fpc (version 2.2-9)

kmeansCBI: Interface functions for clustering methods

Description

These functions provide an interface to several clustering methods implemented in R, for use together with the cluster stability assessment in clusterboot (as parameter clustermethod; "CBI" stands for "clusterboot interface"). In some situations it could make sense to use them to compute a clustering even if you don't want to run clusterboot, because some of the functions contain some additional features (e.g., normal mixture model based clustering of dissimilarity matrices projected into the Euclidean space by MDS or partitioning around medoids with estimated number of clusters, noise/outlier identification in hierarchical clustering).

Usage

kmeansCBI(data,krange,k,scaling=FALSE,runs=1,criterion="ch",...)

hclustCBI(data,k,cut="number",method,scaling=TRUE,noisecut=0,...)

hclusttreeCBI(data,minlevel=2,method,scaling=TRUE,...)

disthclustCBI(dmatrix,k,cut="number",method,noisecut=0,...)

noisemclustCBI(data,G,k,modelNames,nnk,hcmodel=NULL,Vinv=NULL, summary.out=FALSE,...)

distnoisemclustCBI(dmatrix,G,k,modelNames,nnk, hcmodel=NULL,Vinv=NULL,mdsmethod="classical", mdsdim=4, summary.out=FALSE, points.out=FALSE,...)

claraCBI(data,k,usepam=TRUE,diss=inherits(data,"dist"),...)

pamkCBI(data,krange=2:10,k=NULL,criterion="asw", usepam=TRUE, scaling=FALSE,diss=inherits(data,"dist"),...)

tclustCBI(data,k,trim=0.05,...)

dbscanCBI(data,eps,MinPts,diss=inherits(data,"dist"),...)

mahalCBI(data,clustercut=0.5,...)

mergenormCBI(data, G=NULL, k=NULL, modelNames=NULL, nnk=0, hcmodel = NULL, Vinv = NULL, mergemethod="bhat", cutoff=0.1,...)

speccCBI(data,k,...)

pdfclustCBI(data,...)

stupidkcentroidsCBI(dmatrix,k,distances=TRUE)

stupidknnCBI(dmatrix,k)

stupidkfnCBI(dmatrix,k)

stupidkavenCBI(dmatrix,k)

Arguments

data

a numeric matrix. The data matrix - usually a cases*variables-data matrix. claraCBI, pamkCBI and dbscanCBI work with an n*n-dissimilarity matrix as well, see parameter diss.

dmatrix

a squared numerical dissimilarity matrix or a dist-object.

k

numeric, usually integer. In most cases, this is the number of clusters for methods where this is fixed. For hclustCBI and disthclustCBI see parameter cut below. Some methods have a k parameter on top of a G or krange parameter for compatibility; k in these cases does not have to be specified but if it is, it is always a single number of clusters and overwrites G and krange.

scaling

either a logical value or a numeric vector of length equal to the number of variables. If scaling is a numeric vector with length equal to the number of variables, then each variable is divided by the corresponding value from scaling. If scaling is TRUE then scaling is done by dividing the (centered) variables by their root-mean-square, and if scaling is FALSE, no scaling is done before execution.

runs

integer. Number of random initializations from which the k-means algorithm is started.

criterion

"ch" or "asw". Decides whether number of clusters is estimated by the Calinski-Harabasz criterion or by the average silhouette width.

cut

either "level" or "number". This determines how cutree is used to obtain a partition from a hierarchy tree. cut="level" means that the tree is cut at a particular dissimilarity level, cut="number" means that the tree is cut in order to obtain a fixed number of clusters. The parameter k specifies the number of clusters or the dissimilarity level, depending on cut.

method

method for hierarchical clustering, see the documentation of hclust.

noisecut

numeric. All clusters of size <=noisecut in the disthclustCBI/hclustCBI-partition are joined and declared as noise/outliers.

minlevel

integer. minlevel=1 means that all clusters in the tree are given out by hclusttreeCBI or disthclusttreeCBI, including one-point clusters (but excluding the cluster with all points). minlevel=2 excludes the one-point clusters. minlevel=3 excludes the two-point cluster which has been merged first, and increasing the value of minlevel by 1 in all further steps means that the remaining earliest formed cluster is excluded.

