Package ‘vegclust’

August 25, 2022

Type Package
Title Fuzzy Clustering of Vegetation Data
Version 2.0.2
Date 2022-08-24
Description A set of functions to: (1) perform fuzzy clustering of vegetation data (De Cac-
eres et al, 2010) <doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess ecological commu-
nity similarity on the basis of structure and composition (De Cac-
eres et al, 2013) <doi:10.1111/2041-210X.12116>.
Depends R (>= 3.4.0)
Imports vegan
License GPL (>= 2)

URL https://emf-creaf.github.io/vegclust/
LazyLoad yes
Encoding UTF-8
NeedsCompilation yes
RoxygenNote 7.1.1
Suggests knitr, rmarkdown
VignetteBuilder utils, knitr
Author Miquel De Cáceres [aut, cre]
Maintainer Miquel De Cáceres <[email protected]>
Repository CRAN
Date/Publication 2022-08-25 08:50:02 UTC

R topics documented:
vegclust-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
as.memb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
as.vegclust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
CAP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1
2 vegclust-package

CAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
clustcentroid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
clustconst . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
clustvar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
concordance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
conformveg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
crossmemb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
defuzzify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
hcr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
hier.vegclust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
incr.vegclust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
interclustdist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
medreg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
plot.CAP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
plot.CAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
plot.mvegclust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
relate.levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
stratifyvegdata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
treedata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
vegclass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
vegclust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
vegclust2kmeans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
vegclustIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
vegdiststruct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
wetland . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Index 47

vegclust-package Fuzzy Clustering of Vegetation Data Functions for fuzzy and hard clus-
tering of vegetation data

Description
A set of functions to: (1) perform fuzzy clustering of vegetation data (De Caceres et al, 2010)
<doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess ecological community similarity on the ba-
sis of structure and composition (De Caceres et al, 2013) <doi:10.1111/2041-210X.12116>. This
package contains functions used to perform fuzzy and hard clustering of vegetation data under dif-
ferent models.

Details
The DESCRIPTION file:

Package: vegclust
Type: Package
Title: Fuzzy Clustering of Vegetation Data
Version: 2.0.2
vegclust-package 3

Date: 2022-08-24
Authors@R: c( person(’Miquel’, ’De Cáceres’, role=c(’aut’,’cre’), email=’[email protected]’))
Description: A set of functions to: (1) perform fuzzy clustering of vegetation data (De Caceres et al, 2010) <doi:10.11
Depends: R (>= 3.4.0)
Imports: vegan
License: GPL (>= 2)
URL: https://emf-creaf.github.io/vegclust/
LazyLoad: yes
Encoding: UTF-8
NeedsCompilation: yes
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: utils, knitr
Author: Miquel De Cáceres [aut, cre]
Maintainer: Miquel De Cáceres <[email protected]>

Index of help topics:

CAP Cumulative abundance profile (CAP)

CAS Cumulative abundance surface (CAS)
as.memb Turns into membership matrix
as.vegclust Turns into vegclust objects
clustcentroid Cluster centers of a classification
clustconst Constancy table of a classification
clustvar Cluster variance
concordance Concordance between two classifications
conformveg Conform two community data tables
crossmemb Cross-table of two fuzzy classifications
defuzzify Defuzzifies a fuzzy partition
hcr Heterogeneity-constrained random resampling
(HCR)
hier.vegclust Clustering with several number of clusters
incr.vegclust Noise clustering with increasing number of
clusters
interclustdist Calculates the distance between pairs of
cluster centroids
medreg Regeneration of Mediterranean vegetation data
set
plot.CAP Draws cummulative abundance profiles
plot.CAS Draws a cummulative abundance surface
plot.mvegclust Plots clustering results
relate.levels Relates two clustering level results.
stratifyvegdata Reshapes community data from individual into
stratified form
treedata Synthetic vegetation data set with tree data
vegclass Classifies vegetation communities
vegclust Vegetation clustering methods
4 as.memb

vegclust-package Fuzzy Clustering of Vegetation Data Functions

for fuzzy and hard clustering of vegetation
data
vegclust2kmeans Reshapes as kmeans object
vegclustIndex Compute fuzzy evaluation statistics
vegdiststruct Structural and compositional dissimilarity
wetland Wetland vegetation data set

Author(s)
NA Maintainer: NA

References
De Caceres, M., Font, X, Oliva, F. (2010) The management of numerical vegetation classifications
with fuzzy clustering methods. Journal of Vegetation Science 21 (6): 1138-1151.
De Cáceres, M., Legendre, P., & He, F. 2013. Dissimilarity measurements and the size structure of
ecological communities (D. Faith, Ed.). Methods in Ecology and Evolution 4: 1167–1177.

Examples
## Loads data
data(wetland)

## This equals the chord transformation

wetland.chord = as.data.frame(sweep(as.matrix(wetland), 1,
sqrt(rowSums(as.matrix(wetland)^2)), "/"))

## Create noise clustering with 3 clusters. Perform 10 starts from random seeds
## and keep the best solution
wetland.nc = vegclust(wetland.chord, mobileCenters=3, m = 1.2, dnoise=0.75,
method="NC", nstart=10)

as.memb Turns into membership matrix

Description
Attempts to turn its cluster vector argument into a membership matrix

Usage
as.memb(cluster)

Arguments
cluster A vector indicating the hard membership of each object in x to a set of groups.
Can contain NA values.
as.vegclust 5

Value
An matrix with as many rows as the length of cluster and as many columns as different cluster
levels. NA values will have zero membership to all clusters

Author(s)
Miquel De Cáceres, CREAF.

See Also
vegclust, vegclass

Examples
as.memb(factor(c(1,2,NA)))

as.vegclust Turns into vegclust objects

Description
Attempts to turn its arguments into a vegclust object

Usage
as.vegclust(x, y, method="KM", m=1.0, dnoise=NULL, eta=NULL)

Arguments
x A site-by-species data matrix (raw mode), or a site-by-site distance matrix (dis-
tance mode).
y A vector indicating the cluster that each object in x belongs to. Alternatively, a
fuzzy/hard site-by-group matrix of membership values.
method A clustering model from which y was obtained (normally "KM"). Current ac-
cepted models are:
• "KM": K-means or hard c-means (MacQueen 1967)
• "KMdd": Hard c-medoids (Krishnapuram et al. 1999)
• "FCM": Fuzzy c-means (Bezdek 1981)
• "FCMdd": Fuzzy c-medoids (Krishnapuram et al. 1999)
• "NC": Noise clustering (Dave and Krishnapuram 1997)
• "NCdd": Noise clustering with medoids
• "HNC": Hard noise clustering
• "HNCdd": Hard noise clustering with medoids
• "PCM": Possibilistic c-means (Krishnapuram and Keller 1993)
• "PCMdd": Possibilistic c-medoids
6 as.vegclust

m The fuzziness exponent to be used, relevant for all fuzzy models (FCM, FCMdd,
NC, NCdd, PCM and PCMdd)
dnoise The distance to the noise cluster, relevant for noise clustering models (NC, HNC,
NCdd and HNCdd).
eta A vector of reference distances, relevant for possibilistic models (PCM and
PCMdd).

Details
This function is used to generate vegclust objects which can then be used in vegclass to classify
new data. If the input classification is hard (i.e. yes/no membership), cluster centers are calculated
as multivariate means, and the method for assigning new data is assumed to be k-means ("KM"), i.e.
plots will be assigned to the nearest cluster center. If community data is given as site-by-species
data matrix the cluster centroids are added as mobileCenters in the vegclust object. Centroids
will not be computed if community data is given as a site-by-site dissimilarity matrix. Moreover,
current implementation does not allow y to be a membership matrix when x is a distance matrix.

Value
An object of class vegclust.

Author(s)
Miquel De Cáceres, CREAF.

See Also
vegclust, vegclass

Examples
## 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)), "/"))

## Splits wetland data into two matrices of 30x27 and 11x22

wetland.30 = wetland.chord[1:30,]
wetland.30 = wetland.30[,colSums(wetland.30)>0]
dim(wetland.30)
wetland.11 = wetland.chord[31:41,]
wetland.11 = wetland.11[,colSums(wetland.11)>0]
dim(wetland.11)

## Performs a K-means clustering of the data set with 30 sites

wetland.km = kmeans(wetland.30, centers=3, nstart=10)

## Transforms the 'external' classification of 30 sites into a 'vegclust' object

CAP 7

wetland.30.vc = as.vegclust(wetland.30, wetland.km$cluster)

## Assigns the second set of sites according to the (k-means) membership rule
## That is, sites are assigned to the cluster whose cluster centroids is nearest.
wetland.11.km = vegclass(wetland.30.vc, wetland.11)

## A similar 'vegclust' object is obtained when using the distance mode...

wetland.d.vc = as.vegclust(dist(wetland.30), wetland.km$cluster)

## which can be also used to produce the assignment of the second set of objects
wetland.d.11 = as.data.frame(as.matrix(dist(wetland.chord)))[31:41,1:30]
wetland.d.11.km = vegclass(wetland.d.vc,wetland.d.11)

CAP Cumulative abundance profile (CAP)

Description
Functions to calculate cumulative abundance profiles (CAPs), to build matrices from them, and to
summarize several profiles.

