Package: fpc 2.2-12

fpc: Flexible Procedures for Clustering

Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Standardisation of cluster validation statistics by random clusterings and comparison between many clustering methods and numbers of clusters based on this. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.

Authors:Christian Hennig <[email protected]>

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fpc.pdf |fpc.html✨
fpc/json (API)

# Install 'fpc' in R:

install.packages('fpc', repos = c('https://chrhennig.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

tonedata - Tone perception data

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

138 exports 10 stars 7.34 score 13 dependencies 67 dependents 99 mentions 2.3k scripts 13.9k downloads

Last updated 5 months agofrom:6ce07f7497. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 09 2024
R-4.5-win	NOTE	Sep 09 2024
R-4.5-linux	NOTE	Sep 09 2024
R-4.4-win	OK	Sep 09 2024
R-4.4-mac	OK	Sep 09 2024
R-4.3-win	OK	Sep 09 2024
R-4.3-mac	OK	Sep 09 2024

Exports:adcoord ancoord awcoord batcoord batvarcoord bhattacharyya.dist bhattacharyya.matrix calinhara can cat2bin cdbw cgrestandard claraCBI classifdist classifnp clucols clugrey clujaccard clusexpect clustatsum cluster.magazine cluster.stats cluster.varstats clusterbenchstats clusterboot clusym cmahal con.comp confusion cov.wml cqcluster.stats cvnn cweight dbscan dbscanCBI dipp.tantrum diptest.multi discrcoord discrete.recode discrproj distancefactor distcritmulti disthclustCBI disthclusttreeCBI distnoisemclustCBI distrsimilarity dridgeline dudahart2 extract.mixturepars findrep fixmahal fixreg flexmixedruns fpclusters fpclusters.mfpc fpclusters.rfpc fpmi hclustCBI hclusttreeCBI itnumber jittervar kmeansCBI kmeansruns lcmixed localshape mahalanodisc mahalanofix mahalanofuz mahalCBI mahalconf mergenormals mergenormCBI mergeparameters minsize mixdens mixpredictive mvdcoord ncoord neginc noisemclustCBI nselectboot pamk pamkCBI pdfclustCBI piridge piridge.zeroes plot.clboot plot.dbscan plot.mfpc plot.rfpc plot.valstat plotcluster predict.dbscan prediction.strength print.clboot print.clusterbenchstats print.dbscan print.mfpc print.predstr print.rfpc print.summary.cquality print.summary.mergenorm print.summary.mfpc print.summary.rfpc print.valstat print.varwisetables randcmatrix randconf randomclustersim regem regmix rFace rfpi ridgeline ridgeline.diagnosis simmatrix solvecov speccCBI sseg stupidkaven stupidkavenCBI stupidkcentroids stupidkcentroidsCBI stupidkfn stupidkfnCBI stupidknn stupidknnCBI summary.cquality summary.mergenorm summary.mfpc summary.rfpc tclustCBI tdecomp unimodal.ind weightplots wfu xtable zmisclassification.matrix

Dependencies:class cluster DEoptimR diptest flexmix kernlab lattice MASS mclust modeltools nnet prabclus robustbase