G

vector of integers. Number of clusters or numbers of clusters used by mclustBIC. If G has more than one entry, the number of clusters is estimated by the BIC.

modelNames

vector of string. Models for covariance matrices, see documentation of mclustBIC.

nnk

integer. Tuning constant for NNclean, which is used to estimate the initial noise for noisemclustCBI and distnoisemclustCBI. See parameter k in the documentation of NNclean. nnk=0 means that no noise component is fitted.

hcmodel

string or NULL. Determines the initialization of the EM-algorithm for mclustBIC. Documented in hc.

Vinv

numeric. See documentation of mclustBIC.

summary.out

logical. If TRUE, the result of summary.mclustBIC is added as component mclustsummary to the output of noisemclustCBI and distnoisemclustCBI.

mdsmethod

"classical", "kruskal" or "sammon". Determines the multidimensional scaling method to compute Euclidean data from a dissimilarity matrix. See cmdscale, isoMDS and sammon.

mdsdim

integer. Dimensionality of MDS solution.

points.out

logical. If TRUE, the matrix of MDS points is added as component points to the output of noisemclustCBI.

usepam

logical. If TRUE, the function pam is used for clustering, otherwise clara. pam is better, clara is faster.

diss

logical. If TRUE, data will be considered as a dissimilarity matrix. In claraCBI, this requires usepam=TRUE.

krange

vector of integers. Numbers of clusters to be compared.

trim

numeric between 0 and 1. Proportion of data points trimmed, i.e., assigned to noise. See tclust in the tclust package.

eps

numeric. The radius of the neighborhoods to be considered by dbscan.

MinPts

integer. How many points have to be in a neighborhood so that a point is considered to be a cluster seed? See documentation of dbscan.

clustercut

numeric between 0 and 1. If fixmahal is used for fuzzy clustering, a crisp partition is generated and points with cluster membership values above clustercut are considered as members of the corresponding cluster.

mergemethod

method for merging Gaussians, passed on as method to mergenormals.

cutoff

numeric between 0 and 1, tuning constant for mergenormals.

distances

logical (only for stupidkcentroidsCBI). If FALSE, dmatrix is interpreted as cases&variables data matrix.

...

further parameters to be transferred to the original clustering functions (not required).

Value

All interface functions return a list with the following components (there may be some more, see summary.out and points.out above):

result

clustering result, usually a list with the full output of the clustering method (the precise format doesn't matter); whatever you want to use later.

nc

number of clusters. If some points don't belong to any cluster, these are declared "noise". nc includes the "noise cluster", and there should be another component nccl, being the number of clusters not including the noise cluster.

clusterlist

this is a list consisting of a logical vectors of length of the number of data points (n) for each cluster, indicating whether a point is a member of this cluster (TRUE) or not. If a noise cluster is included, it should always be the last vector in this list.

partition

an integer vector of length n, partitioning the data. If the method produces a partition, it should be the clustering. This component is only used for plots, so you could do something like rep(1,n) for non-partitioning methods. If a noise cluster is included, nc=nccl+1 and the noise cluster is cluster no. nc.

clustermethod

a string indicating the clustering method.

The output of some of the functions has further components:
nccl

see nc above.

nnk

by noisemclustCBI and distnoisemclustCBI, see above.

initnoise

logical vector, indicating initially estimated noise by NNclean, called by noisemclustCBI and distnoisemclustCBI.

noise

logical. TRUE if points were classified as noise/outliers by disthclustCBI.

Details

All these functions call clustering methods implemented in R to cluster data and to provide output in the format required by clusterboot. Here is a brief overview. For further details see the help pages of the involved clustering methods.

kmeansCBI

an interface to the function kmeansruns calling kmeans for k-means clustering. (kmeansruns allows the specification of several random initializations of the k-means algorithm and estimation of k by the Calinski-Harabasz index or the average silhouette width.)

hclustCBI

an interface to the function hclust for agglomerative hierarchical clustering with noise component (see parameter noisecut above). This function produces a partition and assumes a cases*variables matrix as input.

hclusttreeCBI

an interface to the function hclust for agglomerative hierarchical clustering. This function gives out all clusters belonging to the hierarchy (upward from a certain level, see parameter minlevel above).

disthclustCBI

an interface to the function hclust for agglomerative hierarchical clustering with noise component (see parameter noisecut above). This function produces a partition and assumes a dissimilarity matrix as input.