Usage
CAP(x, transform=NULL, verbose=FALSE)
CAP2matrix(CAP, type="cumulative",classWeights=NULL)
CAPcenters(CAP, y=NULL)
CAPquantile(CAP, q = 0.5, y = NULL)

Arguments
x A stratified vegetation data set (see function stratifyvegdata).
transform A function or the name of a function to be applied to each cumulative abundance
value.
verbose A logical flag to indicate extra output.
CAP An object of class ’CAP’.
type The type of information that the resulting matrix should contain. Either "profile",
"abundance" or "volume".
classWeights A numerical vector containing the weight for size class. If NULL, then all classes
are assumed to have the same weight.
y A vector used as a factor to calculate average or quantile profiles per each level.
Alternatively, an object of class vegclust for which CAP centroids or medoids
are desired.
q Probability value for which the quantile is desired. By default the median is
given.
8 CAP

Details
Function CAP replaces the abundance value of a size class by the sum of abundances in this and larger
size classes (strata). Thus, upper classes contain smaller abundance values than lower classes, creat-
ing a cumulative abundance profile. Function CAP2matrix takes an object of class ’CAP’ and returns
a data matrix, where values differ depending on parameter type: (1) type="cumulative" simply
reshapes the ’CAP’ object (a list) into a matrix with as many rows as plot records and where columns
are organized in blocks (there are as many blocks as species and each block has as many columns
as size classes); (2) type="total" returns a plot-by-species matrix where each value is the total
abundance of the species in the plot (i.e. the CAP value at the ground level); (3) type="volume"
returns a plot-by-species matrix where each value is the sum of CAP values across size classes (a
measure of the "volume" occupied by the species in the plot). When provided, classWeights are
used to weight size classes of the cumulative abundance profiles (for (1) and (3) only). Function
CAPcenters calculates the average abundance profile for a set of plot records. If y is a factor, it is
used to speficy groups of samples for which average profiles are to be calculated. If y is an object
of class ’vegclust’ then the function returns the CAP centroids or medoids corresponding to the
clustering result. Function CAPquantile calculates a quantile profile for a set of CAPs. The usage
of y is the same as for CAPcenters.

Value
Function CAP returns an object of class ’CAP’, similar to objects of class ’stratifiedvegdata’
but where abundance values of upper size classes have beed added to those of lower size classes.
Function CAP2matrix returns a matrix with species as rows (columns depend on the value of type).
Functions CAPcenters and CAPquantile return an object of class ’CAP’.

Author(s)
Miquel De Cáceres, CREAF.

References
De Cáceres, M., Legendre, P. & He, F. (2013) Dissimilarity measurements and the size structure of
ecological communities. Methods in Ecology and Evolution 4: 1167-1177.
De Cáceres, M., Coll, L., Martín-Alcón, S., González-Olabarria, J.R. (submitted) A general method
for the classification of forest stands using structure and composition.

See Also
stratifyvegdata, plot.CAP, vegdiststruct

Examples
## Load stratified data
data(medreg)

## Check that 'medreg' has correct class

class(medreg)

## Look at the data for the third plot

CAS 9

medreg[[3]]

## Create cumulative abundance profile (CAP) for each plot

medreg.CAP = CAP(medreg)

## Look at the profile of the third plot

medreg.CAP[[3]]

## Create matrix with species abundances

medreg.X = CAP2matrix(medreg.CAP, type="total")
head(medreg.X)

## Generate and plot average profile

average.CAP = CAPcenters(medreg.CAP)
plot(average.CAP)

## Generate and plot median profile

median.CAP = CAPquantile(medreg.CAP, q = 0.5)
plot(median.CAP)

CAS Cumulative abundance surface (CAS)

Description
Functions to calculate cumulative abundance surfaces (CASs), to build matrices from them, and to
summarize several CASs.

Usage
CAS(x, transform=NULL, verbose=FALSE)
CASmargin(CAS, margin=1, verbose=FALSE)
CAS2matrix(CAS, type="cumulative",classWeights=NULL)
CAScenters(CAS, y=NULL)
CASquantile(CAS, q = 0.5, y = NULL)

Arguments
x An object of class ’doublestratifiedvegdata’ (see function stratifyvegdata).
transform A function or the name of a function to be applied to each cumulative abundance
value.
verbose A logical flag to indicate extra output.
CAS An object of class ’CAS’.
margin Indicates whether marginalization should be done in primary (margin = 1) or
secondary (margin = 2) size classes.
type The type of information that the resulting matrix should contain (either "cummulative"
or "total").
10 CAS

classWeights A numerical matrix containing the weight for each combination of size classes.
If NULL, then all classes are assumed to have the same weight.
y A vector used as a factor to calculate average or quantile surfaces per each level.
Alternatively, an object of class vegclust for which CAS centroids or medoids
are desired.
q Probability value for which the quantile is desired. By default the median is
given.

Details
Function CAS replaces the abundance value of each combination of size classes by the sum of abun-
dances in this and larger size classes. This creates a cumulative abundance surface (similar to a
bivariant cummulative distribution function). Function CASmargin takes an object of class ’CAS’
and returns an object of class ’CAP’ that corresponds marginal profile in either the primary or the
secondary size classes. Function CAS2matrix takes an object of class ’CAS’ and returns a data ma-
trix, where values differ depending on parameter type: (1) type="cummulative" simply reshapes
the ’CAS’ object (a list) into a matrix with as many rows as plot records and where columns are
organized in blocks (there are as many blocks as species and each block has as many columns as
combinations of size classes); (2) type="total" returns a plot-by-species matrix where each value
is the total abundance of the species in the plot (i.e. the CAS value at the ground level). When
provided, classWeights are used to weight size classes of the cumulative abundance surfaces (for
(1) only). Function CAScenters calculates the average abundance surface for a set of plot records.
If y is a factor, it is used to speficy groups of samples for which average profiles are to be calcu-
lated. If y is an object of class ’vegclust’ then the function returns the CAS centroids or medoids
corresponding to the clustering result. Function CASquantile calculates a quantile surface for a set
of CASs. The usage of y is the same as for CAScenters.

Value
Function CAS returns an object of class ’CAS’, similar to objects of class ’doublestratifiedvegdata’
but where abundance values of upper size classes have beed added to those of lower size classes.
Function CAS2matrix returns a matrix with species as rows (columns depend on the value of type).
Functions CAScenters and CASquantile return an object of class ’CAS’.

Author(s)
Miquel De Cáceres, CREAF.

References
De Cáceres, M., Legendre, P. & He, F. (2013) Dissimilarity measurements and the size structure of
ecological communities. Methods in Ecology and Evolution 4: 1167-1177.
De Cáceres, M., Coll, L., Martín-Alcón, S., González-Olabarria, J.R. (submitted) A general method
for the classification of forest stands using structure and composition.

See Also
stratifyvegdata, plot.CAS, vegdiststruct
clustcentroid 11

Examples
## Load tree data
data(treedata)

## Define stratum thresholds (4 strata)

heights = seq(0,4, by=0.5)
diameters = seq(0,2, by=0.5)

## Stratify tree data using heights and diameters as structural variables

X = stratifyvegdata(treedata, sizes1=heights, sizes2=diameters, plotColumn="plotID",
speciesColumn="species", size1Column="height", size2Column="diam",
counts=TRUE)
X[[2]]

## Build cummulative abundance surface

Y = CAS(X)

Y[[2]]

## Extracts the first and second marginal (i.e. CAP on heights or diameters respectively)
Y.M1 = CASmargin(Y, margin = 1)
Y.M1[[2]]

Y.M2 = CASmargin(Y, margin = 2)

Y.M2[[2]]

## For comparison we calculate the same profiles using the stratifyvegdata and CAP functions
Y1 = CAP(stratifyvegdata(treedata, sizes1=heights, plotColumn="plotID",
speciesColumn="species", size1Column="height",
counts=TRUE))
Y1[[2]]
Y2 = CAP(stratifyvegdata(treedata, sizes1=diameters, plotColumn="plotID",
speciesColumn="species", size1Column="diam",
counts=TRUE))
Y2[[2]]

## Compare Y.M1[[2]] with Y1[[2]] and Y.M2[[2]] with Y2[[2]]

clustcentroid Cluster centers of a classification

Description

Function clustcentroid calculates the centroid (multivariate average) coordinates of a classifica-

tion. Function clustmedoid determines the medoid (object whose average dissimilarity to all the
other objects is minimal) for each cluster in the classification.
12 clustcentroid

Usage
clustcentroid(x, y, m = 1)
clustmedoid(x, y, m = 1)

Arguments
x Community data, a site-by-species data frame. In function clustmedoid, x can
alternatively be an object of class dist (otherwise, the dissimilarity measure is
assumed to be the Euclidean distance).
y It can be (a) A vector indicating the cluster that each object in x belongs to; (b)
a fuzzy/hard site-by-group matrix of membership values; (c) an object of class
vegclust or vegclass
m Fuzziness exponent, only effective when y is a fuzzy membership matrix.