Help page	Topics
fpc package overview	fpc-package
Asymmetric discriminant coordinates	adcoord
Asymmetric neighborhood based discriminant coordinates	ancoord
Asymmetric weighted discriminant coordinates	awcoord
Bhattacharyya discriminant projection	batcoord batvarcoord
Bhattacharyya distance between Gaussian distributions	bhattacharyya.dist
Matrix of pairwise Bhattacharyya distances	bhattacharyya.matrix
Calinski-Harabasz index	calinhara
Generation of the tuning constant for regression fixed point clusters	can
Recode nominal variables to binary variables	cat2bin
CDbw-index for cluster validation	cdbw
Standardise cluster validation statistics by random clustering results	cgrestandard
Classification of unclustered points	classifdist classifnp
Sets of colours and symbols for cluster plotting	clucols clugrey clusym
Jaccard similarity between logical vectors	clujaccard
Expected value of the number of times a fixed point cluster is found	clusexpect
Compute and format cluster validation statistics	clustatsum
Run many clustering methods on many numbers of clusters	cluster.magazine
Cluster validation statistics	cluster.stats
Variablewise statistics for clusters	cluster.varstats print.varwisetables
Run and validate many clusterings	clusterbenchstats print.clusterbenchstats
Clusterwise cluster stability assessment by resampling	clusterboot plot.clboot print.clboot
Generation of tuning constant for Mahalanobis fixed point clusters.	cmahal
Connectivity components of an undirected graph	con.comp
Misclassification probabilities in mixtures	confusion
Weighted Covariance Matrices (Maximum Likelihood)	cov.wml
Cluster validation statistics (version for use with clusterbenchstats	cqcluster.stats print.summary.cquality summary.cquality
Cluster validation based on nearest neighbours	cvnn
Weight function for AWC	cweight
DBSCAN density reachability and connectivity clustering	dbscan plot.dbscan predict.dbscan print.dbscan
Simulates p-value for dip test	dipp.tantrum
Diptest for discriminant coordinate projection	diptest.multi
Discriminant coordinates/canonical variates	discrcoord
Recodes mixed variables dataset	discrete.recode
Linear dimension reduction for classification	discrproj
Factor for dissimilarity of mixed type data	distancefactor
Distance based validity criteria for large data sets	distcritmulti
Similarity of within-cluster distributions to normal and uniform	distrsimilarity
Density along the ridgeline	dridgeline
Duda-Hart test for splitting	dudahart2
Extract parameters for certain components from mclust	extract.mixturepars
Finding representatives for cluster border	findrep
Mahalanobis Fixed Point Clusters	fixmahal fpclusters.mfpc fpmi plot.mfpc print.mfpc print.summary.mfpc summary.mfpc
Linear Regression Fixed Point Clusters	fixreg fpclusters.rfpc plot.rfpc print.rfpc print.summary.rfpc rfpi summary.rfpc
Fitting mixed Gaussian/multinomial mixtures with flexmix	flexmixedruns
Extracting clusters from fixed point cluster objects	fpclusters
Number of regression fixed point cluster iterations	itnumber
Jitter variables in a data matrix	jittervar
Interface functions for clustering methods	claraCBI dbscanCBI disthclustCBI disthclusttreeCBI distnoisemclustCBI emskewCBI hclustCBI hclusttreeCBI kmeansCBI mahalCBI mergenormCBI noisemclustCBI pamkCBI pdfclustCBI speccCBI stupidkavenCBI stupidkcentroidsCBI stupidkfnCBI stupidknnCBI tclustCBI
k-means with estimating k and initialisations	kmeansruns
flexmix method for mixed Gaussian/multinomial mixtures	lcmixed
Local shape matrix	localshape
Mahalanobis for AWC	mahalanodisc
Mahalanobis distances from center of indexed points	mahalanofix mahalanofuz
Mahalanobis fixed point clusters initial configuration	mahalconf
Clustering by merging Gaussian mixture components	mergenormals print.summary.mergenorm summary.mergenorm
New parameters from merging two Gaussian mixture components	mergeparameters
Minimum size of regression fixed point cluster	minsize
Density of multivariate Gaussian mixture, mclust parameterisation	mixdens
Prediction strength of merged Gaussian mixture	mixpredictive
Mean/variance differences discriminant coordinates	mvdcoord
Neighborhood based discriminant coordinates	ncoord
Neg-entropy normality index for cluster validation	neginc
Selection of the number of clusters via bootstrap	nselectboot
Partitioning around medoids with estimation of number of clusters	pamk
Ridgeline Pi-function	piridge
Extrema of two-component Gaussian mixture	piridge.zeroes
Simulation-standardised plot and print of cluster validation statistics	plot.valstat print.valstat
Discriminant projection plot.	plotcluster
Prediction strength for estimating number of clusters	prediction.strength print.predstr
Random partition matrix	randcmatrix
Generate a sample indicator vector	randconf
Simulation of validity indexes based on random clusterings	randomclustersim
Mixture Model ML for Clusterwise Linear Regression	regem regmix
"Face-shaped" clustered benchmark datasets	rFace
Ridgeline computation	ridgeline
Ridgeline plots, ratios and unimodality	ridgeline.diagnosis
Extracting intersections between clusters from fpc-object	simmatrix
Inversion of (possibly singular) symmetric matrices	solvecov
Position in a similarity vector	sseg
Stupid average dissimilarity random clustering	stupidkaven
Stupid k-centroids random clustering	stupidkcentroids
Stupid farthest neighbour random clustering	stupidkfn
Stupid nearest neighbour random clustering	stupidknn
Root of singularity-corrected eigenvalue decomposition	tdecomp
Tone perception data	tonedata
Is a fitted denisity unimodal or not?	unimodal.ind
Cluster validation statistics - object	valstat.object
Ordered posterior plots	weightplots
Weight function (for Mahalabobis distances)	wfu
Partition crosstable with empty clusters	xtable
Matrix of misclassification probabilities between mixture components	zmisclassification.matrix

Package: fpc 2.2-12

fpc: Flexible Procedures for Clustering

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