of class "numeric" giving the number of partitions.

Class "VegsoupPartition" extends "Vegsoup" directly and all methods defined for the latter class apply.

Methods defined for class "VegsoupPartition" include the following:

1) Getter methods

partitioning: signature(obj = "VegsoupPartition"): Return partitioning (clustering) vector. See partitioning.
getK: signature(obj = "VegsoupPartition"): Return the number of partitions (clusters). See getK.

2) Indexing

[: signature(x = "VegsoupPartition", i = "ANY", j = "ANY"): Traditional row and column indexing. Note, that subsetting may also affect slots 'part', 'method', and 'k' if necessary.
partition: signature(obj = "VegsoupPartition"): Retrieve a single partition by it's value. See partition.
seriation: signature(obj = "VegsoupPartition"): Modify an objects internal order as to reflect a vegetation table. See seriation.

3) Replacement

partitioning<-: signature(obj = "VegsoupPartition", value = "numeric"): Experimental. See partitioning.

4) Object summary and print methods

summary: signature(object = "VegsoupPartition"): Summary method for "VegsoupPartition" objects.
head: signature(x = "VegsoupPartition"): Print method. See head.

5) Cluster optimization methods

optindval: signature(obj = "VegsoupPartition"): Optimize partition by maximizing Dufrene and Legendre's Indicator value. See optindval.
optsil: signature(obj = "VegsoupPartition"): Optimize partition by maximizing mean silhouette width of partitions. See optsil.

6) Table Summaries

contingency: signature(obj = "VegsoupPartition"): Contingency table. See contingency.
constancy: signature(obj = "VegsoupPartition"): Constancy table. See constancy
importance: signature(obj = "VegsoupPartition"): Importance table. See importance.

7) Descriptive statistics and and additional summaries

quantile: signature(obj = "VegsoupPartition"): Sample quantiles for each species in each partition (cluster). See quantile.
FisherTest: signature(obj = "VegsoupPartition"): Partitioning (classification) validity based Fisher Text. See FisherTest.
Tabdev: signature(obj = "VegsoupPartition"): Partition (classification) validity assessment by table deviance.
Partana: signature(obj = "VegsoupPartition"): Calculate mean object-to-partition(cluster) similarity. See partana.
richness: signature(obj = "VegsoupPartition"): Retrieve dataset, sample or species richness grouped by partitions (clusters). See richness.
spread: signature(object = "VegsoupPartition"): List occurrences of species in partitions (clusters).
shared: signature(obj = "VegsoupPartition"): Computes a diagonal matrix showing percentages of shared species between partitions (clusters). See shared.
typal: signature(obj = "VegsoupPartition"): Identifies samples (plots) that typify clusters in a partition based on dissimilarity. See typal.
partitioningMatrix: signature(obj = "VegsoupPartition"): Create a matrix of memberships of plots to partitions. See partitioningMatrix.
partitioningCombinations: signature(obj = "VegsoupPartition"): Tabulate all possible combination of partitions. See partitioningCombinations.

8) Cluster validation

disdiam: signature(obj = "VegsoupPartition"): Maximum within-cluster dissimilarity of all partitions. See disdiam.
silhouette: signature(obj = "VegsoupPartition"): Compute silhouette information. See silhouette.

9) Indicator species (fidelity) methods

fidelity: signature(obj = "VegsoupPartition"): Calculate fidelity values and promote to class "VegsoupPartitionFidelity". See fidelity and VegsoupPartitionFidelity.
SigFidelity: signature(obj = "VegsoupPartition"): Experimental. See SigFidelity.
Phi: signature(obj = "VegsoupPartition"): Calculate Phi statistic based on partitioning vector. See Phi.
Indval: signature(obj = "VegsoupPartition"): Dufrene-Legendre Indicator Species Analysis See Indval.
isamic: signature(obj = "VegsoupPartition"): Indicator species analysis to minimize intermediate constancy See isamic.
murdoch: signature(obj = "VegsoupPartition"): Indicator Species Analysis by Murdoch Preference Function. See murdoch.

10) Plot methods

plot: signature(x = "VegsoupPartition", y = "missing"): Ordination plot highlighting partitions.
rectangles: signature(obj = "VegsoupPartition"): Create a plot of matrix dimensions of each partition (cluster). See rectangles.
ellipsoidhull: signature(x = "VegsoupPartition"): Computes the ellipsoid hull such that all given plot locations lie just inside or on the boundary of the ellipsoid and adds it to a map. See ellipsoidhull.

11) Typesetting and text output methods

Latex: signature(obj = "VegsoupPartition"): Save a LaTex file- See Latex.
write.verbatim: signature(obj = "VegsoupPartition"): Output fixed column width table. See write.verbatim.

12) Spatial output methods

KML: signature(obj = "VegsoupPartition"): Save KML file for visualization in Goolge Earth. See KML.

1) Comparisons of two objects.

accuracy: signature(obj1 = "VegsoupPartition", obj2 = "VegsoupPartition"): Accuracy Statistics of two objects under comparison. See accuracy.
confusion: signature(obj1 = "VegsoupPartition", obj2 = "VegsoupPartition"): confusionion matrix of two objects. See confusion.

Roland Kaiser

Vegsoup