Value
Function clustcentroid returns a group-by-species matrix containing species average abundance
values (i.e. the coordinates of each cluster centroid). Function clustmedoid returns a vector of
indices (medoids).

Note
In order to assign new plot record data into a predefined set of classes, one should use functions
as.vegclust and vegclass instead.

Author(s)
Miquel De Cáceres, CREAF

See Also
as.vegclust, vegclass, vegclust, kmeans

Examples
## Loads stats
library(stats)

## 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)), "/"))

## Performs a K-means clustering

wetland.km = kmeans(wetland.chord, centers=3, nstart=10)

## Gets the coordinates corresponding to the centroids of KM clusters

clustconst 13

clustcentroid(wetland.chord, y=wetland.km$cluster)

## Gets the object indices corresponding to the medoids of KM clusters

clustmedoid(wetland.chord, y=wetland.km$cluster)

clustconst Constancy table of a classification

Description
Allows studying the constancy table (i.e. the frequency of species in each class) of a classification
represented in the form of a membership data matrix.

Usage
clustconst(x, memb)
## S3 method for class 'clustconst'
summary(object, mode="all", name=NULL, sort=TRUE, minconst=0.5, digits=3, ...)

Arguments
x Community data, a site by species data frame.
memb An site-by-group matrix indicating the (hard or fuzzy) membership of each ob-
ject in x to a set of groups.
object An object of class ’clustconst’.
mode Use mode="all" to print the constancy table, mode="cluster" to print con-
stancy values for one cluster, and mode="species", to print constancy values
for one species.
name A string with the name of a cluster (in mode="cluster"), or the name of a
species (in mode="species").
sort A flag to indicate whether constancy table should be sorted in descending order.
minconst A threshold used to limit the values shown.
digits The number of digits for rounding.
... Additional parameters for summary (actually not used).

Details
The constancy value of a species in a vegetation unit is the relative frequency of occurrence of the
species in plot records that belong to the unit. In case of a fuzzy vegetation unit the constancy value
is the sum of memberships of sites that contain the species divided by the sum of memberships
of all sites. Use the ’summary’ function to obtain information about: (1) which species are more
frequent on a given vegetation unit; (2) which vegetation units have higher frequencies of a given
target species. Additionally, the ’summary’ function can sort a constancy table if mode="all" and
sort=TRUE are indicated.
14 clustvar

Value
Function clustconst returns an object of type ’clustconst’, in fact a data frame with the constancy
value of each species (rows) on each cluster (column).

Author(s)
Miquel De Cáceres, CREAF

See Also
vegclust, kmeans

Examples
## Loads stats
library(stats)

## 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)), "/"))

## Performs a K-means clustering

wetland.km = kmeans(wetland.chord, centers=3, nstart=10)

## Gets constancy table of KM (i.e. hard) clusters

c=clustconst(wetland.chord, memb=as.memb(wetland.km$cluster))

## Prints constancy values ordered and store the result in d

d=summary(c, mode="all")

## Prints the most frequent species in the first cluster

summary(c, mode="cluster", name=names(c)[1])

clustvar Cluster variance

Description
Computes the variation in community composition (i.e. beta diversity) found within the sites of a
set of hard or fuzzy clusters.

Usage
clustvar(x, cluster = NULL, defuzzify=FALSE,...)
clustvar 15

Arguments
x Community data. Either a site-by-species matrix or a site-by-site matrix of com-
positional distances between sites (i.e., an object of class dist). Alternatively,
this can be an object of class vegclust or vegclass, and in this case it is un-
necessary to provide cluster.
cluster A vector indicating the hard membership of each object in x to a set of groups.
defuzzify A flag indicating whether fuzzy memberships should be defuzzified (see func-
tion defuzzify). Only applies to the case where an object of class vegclust or
vegclass is supplied in x.
... Additional parameters for function defuzzify.

Details
This function can be used in two ways:
• if x is a data matrix (site by species or distances among sites) and cluster is null, the function
assumes a single cluster of all points in x. When cluster is provided, the function computes
cluster variance for each (hard) group and this computation implies setting the centroid of the
group. Cluster variance is defined as the average squared distance to the centroid.
• If x is an object of class vegclust or vegclass, the function uses the information contained
there (distances to cluster centers, memberships and exponent of fuzziness) in order to com-
pute cluster variances. Cluster centers do not need to be recomputed, and the distances to
cluster centers are used directly. For centroid-based cluster models (KM, FCM, NC, HNC and
PCM) the variance is defined as the average squared distance to the centroid. For medoid-
based cluster models (KMdd, FCMdd, NCdd, HNCdd and PCMdd) the variance is defined as
average distance to the medoid. The variance for both mobile and fixed clusters is returned.
Additionally, membership matrices may be defuzzified if defuzzify=TRUE.

Value
A double value (for one cluster) or a vector of values, one per each cluster.

Author(s)
Miquel De Cáceres, CREAF

See Also
vegclust, kmeans,defuzzify

Examples
## 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)), "/"))
16 concordance

## Create noise clustering with 3 clusters. Perform 10 starts from random seeds
## and keep the best solution
wetland.nc = vegclust(wetland.chord, mobileCenters=3, m = 1.2, dnoise=0.75,
method="NC", nstart=10)

## Gets cluster variance of fuzzy clusters

clustvar(wetland.nc)

## Gets cluster variance of fuzzy clusters after defuzzification

clustvar(wetland.nc, defuzzify=TRUE)

## Similar to the previous, this gets cluster variance of defuzzified (i.e. hard) clusters
clustvar(wetland.chord, cluster=defuzzify(wetland.nc)$cluster)

## Gets cluster variance of K-means (i.e. hard) clusters

clustvar(wetland.chord, cluster=kmeans(wetland.chord, centers=3, nstart=10)$cluster)

concordance Concordance between two classifications

Description
Computes an index to compare two classifications.

Usage
concordance(x, y, method="adjustedRand",...)

Arguments
x,y Classification vector or membership matrix. Alternatively, objects of type vegclust
or vegclass.
method A string vector to indicate the desired indices (see details).
... Additional parameters for function defuzzify, which will be called if x or y are
of type matrix, vegclust or vegclass.

Details
Several indices for comparison of partitions are available:

• method="Rand": Rand (1971) index.

• method="adjustedRand": Rand index adjusted for random effects (Hubert & Arabie 1985).
• method="Wallace": Wallace (1983) index (for asymmetrical comparisons). This index (and
its adjusted version) is useful to quantify how much x is nested into y.
• method="adjustedWallace": Wallace index adjusted for random effects (Pinto et al. 2008).
conformveg 17

Value
A numeric vector with the desired index values.

Author(s)
Miquel De Cáceres, CREAF

References
Hubert, L. & Arabie, P. (1985). Comparing partitions. Journal of Classification, 2, 193–218.
Pinto, F.R., Melo-Cristino, J. & Ramirez, M. (2008). A confidence interval for the wallace coeffi-
cient of concordance and its application to microbial typing methods. PLoS ONE, 3.
Rand, W.M. (1971). Objective Criteria for the Evaluation of Clustering Methods. Journal of the
American Statistical Association, 66, 846–850.
Wallace, D.L. (1983). A method for comparing two hierarchical clusterings: Comment. Journal of
the American Statistical Association, 78, 569–576.

See Also
vegclust, vegclass, defuzzify

conformveg Conform two community data tables

Description
Conforms two community data tables to have the same set of columns (species)

Usage
conformveg(x, y, fillvalue = 0, verbose=FALSE)

Arguments
x Community data, a site-by-species matrix.
y Community data, a site-by-species matrix.
fillvalue The value to be used to fill new entries in inflated matrices.
verbose Displays information about the number of species shared between x and y, as
well as the number of species that are in one of the data tables but not in the
other.

Details
This function adds to x as many new columns as columns of y that are not in x. The same is done
for y, so the two tables have the same set of columns when they are returned.
18 crossmemb

Value
A list with the two inflated matrices x and y.