% \item{disthclusttreeCBI}{an interface to the function % \code{hclust} for agglomerative hierarchical clustering. This % function gives out all clusters belonging to the hierarchy % (upward from a certain level, see parameter \code{minlevel} % above), and assumes a dissimilarity matrix as input.}
noisemclustCBI

an interface to the function mclustBIC, for normal mixture model based clustering. Warning: mclustBIC often has problems with multiple points. In clusterboot, it is recommended to use this together with multipleboot=FALSE.

distnoisemclustCBI

an interface to the function mclustBIC for normal mixture model based clustering. This assumes a dissimilarity matrix as input and generates a data matrix by multidimensional scaling first. Warning: mclustBIC often has problems with multiple points. In clusterboot, it is recommended to use this together with multipleboot=FALSE.

claraCBI

an interface to the functions pam and clara for partitioning around medoids.

pamkCBI

an interface to the function pamk calling pam for partitioning around medoids. The number of clusters is estimated by the Calinski-Harabasz index or by the average silhouette width.

tclustCBI

an interface to the function tclust in the tclust package for trimmed Gaussian clustering. This assumes a cases*variables matrix as input.

% % NOTE: This package is currently only available in CRAN as % archived version. Therefore I cannot currently offer the % \code{tclustCBI}-function in \code{fpc}. The code for the % function is below in the Examples-Section, so if you need it, % run that code first.} % \item{disttrimkmeansCBI}{an interface to the function % \code{\link[trimcluster]{trimkmeans}} for trimmed k-means % clustering. This assumes a dissimilarity matrix as input and % generates a data matrix by multidimensional scaling first.}
dbscanCBI

an interface to the function dbscan for density based clustering.

mahalCBI

an interface to the function fixmahal for fixed point clustering. This assumes a cases*variables matrix as input.

mergenormCBI

an interface to the function mergenormals for clustering by merging Gaussian mixture components. Unlike mergenormals, mergenormCBI includes the computation of the initial Gaussian mixture. This assumes a cases*variables matrix as input.

speccCBI

an interface to the function specc for spectral clustering. See the specc help page for additional tuning parameters. This assumes a cases*variables matrix as input.

pdfclustCBI

an interface to the function pdfCluster for density-based clustering. See the pdfCluster help page for additional tuning parameters. This assumes a cases*variables matrix as input.

% \item{emskewCBI}{an interface to the function % \code{\link[EMMIXskew]{EmSkew}} for clustering with the % EM-algorithm based on Gaussian, skew Gaussian, t or skew-t % mixtures. See % help page of \code{\link[EMMIXskew]{EmSkew}}. This assumes a % cases*variables matrix as input. Note that by September 2020, % package \code{EMMIXskew} is not available on CRAN but only % in the CRAN archives; CRAN states that it needs an update.}
stupidkcentroidsCBI

an interface to the function stupidkcentroids for random centroid-based clustering. See the stupidkcentroids help page. This can have a distance matrix as well as a cases*variables matrix as input, see parameter distances.

stupidknnCBI

an interface to the function stupidknn for random nearest neighbour clustering. See the stupidknn help page. This assumes a distance matrix as input.

stupidkfnCBI

an interface to the function stupidkfn for random farthest neighbour clustering. See the stupidkfn help page. This assumes a distance matrix as input.

stupidkavenCBI

an interface to the function stupidkaven for random average dissimilarity clustering. See the stupidkaven help page. This assumes a distance matrix as input.

See Also

clusterboot, dist, kmeans, kmeansruns, hclust, mclustBIC, pam, pamk, clara, dbscan, fixmahal, tclust, pdfCluster

Examples

# NOT RUN {
  options(digits=3)
  set.seed(20000)
  face <- rFace(50,dMoNo=2,dNoEy=0,p=2)
  dbs <- dbscanCBI(face,eps=1.5,MinPts=4)
  dhc <- disthclustCBI(dist(face),method="average",k=1.5,noisecut=2)
  table(dbs$partition,dhc$partition)
  dm <- mergenormCBI(face,G=10,modelNames="EEE",nnk=2)
  dtc <- tclustCBI(face,6,trim=0.1,restr.fact=500)
  table(dm$partition,dtc$partition)

# }