VegsoupPartition-class: VegsoupPartition Class

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

Description

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

Objects from the Class

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.

Slots

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.

Extends

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

Methods

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.

Author(s)

Roland Kaiser

See Also

Vegsoup

Examples

1
showClass("VegsoupPartition")

vegsoup documentation built on Feb. 24, 2021, 3 a.m.