Author(s)
Miquel De Cáceres, Centre Tecnologic Forestal de Catalunya.

See Also
vegclust, vegclass

Examples
## Loads data (38 columns and 33 species)
data(wetland)
dim(wetland)

## Splits wetland data into two matrices of 30x27 and 11x22

wetland.30 = wetland[1:30,]
wetland.30 = wetland.30[,colSums(wetland.30)>0]
dim(wetland.30)
wetland.11 = wetland[31:41,]
wetland.11 = wetland.11[,colSums(wetland.11)>0]
dim(wetland.11)

## Conforms the two matrices so they can eventually be merged

wetland.cf = conformveg(wetland.30, wetland.11)
dim(wetland.cf$x)
dim(wetland.cf$y)
names(wetland.cf$x)==names(wetland.cf$y)

crossmemb Cross-table of two fuzzy classifications

Description
Calculates a cross-tabulated matrix relating two fuzzy membership matrices

Usage
crossmemb(x, y, relativize = TRUE)

Arguments
x A site-by-group fuzzy membership matrix. Alternatively, an object of class ’veg-
clust’ or ’vegclass’.
y A site-by-group fuzzy membership matrix. Alternatively, an object of class ’veg-
clust’ or ’vegclass’.
relativize If TRUE expresses the cross-tabulated values as proportions of cluster size in x.
defuzzify 19

Value

A cross-tabulated matrix comparing the two classifications. In general, each cell’s value is the
(fuzzy) number of objects that in x are assigned to the cluster corresponding to the row and in y are
assigned to the cluster corresponding to the column. If relativize=TRUE then the values of each
row are divided by the (fuzzy) size of the corresponding cluster in x.

Author(s)

Miquel De Cáceres, CREAF.

See Also

defuzzify, vegclust

Examples
## 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 clustering with 3 clusters. Perform 10 starts from random seeds

## and keep the best solution. Try both FCM and NC methods:
wetland.fcm = vegclust(wetland.chord, mobileCenters=3, m = 1.2, method="FCM", nstart=10)
wetland.nc = vegclust(wetland.chord, mobileCenters=3, m = 1.2, dnoise=0.75, method="NC",
nstart=10)

## Compare the results

crossmemb(wetland.fcm, wetland.nc, relativize=FALSE)

defuzzify Defuzzifies a fuzzy partition

Description

Transforms a fuzzy classification into a crisp (hard) classification.

Usage

defuzzify(object, method = "max", alpha = 0.5, na.rm = FALSE)

20 defuzzify

Arguments
object A site-by-group fuzzy membership matrix. Alternatively, an object of class ’veg-
clust’ or ’vegclass’.
method Either "max" to choose for the maximum membership value across clusters, or
"cut" for an alpha-cut.
alpha Threshold for the alpha-cut, bounded between 0 and 1.
na.rm If TRUE removes the objects that do not belong to any cluster when using method="cut".

Details
Alpha-cut means that memberships lower than alpha are transformed into 0 while memberships
higher than alpha are transformed into 1. This means that if alpha values are low (i.e. close to 0), an
object may belong to more than one group after defuzzification. These will generate a concatenation
of cluster names in the output cluster vector and a row with sum more than one in the memb matrix).
Similarly, if alpha is high (i.e. close to 1) there are objects that may be left unclassified. These will
get NA in the cluster vector and zero row in the memb matrix.

Value
A list with the following items:

memb A data frame with the hard membership partition.

cluster A vector (factor) with the name of the cluster for each object.

Author(s)
Miquel De Cáceres, CREAF.

References
Davé, R. N. and R. Krishnapuram (1997) Robust clustering methods: a unified view. IEEE Trans-
actions on Fuzzy Systems 5, 270-293.

See Also
vegclust

Examples
## 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 with 3 clusters. Perform 10 starts from random seeds
## and keep the best solution
hcr 21

wetland.nc = vegclust(wetland.chord, mobileCenters=3, m = 1.2, dnoise=0.75,

method="NC", nstart=10)

## Defuzzification using an alpha-cut (alpha=0.5)

wetland.nc.df = defuzzify(wetland.nc$memb, method="cut")

## Cluster vector, with 'N' for objects that are unclassified,

## and 'NA' for objects that are intermediate
print(wetland.nc.df$cluster)

## Hard membership matrix (site 22 does not get any cluster assigned)
print(wetland.nc.df$memb)

hcr Heterogeneity-constrained random resampling (HCR)

Description
Returns a set of indices of the original data set that maximizes the mean and minimizes the variance
of the distances between pairs of plot records.

Usage
hcr(d, nout, nsampl=1000)

Arguments
d An object of class dist containing the distance values between pairs of sites
(plot records).
nout The number of sites (plot records) to be chosen among those available in d.
nsampl The number of resampling trials to be compared.

Details
Many subsets of the input data are selected randomly. These subsets are sorted by decreasing mean
dissimilarity between pairs of plot records, and then sorted again by increasing variance of these
dissimilarities. Ranks from both sortings are summed for each subset, and the subset with the lowest
summed rank is considered as the most representative.

Value
Returns a vector containing the indices of the selected sites (plot records) to be used for sub-setting
the original table.

Author(s)
Miquel De Cáceres, CREAF
22 hier.vegclust

References
Lengyel, A., Chytry, M., Tichy, L. (2011) Heterogeneity-constrained random resampling of phy-
tosociological databases. Journal of Vegetation Science 22: 175-183.

Examples
## Loads data (38 columns and 33 species)
data(wetland)
dim(wetland)

## Constructs the chord distance matrix

## (see also \code{\link{decostand}} in package vegan)
wetland.chord =dist(as.data.frame(sweep(as.matrix(wetland), 1,
sqrt(rowSums(as.matrix(wetland)^2)), "/")))

## Performs HCR resampling. Returns indices of objects

sel = hcr(wetland.chord, nout=20, nsampl=1000)

## Prints the names of the plot records

print(row.names(wetland)[sel])

## Subset the original distance matrix

sel.chord = as.dist(as.matrix(wetland.chord)[sel,sel])

hier.vegclust Clustering with several number of clusters

Description
Performs several runs of function ’vegclust’ (or ’vegclustdist’) on a community data matrix (or
distance matrix) using different number of clusters

Usage
hier.vegclust(x, hclust, cmin=2,cmax=20, min.size=NULL, verbose=TRUE, ...)
hier.vegclustdist(x, hclust, cmin=2,cmax=20, min.size=NULL, verbose=TRUE, ...)
random.vegclust(x, cmin=2, cmax=20, nstart=10, min.size=NULL, verbose=TRUE, ...)
random.vegclustdist(x, cmin=2, cmax=20, nstart=10, min.size=NULL, verbose=TRUE, ...)

Arguments
x For hier.vegclust and random.vegclust, a site (rows) by species (columns)
matrix or data frame. For hier.vegclustdist and random.vegclustdist, a square
distance matrix.
hclust A hierarchical clustering represented in an object of type hclust.
cmin Number of minimum mobile clusters.
cmax Number of maximum mobile clusters.
hier.vegclust 23

nstart A number indicating how many random trials should be performed for each
number of groups
min.size If min.size != NULL, it specifies the minimum size of clusters. If some clus-
ters are smaller, the algorithm will return the solutions corresponding to lower
numbers of clusters.
verbose Flag used to print which number of clusters is currently running.
... Additional parameters for function vegclust or vegclustdist.

Details
Function hier.vegclust takes starting cluster configurations from cuts of a dendrogram given
by object hclust. Function random.vegclust chooses random objects as cluster centroids and for
each number of clusters performs nstart trials. Functions hier.vegclustdist and random.vegclustdist
are analogous to hier.vegclust and random.vegclust but accept distance matrices as input.

Value
Returns an object of type ’mvegclust’ (multiple vegclust), which contains a list vector with objects
of type vegclust.

Author(s)
Miquel De Cáceres, CREAF

See Also
vegclust, vegclustdist, vegclass, defuzzify, hclust

Examples
## 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.nc1 = hier.vegclust(wetland.chord, wetland.hc, cmin=2, cmax=5,
m = 1.2, dnoise=0.75, method="NC")

## Create noise clustering from random seeds at different levels

wetland.nc2 = random.vegclust(wetland.chord, cmin=2, cmax=5, nstart=10,
m = 1.2, dnoise=0.75, method="NC")
24 incr.vegclust

incr.vegclust Noise clustering with increasing number of clusters

Description
Performs several runs of function ’vegclust’ on a community data matrix using an increasing number
of clusters until some conditions are met.

Usage
incr.vegclust(x, method="NC", ini.fixed.centers = NULL,
min.size = 10, max.var=NULL, alpha = 0.5,
nstart=100, fix.previous = TRUE, dnoise=0.75, m=1.0,...)

Arguments
x Community data table. A site (rows) by species (columns) matrix or data frame.
method A clustering model. Current accepted models are of the noise clustering family:
• "NC": Noise clustering (Dave and Krishnapuram 1997)
• "NCdd": Noise clustering with medoids
• "HNC": Hard noise clustering
• "HNCdd": Hard noise clustering with medoids
ini.fixed.centers
The coordinates of initial fixed cluster centers. These will be used as fixedCenters
in all calls to vegclust. If method="NCdd" or method="HNCdd" then ini.fixed.centers
can be specified as a vector of indices for medoids.
min.size The minimum size (cardinality) of clusters. If any of the current k clusters does
not have enough members the algorithm will stop and return the solution with
k-1 clusters.
max.var The maximum variance allowed for clusters (see function clustvar). If speci-
fied, the algorithm will stop when any of the clusters is at the same time small
and has large variance. If max.var = NULL then this criterion is not used.
alpha Criterion to choose cluster seeds from the noise class. Specifically, an object
is considered as cluster seed if the membership to the noise class is larger than
alpha.
nstart A number indicating how many random trials should be performed for number
of groups. Each random trial uses the k-1 cluster centers plus the coordinates of
the current cluster seed as initial solution for vegclust. Thus, if there are less
cluster seed candidates than nstart, then not all runs are conducted.
fix.previous Flag used to indicate that the cluster centers found when determining k-1 clusters
are fixed when determining k clusters.
m The fuzziness exponent.
dnoise The distance to the noise cluster.
... Additional parameters for function vegclust.
interclustdist 25

Details
Function hier.vegclust takes starting cluster configurations from cuts of a dendrogram given by
object hclust. Function random.vegclust chooses random objects as cluster centroids and for
each number of clusters performs nstart trials.

Value
Returns an object of class vegclust; or NULL if the initial cluster does not contain enough members.

Author(s)
Miquel De Cáceres, CREAF

References
Davé, R. N. and R. Krishnapuram (1997) Robust clustering methods: a unified view. IEEE Trans-
actions on Fuzzy Systems 5, 270-293.

See Also
vegclust,hier.vegclust

Examples
## 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)), "/"))

## Call incremental noise clustering

wetland.nc = incr.vegclust(wetland.chord, method="NC", m = 1.2, dnoise=0.75,
min.size=5)

## Inspect cluster sizes

print(wetland.nc$size)

interclustdist Calculates the distance between pairs of cluster centroids

Description
Calculates the distance between pairs of cluster centroids, given a distance matrix and a cluster
vector.
26 medreg

Usage
interclustdist(x, cluster)

Arguments
x A site-by-site data matrix or an object of class dist containing the distance
values between pairs of sites (plot records).
cluster A vector indicating the hard membership of each object in x to a set of groups.
Can contain NA values.

Value
An object of class dist containing the distances between cluster centers.

Author(s)
Miquel De Cáceres, CREAF

Examples
##TO BE DONE##

medreg Regeneration of Mediterranean vegetation data set

Description
A stratified vegetation data set containing with several plot records laid to assess vegetation recovery
three years after a wildfire. Collected in 2012 by Miquel De Caceres and Albert Petit in Horta de
Sant Joan (Catalonia, Spain).

Usage
data(medreg)

Format
An object of class ’stratifiedvegdata’ with 96 elements (plots), each of them consisting of a data.frame
where rows correspond to species groups and columns correspond to vegetation strata. Abundance
values are percentage cover.

See Also
CAP, plot.CAP

Examples
data(medreg)
plot.CAP 27

plot.CAP Draws cummulative abundance profiles

Description
Create plots used to inspect one or more cumulative abundance profiles.

Usage
## S3 method for class 'CAP'
plot(x, sizes=NULL, species=NULL, plots=NULL, switchAxes=FALSE,
add=FALSE, drawAxes = TRUE, xlab="", ylab="", type="s",...)
## S3 method for class 'stratifiedvegdata'
plot(x, sizes=NULL, species=NULL, plots=NULL, switchAxes=FALSE,
add=FALSE, drawAxes = TRUE, xlab="", ylab="", type="s",...)

Arguments
x An object returned from function CAP or an object of class stratifiedvegdata
(see documentation for function stratifyvegdata).
sizes A vector containing the size values associated to each size class. If NULL the
y-axis will be defined using the size class order in x.
species A vector of strings indicating the species whose profile is to be drawn. If NULL
all species are plotted.
plots A vector indicating the plot records whose profile is to be drawn. Can be a
character vector (for plot names), a numeric vector (for plot indices) or a
logical vector (for TRUE/FALSE selection). If NULL all plot records are plot-
ted.
switchAxes A flag indicating whether ordinate and abscissa axes should be interchanged.
add A flag indicating whether profiles should be drawn on top of current drawing
area. If add=FALSE a new plot is created.
drawAxes A flag indicating whether axes should be drawn.
xlab String label for the x axis.
ylab String label for the y axis.
type Type of plot to be drawn ("p" for points, "l" for lines, "s" for steps, ...).
... Additional plotting parameters.

Author(s)
Miquel De Cáceres, CREAF

References
De Cáceres, M., Legendre, P. & He, F. (2013) Dissimilarity measurements and the size structure of
ecological communities. Methods in Ecology and Evolution 4: 1167-1177.
28 plot.CAS

See Also
CAP

Examples
## Load stratified data
data(medreg)

## Check that 'medreg' has correct class

class(medreg)

## Create cumulative abundance profile (CAP) for each plot

medreg.CAP = CAP(medreg)

## Draw the stratified data and profile corresponding to the third plot
plot(medreg, plots="3")
plot(medreg.CAP, plots="3")

## Look at the plot and CAP of the same plot

medreg[["3"]]
medreg.CAP[["3"]]

plot.CAS Draws a cummulative abundance surface

Description
Create plots used to inspect one or more cumulative abundance profiles.

Usage
## S3 method for class 'CAS'
plot(x, plot=NULL, species=NULL, sizes1=NULL, sizes2 = NULL,
palette = colorRampPalette(c( "light blue","light green","white",
"yellow","orange","red")), zlim=NULL,...)

Arguments
x An object of class CAS.
plot A string indicating the plot record whose surface is to be drawn.
species A string indicating the species whose profile is to be drawn.
sizes1 A vector containing the size values associated to each primary size class. If NULL
the x-axis will be defined using the primary size class order in x.
sizes2 A vector containing the size values associated to each secondary size class. If
NULL the y-axis will be defined using the secondary size class order in x.
palette Color palette for z values.
zlim The limits for the z-axis.
... Additional plotting parameters for function persp.
plot.mvegclust 29

Author(s)
Miquel De Cáceres, CREAF

References
De Cáceres, M., Legendre, P. & He, F. (2013) Dissimilarity measurements and the size structure of
ecological communities. Methods in Ecology and Evolution 4: 1167-1177.

See Also
CAS, persp

Examples
## Create synthetic tree data
pl = rep(1,100) # All trees in the same plot
sp = ifelse(runif(100)>0.5,1,2) # Random species identity (species 1 or 2)
h=rgamma(100,10,2) # Heights (m)
d = rpois(100, lambda=h^2) # Diameters (cm)
m = data.frame(plot=pl,species=sp, height=h,diameter=d)
m$ba = pi*(m$diameter/200)^2
print(head(m))

## Size classes
heights = seq(0,4, by=.25)^2 # Quadratic classes
diams = seq(0,130, by=5) # Linear classes

## Stratify tree data

X<-stratifyvegdata(m, sizes1=heights, sizes2=diams,
plotColumn = "plot", speciesColumn = "species",
size1Column = "height", size2Column = "diameter",
abundanceColumn = "ba")

## Build cummulative abundance surface

Y = CAS(X)

## Plot the surface of species '1' in plot '1' using heights and diameters
plot(Y, species=1, sizes1=heights[-1], xlab="height (m)",
ylab="diameter (cm)", sizes2=diams[-1], zlab="Basal area (m2)",
zlim = c(0,6), main="Species 1")

plot.mvegclust Plots clustering results

Description
Create plots used to study vegclust clustering results for an increasing number of clusters
30 plot.mvegclust

Usage
## S3 method for class 'mvegclust'
plot(x, type="hnc", excludeFixed=TRUE, verbose=FALSE, ylim=NULL,
xlab=NULL, ylab=NULL, maxvar=0.6, minsize=20,...)

Arguments
x An object returned from functions hier.vegclust or random.vegclust.
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 type="valid" plot.
minsize Minimum cluster size allowed for the type="valid" plot.
... Additional plotting parameters.

Value
Different information is returned depending on the type of plot chosen.

Author(s)
Miquel De Cáceres, CREAF

Examples
## 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,

relate.levels 31

## 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")

relate.levels Relates two clustering level results.

Description

Analyzes how lower level clusters are assigned into upper level ones. The analysis is made for
several number of clusters.

Usage

relate.levels(lower, upper, defuzzify = FALSE, excludeFixed = FALSE, verbose=FALSE, ...)

Arguments

lower A list of objects of type vegclust or vegclass that represent classifications at

a finer level of resolution.
upper A list of objects of type vegclust or vegclass that represent classifications at
an broader level of resolution.
defuzzify A logical flag used to indicate whether the result of calling crossmemb should
be deffuzified.
excludeFixed A logical used to indicate whether fixed clusters should be excluded from the
comparison of levels.
verbose A flag used to ask for extra screen output.
... Additional parameters for function defuzzify.

Details

For each pair of vegclust (or vegclass) objects in upper and lower, the function calls func-
tion crossmemb and then, if asked, deffuzifies the resulting memberships (by calling function
defuzzify) and several quantities are calculated (see ’value’ section).
32 relate.levels

Value

A list with several data frames (see below). In each of them, the rows are items of upper and
columns are items of lower. The names of rows and columns are the number of clusters of each
vegclust (or vegclass) object.

nnoise The number of low level clusters that are assigned to the Noise class (for upper
objects using Noise clustering).
maxnoise The maximum membership value of low level clusters to the Noise class (for
upper objects using Noise clustering).
minmaxall The minimum value (across upper level clusters) of the maximum membership
value observed among the lower level clusters.
minallsize The minimum value (across upper level clusters) of the sum of membership
values across lower level clusters.
empty The number of upper level clusters (mobile or fixed) that do not have any mem-
ber among the lower level clusters.

Author(s)

Miquel De Cáceres, CREAF

See Also

vegclust, vegclass, defuzzify

Examples

## 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 cluster

wetland.hc = hclust(dist(wetland.chord),method="ward")
wetland.nc1 = hier.vegclust(wetland.chord, wetland.hc, cmin=2, cmax=6, m = 1.2,
dnoise=0.75, method="NC")
wetland.nc2 = hier.vegclust(wetland.chord, wetland.hc, cmin=2, cmax=4, m = 1.2,
dnoise=0.85, method="NC")

## Studies the assignment of levels

relate.levels(wetland.nc1, wetland.nc2, method="cut")
stratifyvegdata 33

stratifyvegdata Reshapes community data from individual into stratified form

Description
Function stratifyvegdata reshapes individual abundance values into species abundance values
per size class or combination of size classes. Function as.stratifiedvegdata checks if the input
list has appropriate properties and turns it into an object of class ’stratifiedvegdata’.

Usage
stratifyvegdata(x, sizes1, sizes2 = NULL, treeSel=NULL, spcodes = NULL,
plotColumn="plot", speciesColumn = "species",
abundanceColumn="abundance", size1Column = "size", size2Column = NULL,
cumulative=FALSE, counts=FALSE, mergeSpecies=FALSE, verbose=FALSE)
as.stratifiedvegdata(X)

Arguments
x A data frame containing individual plant data. Individuals are in rows, while
measurements are in columns.
sizes1 A numerical vector containing the breaks for primary size classes in ascending
order.
sizes2 A numerical vector containing the breaks for secondary size classes in ascending
order.
treeSel A logical vector specifying which rows in x to be used. By default (treeSel =
NULL) all rows are taken.
spcodes A character vector indicating the codes of species to be used for stratification
(species codes beyond those appearing in x are possible). If spcodes = NULL
then all species in x are used.
plotColumn The name of the column in x that contains plot identifiers.
speciesColumn The name of the column in x that contains species names.
abundanceColumn
The name of the column in x that contains abundance values.
size1Column The name of the column in x that contains values for primary size classes.
size2Column The name of the column in x that contains values for secondary size classes.
cumulative A flag to indicate that cumulative abundance profiles or surfaces are desired.
counts A flag to indicate that the output should be individual counts instead of added
abundance values.
mergeSpecies A flag to indicate that species identity should be ignored. This leads to analyzing
the structure of biomass disregarding species identity.
verbose A logical flag to indicate extra output.
34 stratifyvegdata

X A list with as many elements as plot records. Each element should be of class
’matrix’ or ’data.frame’ with species in rows and strata in columns. Further-
more, the number of rows (species) and columns (strata) should be the same for
all elements.

Details
For each individual (row) in x, stratifyvegdata assigns it to the size class (stratum) containing
its size. The corresponding abundance value (e.g. crown cover) of the individual is added to the
abundance of the corresponding species at the size class (stratum). If sizes2 and size2Column are
supplied, the function assigns each individual (row) in x to the combination of size classes (e.g. tree
height and diameter).

Value
Both functions return an object of class ’stratifiedvegdata’, which is a list of matrices, one for
each plot record. Each element (matrix) has as many rows as species and as many columns as size
classes (i.e., as many as elements in vector sizes1). Columns are named starting with ’S’ and
continuing with the size class (stratum) number. If mergeSpecies=TRUE then all matrices have a
single row (whose name is "all"). If sizes2 and size2Column are supplied to stratifyvegdata,
the function returns an object of class ’doublestratifiedvegdata’, which is a list of arrays, one
for each plot record. Each element (array) has three dimensions corresponding to species, primary
sizes (number of elements in in vector sizes1) and secondary sizes (number of elements in in vector
sizes2). If cumulative=TRUE then the function returns cumulative abundances (see CAP and CAS).

Author(s)
Miquel De Cáceres, CREAF.

References
De Cáceres, M., Legendre, P. & He, F. (2013) Dissimilarity measurements and the size structure of
ecological communities. Methods in Ecology and Evolution 4: 1167-1177.

See Also
reshape, CAP, CAS

Examples
## Load tree data
data(treedata)

## Inspect tree data

head(treedata)

## Define stratum thresholds (4 strata)

heights = seq(0,4, by=0.5)
diameters = seq(0,2, by=0.5)

## Stratify tree data using heights as structural variable

treedata 35

X = stratifyvegdata(treedata, sizes1=heights, plotColumn="plotID",

speciesColumn="species", size1Column="height", counts=TRUE)

## Inspect the second plot record

X[[2]]

## Stratify tree data using heights as structural variable and cover as abundance
Y = stratifyvegdata(treedata, sizes1=heights, plotColumn="plotID",
speciesColumn="species", size1Column="height",
abundanceColumn="cover")
Y[[2]]

## Stratify tree data using heights and diameters as structural variables

Z = stratifyvegdata(treedata, sizes1=heights, sizes2=diameters, plotColumn="plotID",
speciesColumn="species", size1Column="height", size2Column="diam",
counts=TRUE)
Z[[2]]

treedata Synthetic vegetation data set with tree data

Description

A synthetic data set used to illustrate the stratification of data originally collected on an individual
basis (e.g. forest inventory).

Usage

data(treedata)

Format

A data frame where each row corresponds to a different tree. Columns are plot code, species
identity, tree height, tree diameter and cover value.

See Also

stratifyvegdata
36 vegclass

vegclass Classifies vegetation communities

Description

Classifies vegetation communities into a previous fuzzy or hard classification.

Usage

vegclass(y, x)

Arguments

y An object of class vegclust that represents a previous knowledge.

x Community data to be classified, in form of a site by species matrix (if the
vegclust object is in raw mode) or a data frame containing the distances between
the new sites in rows and the old sites in columns (if the vegclust object is in
distance mode).

Details

This function uses the classification model specified in y to classify the communities (rows) in x.
When vegclust is in raw mode, the function calls first to conformveg in order to cope with different
sets of species. See the help of as.vegclust to see an example of vegclass with distance matrices.

Value

Returns an object of type vegclass with the following items:

method The clustering model used in y

m The fuzziness exponent in y
dnoise The distance to the noise cluster used for noise clustering (models NC, NCdd,
HNC, HNCdd). This is set to NULL for other models.
eta The reference distance vector used for possibilistic clustering (models PCM and
PCMdd). This is set to NULL for other models.
memb The fuzzy membership matrix.
dist2clusters The matrix of object distances to cluster centers.

Author(s)

Miquel De Cáceres, CREAF.

vegclass 37

References
Davé, R. N. and R. Krishnapuram (1997) Robust clustering methods: a unified view. IEEE Trans-
actions on Fuzzy Systems 5, 270-293.
Bezdek, J. C. (1981) Pattern recognition with fuzzy objective functions. Plenum Press, New York.
Krishnapuram, R. and J. M. Keller. (1993) A possibilistic approach to clustering. IEEE transactions
on fuzzy systems 1, 98-110.
De Cáceres, M., Font, X, Oliva, F. (2010) The management of numerical vegetation classifications
with fuzzy clustering methods [Related software]. Journal of Vegetation Science 21 (6): 1138-1151.

See Also
vegclust, as.vegclust, kmeans, conformveg

Examples
## Loads data (38 columns and 33 species)
data(wetland)
dim(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)), "/"))

## Splits wetland data into two matrices of 30x27 and 11x22

wetland.30 = wetland.chord[1:30,]
wetland.30 = wetland.30[,colSums(wetland.30)>0]
dim(wetland.30)
wetland.11 = wetland.chord[31:41,]
wetland.11 = wetland.11[,colSums(wetland.11)>0]
dim(wetland.11)

## Create noise clustering with 3 clusters from the data set with 30 sites.
wetland.30.nc = vegclust(wetland.30, mobileCenters=3, m = 1.2, dnoise=0.75,
method="NC", nstart=10)

## Cardinality of fuzzy clusters (i.e., the number of objects belonging to)

wetland.30.nc$size

## Classifies the second set of sites according to the clustering of the first set
wetland.11.nc = vegclass(wetland.30.nc, wetland.11)

## Fuzzy membership matrix

wetland.11.nc$memb

## Obtains hard membership vector, with 'N' for objects that are unclassified
defuzzify(wetland.11.nc$memb)$cluster
38 vegclust

vegclust Vegetation clustering methods

Description
Performs hard or fuzzy clustering of vegetation data

Usage
vegclust(x, mobileCenters, fixedCenters = NULL, method="NC", m = 2, dnoise = NULL,
eta = NULL, alpha=0.001, iter.max=100, nstart=1, maxminJ = 10, seeds=NULL,
verbose=FALSE)
vegclustdist(x, mobileMemb, fixedDistToCenters = NULL, method="NC", m = 2, dnoise = NULL,
eta = NULL, alpha=0.001, iter.max=100, nstart=1, seeds=NULL, verbose=FALSE)

Arguments
x Community data. A site-by-species matrix or data frame (for vegclust) or a
site-by-site dissimilarity matrix or dist object (for vegclustdist).
mobileCenters A number, a vector of seeds, or coordinates for mobile clusters.
fixedCenters A matrix or data frame with coordinates for fixed (non-mobile) clusters.
mobileMemb A number, a vector of seeds, or starting memberships for mobile clusters.
fixedDistToCenters
A matrix or data frame with the distances to fixed cluster centers.
method A clustering model. Current accepted models are:
• "KM": K-means or hard c-means (MacQueen 1967)
• "KMdd": Hard c-medoids (Krishnapuram et al. 1999)
• "FCM": Fuzzy c-means (Bezdek 1981)
• "FCMdd": Fuzzy c-medoids (Krishnapuram et al. 1999)
• "NC": Noise clustering (Dave and Krishnapuram 1997)
• "NCdd": Noise clustering with medoids
• "HNC": Hard noise clustering
• "HNCdd": Hard noise clustering with medoids
• "PCM": Possibilistic c-means (Krishnapuram and Keller 1993)
• "PCMdd": Possibilistic c-medoids
m The fuzziness exponent to be used (this is relevant for all models except for
kmeans)
dnoise The distance to the noise cluster, relevant for noise clustering (NC).
eta A vector of reference distances, relevant for possibilistic C-means (PCM).
alpha Threshold used to stop iterations. The maximum difference in the membership
matrix of the current vs. the previous iteration will be compared to this value.
iter.max The maximum number of iterations allowed.
vegclust 39

nstart If mobileCenters or mobileMemb is a number, how many random sets should

be chosen?
maxminJ When random starts are used, these will stop if at least maxminJ runs ended up
in the same functional value.
seeds If mobileCenters or mobileMemb is a number, a vector indicating which objects
are potential initial centers. If NULL all objects are valid seeds.
verbose Flag to print extra output.

Details
Functions vegclust and vegclustdist try to generalize the kmeans function in stats in three
ways.
Firstly, they allows different clustering models. Clustering models can be divided in (a) fuzzy or
hard; (b) centroid-based or medoid-based; (c) Partitioning (KM and FCM family), noise clustering
(NC family), and possibilistic clustering (PCM and PCMdd). The reader should refer to the original
publications to better understand the differences between models.
Secondly, users can specify fixed clusters (that is, centroids that do not change their positions during
iterations). Fixed clusters are intended to be used when some clusters were previously defined and
new data has been collected. One may allow some of these new data points to form new clusters,
while some other points will be assigned to the original clusters. In the case of models with cluster
repulsion (such as KM, FCM or NC) the new (mobile) clusters are not allowed to ’push’ the fixed
ones. As a result, mobile clusters will occupy new regions of the reference space.
Thirdly, vegclustdist implements the distance-based equivalent of vegclust. The results of
vegclust and vegclustdist will be the same (if seeds are equal) if the distance matrix is cal-
culated using the Euclidean distance (see function dist). Otherwise, the equivalence holds by
resorting on principal coordinates analysis.
Note that all data frames or matrices used as input of vegclust should be defined on the same
space of species (see conformveg). Unlike kmeans, which allows different specific algorithms,
here updates of prototypes (centroids or medoids) are done after all objects have been reassigned
(Forgy 1965). In order to obtain hard cluster definitions, users can apply the function defuzzify to
the vegclust object.

Value
Returns an object of type vegclust with the following items:

mode raw for function vegclust and dist for function vegclustdist.
method The clustering model used
m The fuzziness exponent used (m=1 in case of kmeans)
dnoise The distance to the noise cluster used for noise clustering (NC, HNC, NCdd or
HNCdd). This is set to NULL for other models.
eta The reference distance vector used for possibilistic clustering (PCM or PCMdd).
This is set to NULL for other models.
memb The fuzzy membership matrix. Columns starting with "M" indicate mobile clus-
ters, whereas columns starting with "F" indicate fixed clusters.
40 vegclust

mobileCenters If vegclust is used, this contains a data frame with the coordinates of the mo-
bile centers (centroids or medoids). If vegclustdist is used, it will contain
the indices of mobile medoids for models KMdd, FCMdd, HNCdd, NCdd and
PCMdd; or NULL otherwise.
fixedCenters If vegclust is used, this contains a data frame with the coordinates of the fixed
centers (centroids or medoids). If vegclustdist is used, it will contain the in-
dices of fixed medoids for models KMdd, FCMdd, HNCdd, NCdd and PCMdd;
or NULL otherwise.
dist2clusters The matrix of object distances to cluster centers. Columns starting with "M"
indicate mobile clusters, whereas columns starting with "F" indicate fixed clus-
ters.
withinss In the case of methods KM, FCM, NC, PCM and HNC it contains the within-
cluster sum of squares for each cluster (squared distances to cluster center weighted
by membership). In the case of methods KMdd, FCMdd, NCdd, HNCdd and
PCMdd it contains the sum of distances to each cluster (weighted by member-
ship).
size The number of objects belonging to each cluster. In case of fuzzy clusters the
sum of memberships is given.
functional The objective function value (the minimum value attained after all iterations).

Author(s)
Miquel De Cáceres, CREAF

References
Forgy, E. W. (1965) Cluster analysis of multivariate data: efficiency vs interpretability of classifica-
tions. Biometrics 21, 768-769.
MacQueen, J. (1967) Some methods for classification and analysis of multivariate observations. In
Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, eds L.
M. Le Cam and J. Neyman, 1, pp. 281-297. Berkeley, CA: University of California Press.
Davé, R. N. and R. Krishnapuram (1997) Robust clustering methods: a unified view. IEEE Trans-
actions on Fuzzy Systems 5, 270-293.
Bezdek, J. C. (1981) Pattern recognition with fuzzy objective functions. Plenum Press, New York.
Krishnapuram, R., Joshi, A., & Yi, L. (1999). A Fuzzy relative of the k-medoids algorithm
with application to web document and snippet clustering. IEEE International Fuzzy Systems (pp.
1281–1286).
Krishnapuram, R. and J. M. Keller. (1993) A possibilistic approach to clustering. IEEE transactions
on fuzzy systems 1, 98-110.
De Cáceres, M., Font, X, Oliva, F. (2010) The management of numerical vegetation classifications
with fuzzy clustering methods. Journal of Vegetation Science 21 (6): 1138-1151.

See Also
hier.vegclust,incr.vegclust,kmeans,vegclass,defuzzify,clustvar
vegclust2kmeans 41

Examples
## Loads data
data(wetland)

## This equals the chord transformation

## (see also 'decostand' in package vegan)
wetland.chord = as.data.frame(sweep(as.matrix(wetland), 1,
sqrt(rowSums(as.matrix(wetland)^2)), "/"))

## Create noise clustering with 3 clusters. Perform 10 starts from random seeds
## and keep the best solution
wetland.nc = vegclust(wetland.chord, mobileCenters=3, m = 1.2, dnoise=0.75,
method="NC", nstart=10)

## Fuzzy membership matrix

wetland.nc$memb

## Cardinality of fuzzy clusters (i.e., the number of objects belonging to each cluster)
wetland.nc$size

## Obtains hard membership vector, with 'N' for objects that are unclassified
defuzzify(wetland.nc$memb)$cluster

## The same result is obtained with a matrix of chord distances

wetland.d = dist(wetland.chord)
wetland.d.nc = vegclustdist(wetland.d, mobileMemb=3, m = 1.2, dnoise=0.75,
method="NC", nstart=10)

vegclust2kmeans Reshapes as kmeans object

Description
This function casts an object of class vegclust into an object of class kmeans.

Usage
vegclust2kmeans(x)

Arguments
x An object of class vegclust to be casted, where method="KM" and mode="raw".

Author(s)
Miquel De Cáceres, CREAF

See Also
vegclust, kmeans
42 vegclustIndex

Examples
## 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 with 3 clusters. Perform 10 starts from random seeds
wetland.vc = vegclust(wetland.chord, mobileCenters=3,
method="KM", nstart=10)

## Reshapes as kmeans object

wetland.km = vegclust2kmeans(wetland.vc)
wetland.km

vegclustIndex Compute fuzzy evaluation statistics

Description
Computes several evaluation statistics on the fuzzy clustering results on objects of class vegclust.

Usage
vegclustIndex(y)

Arguments
y An object of class vegclust or a membership matrix.

Details
These statistics were conceived to be computed on fuzzy partitions, such as the ones coming from
Fuzzy C-means (Bezdek 1981). Maximum values of PCN or minimum values of PEN can be used
as criteria to choose the number of clusters.

Value
Returns an vector of four values: partition coefficient (PC), normalized partition coefficient (PCN),
partition entropy (PE) and normalized partition entropy (PEN).

Author(s)
Miquel De Cáceres, CREAF.
vegdiststruct 43

References

Bezdek, J. C. (1981) Pattern recognition with fuzzy objective functions. Plenum Press, New York.

See Also

vegclust

Examples

## 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 with 2, 3 and 4 clusters. Perform 10 starts from random seeds
## and keep the best solutions
wetland.fcm2 = vegclust(wetland.chord, mobileCenters=2, m = 1.2, method="FCM", nstart=10)
wetland.fcm3 = vegclust(wetland.chord, mobileCenters=3, m = 1.2, method="FCM", nstart=10)
wetland.fcm4 = vegclust(wetland.chord, mobileCenters=4, m = 1.2, method="FCM", nstart=10)

## Compute statistics. Both PCN and PEN indicate that three groups are more advisable
## than 2 or 4.
print(vegclustIndex(wetland.fcm2))
print(vegclustIndex(wetland.fcm3))
print(vegclustIndex(wetland.fcm4))

vegdiststruct Structural and compositional dissimilarity

Description

Function to calculate the dissimilarity between ecological communities taking into account both
their composition and the size of organisms.

Usage

vegdiststruct(x, y=NULL, paired=FALSE, type="cumulative", method="bray",

transform=NULL, classWeights=NULL)
44 vegdiststruct

Arguments
x A stratified vegetation data set (see function stratifyvegdata), a set of cum-
mulative abundance profiles (see function CAP) or a set of cummulative abun-
dance surfaces (see function CAS).
y A second stratified vegetation data set (see function stratifyvegdata), a sec-
ond set of cummulative abundance profiles (see function CAP) or a second set
of cummulative abundance surfaces (see function CAS) against which object x
should be compared.
paired Only relevant when y != NULL. If paired = TRUE pairwise comparisons are cal-
culated between elements in x and y (and x and y need to be of the same length).
If paired = FALSE then all objects in x are compared to all objects in y.
type Whether dissimilarities between pairs of sites should be calculated from differ-
ences in cummulative abundance ("cumulative"), in total abundance ("total")
or in volumes of cumulative abundance profiles ("volume").
method The dissimilarity coefficient to calculate (see details).
transform A function or the name of a function to be applied to each cumulative abundance
value.
classWeights A numerical vector or a matrix containing the weight of each size class or com-
bination of size classes (see functions CAP2matrix and CAS2matrix). If NULL,
then the function assumes classes of equal weight.

Details
The six different coefficients available are described in De Caceres et al. (2013): (1) method="bray"
for percentage difference (alias Bray-Curtis dissimilarity); (2) method="ruzicka" for Ruzicka in-
dex (a generalization of Jaccard); (3) method="kulczynski" for the Kulczynski dissimilarity in-
dex; (4) method="ochiai" for the complement of a quantitative generalization of Ochiai index of
similarity; (5) method="canberra" for the Canberra index (Adkins form); (6) method="relman"
for the relativized Manhattan coefficient (Whittaker’s index of association). Currently, the function
also supports (7) method="manhattan" for the city block metric.

Value
Returns an object of class ’dist’.

Author(s)
Miquel De Cáceres, CREAF.

References
De Cáceres, M., Legendre, P. & He, F. (2013) Dissimilarity measurements and the size structure of
ecological communities. Methods in Ecology and Evolution 4: 1167-1177.

See Also
stratifyvegdata, vegdist
wetland 45

Examples
## Load stratified data
data(medreg)

## Check that 'medreg' has correct class

class(medreg)

## Create cumulative abundance profile (CAP) for each plot

medreg.CAP = CAP(medreg)

## Create dissimilarity (percentage difference) matrix using profiles

medreg.D = vegdiststruct(medreg, method="bray")

## Create dissimilarity (percentage difference) matrix using abundances

medreg.D2 = vegdiststruct(medreg, method="bray", type="total")

## Calculate correlation
cor(as.vector(medreg.D), as.vector(medreg.D2))

wetland Wetland vegetation data set

Description
Vegetation of the Adelaide river alluvial plain (Australia). This data set was published by Bowman
& Wilson (1987) and used in Dale (1988) to compare fuzzy classification approaches.

Usage
data(wetland)

Format
A data frame with 41 sites (rows) and 33 species (columns). Abundance values are represented in
abundance classes.

Source
Bowman, D. M. J. S. and B. A. Wilson. 1986. Wetland vegetation pattern on the Adelaide River
flood plain, Northern Territory, Australia. Proceedings of the Royal Society of Queensland 97:69-
77.

References
Dale, M. B. 1988. Some fuzzy approaches to phytosociology. Ideals and instances. Folia geobotan-
ica et phytotaxonomica 23:239-274.
46 wetland

Examples
data(wetland)
Index

∗ datasets kmeans, 12, 14, 15, 37, 39–41

medreg, 26
treedata, 35 medreg, 26
wetland, 45
∗ package persp, 28, 29
vegclust-package, 2 plot.CAP, 8, 26, 27
plot.CAS, 10, 28
as.memb, 4 plot.mvegclust, 29
as.stratifiedvegdata (stratifyvegdata), plot.stratifiedvegdata (plot.CAP), 27
33
as.vegclust, 5, 12, 36, 37 random.vegclust, 30
random.vegclust (hier.vegclust), 22
CAP, 7, 26–28, 34, 44 random.vegclustdist (hier.vegclust), 22
CAP2matrix, 44 relate.levels, 31
CAP2matrix (CAP), 7 reshape, 34
CAPcenters (CAP), 7
CAPquantile (CAP), 7 stratifyvegdata, 7–10, 27, 33, 35, 44
CAS, 9, 28, 29, 34, 44 summary.clustconst (clustconst), 13
CAS2matrix, 44
CAS2matrix (CAS), 9 treedata, 35
CAScenters (CAS), 9
vegclass, 5, 6, 12, 15–18, 23, 31, 32, 36, 40
CASmargin (CAS), 9
vegclust, 5–8, 10, 12, 14–20, 23–25, 31, 32,
CASquantile (CAS), 9
36, 37, 38, 41–43
clustcentroid, 11
vegclust-package, 2
clustconst, 13
vegclust2kmeans, 41
clustmedoid (clustcentroid), 11
vegclustdist, 23
clustvar, 14, 24, 40
vegclustdist (vegclust), 38
concordance, 16
vegclustIndex, 42
conformveg, 17, 36, 37, 39
vegdist, 44
crossmemb, 18, 31
vegdiststruct, 8, 10, 43
defuzzify, 15–17, 19, 19, 23, 31, 32, 39, 40
wetland, 45
dist, 12, 15, 21, 26, 38, 39, 44

hclust, 22, 23
hcr, 21
hier.vegclust, 22, 25, 30, 40
hier.vegclustdist (hier.vegclust), 22

incr.vegclust, 24, 40
interclustdist, 25

47