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. 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.

AuthorChristian Hennig <c.hennig@ucl.ac.uk>
Date of publication2015-08-14 08:27:19
MaintainerChristian Hennig <c.hennig@ucl.ac.uk>

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Man pages

adcoord: Asymmetric discriminant coordinates

ancoord: Asymmetric neighborhood based discriminant coordinates

awcoord: Asymmetric weighted discriminant coordinates

batcoord: Bhattacharyya discriminant projection

bhattacharyya.dist: Bhattacharyya distance between Gaussian distributions

bhattacharyya.matrix: Matrix of pairwise Bhattacharyya distances

calinhara: Calinski-Harabasz index

can: Generation of the tuning constant for regression fixed point...

cat2bin: Recode nominal variables to binary variables

classifdist: Classification of unclustered points

clucols: Sets of colours and symbols for cluster plotting

clujaccard: Jaccard similarity between logical vectors

clusexpect: Expected value of the number of times a fixed point cluster...

clusterboot: Clusterwise cluster stability assessment by resampling

cluster.stats: Cluster validation statistics

cluster.varstats: Variablewise statistics for clusters

cmahal: Generation of tuning constant for Mahalanobis fixed point...

concomp: Connectivity components of an undirected graph

confusion: Misclassification probabilities in mixtures

cov.wml: Weighted Covariance Matrices (Maximum Likelihood)

cweight: Weight function for AWC

dbscan: DBSCAN density reachability and connectivity clustering

dipp.tantrum: Simulates p-value for dip test

diptest.multi: Diptest for discriminant coordinate projection

discrcoord: Discriminant coordinates/canonical variates

discrete.recode: Recodes mixed variables dataset

discrproj: Linear dimension reduction for classification

distancefactor: Factor for dissimilarity of mixed type data

distcritmulti: Distance based validity criteria for large data sets

dridgeline: Density along the ridgeline

dudahart2: Duda-Hart test for splitting

extract.mixturepars: Extract parameters for certain components from mclust

fixmahal: Mahalanobis Fixed Point Clusters

fixreg: Linear Regression Fixed Point Clusters

flexmixedruns: Fitting mixed Gaussian/multinomial mixtures with flexmix

fpclusters: Extracting clusters from fixed point cluster objects

fpc-package: fpc package overview

itnumber: Number of regression fixed point cluster iterations

jittervar: Jitter variables in a data matrix

kmeansCBI: Interface functions for clustering methods

kmeansruns: k-means with estimating k and initialisations

lcmixed: flexmix method for mixed Gaussian/multinomial mixtures

localshape: Local shape matrix

mahalanodisc: Mahalanobis for AWC

mahalanofix: Mahalanobis distances from center of indexed points

mahalconf: Mahalanobis fixed point clusters initial configuration

mergenormals: Clustering by merging Gaussian mixture components

mergeparameters: New parameters from merging two Gaussian mixture components

minsize: Minimum size of regression fixed point cluster

mixdens: Density of multivariate Gaussian mixture, mclust...

mixpredictive: Prediction strength of merged Gaussian mixture

mvdcoord: Mean/variance differences discriminant coordinates

ncoord: Neighborhood based discriminant coordinates

nselectboot: Selection of the number of clusters via bootstrap

pamk: Partitioning around medoids with estimation of number of...

piridge: Ridgeline Pi-function

piridge.zeroes: Extrema of two-component Gaussian mixture

plotcluster: Discriminant projection plot.

prediction.strength: Prediction strength for estimating number of clusters

randcmatrix: Random partition matrix

randconf: Generate a sample indicator vector

regmix: Mixture Model ML for Clusterwise Linear Regression

rFace: "Face-shaped" clustered benchmark datasets

ridgeline: Ridgeline computation

ridgeline.diagnosis: Ridgeline plots, ratios and unimodality

simmatrix: Extracting intersections between clusters from fpc-object

solvecov: Inversion of (possibly singular) symmetric matrices

sseg: Position in a similarity vector

tdecomp: Root of singularity-corrected eigenvalue decomposition

tonedata: Tone perception data

unimodal.ind: Is a fitted denisity unimodal or not?

weightplots: Ordered posterior plots

wfu: Weight function (for Mahalabobis distances)

zmisclassification.matrix: Matrix of misclassification probabilities between mixture...

Files in this package

fpc/R/dbscan.R fpc/R/addclustermethods.R fpc/R/mergenormals.R fpc/R/localshape.R fpc/R/clusterboot.R fpc/R/fpc.R fpc/R/discrproj.R fpc/R/rFace.R fpc/R/discrproj2.R fpc/R/lcmixed.R fpc/R/fixreg.R fpc/R/regmix.R
fpc/man/clucols.Rd fpc/man/ncoord.Rd fpc/man/zmisclassification.matrix.Rd fpc/man/unimodal.ind.Rd fpc/man/classifdist.Rd fpc/man/ridgeline.Rd fpc/man/extract.mixturepars.Rd fpc/man/ridgeline.diagnosis.Rd fpc/man/bhattacharyya.matrix.Rd fpc/man/kmeansCBI.Rd fpc/man/randconf.Rd fpc/man/nselectboot.Rd fpc/man/discrcoord.Rd fpc/man/flexmixedruns.Rd fpc/man/cluster.varstats.Rd fpc/man/dipp.tantrum.Rd fpc/man/dudahart2.Rd fpc/man/plotcluster.Rd fpc/man/dridgeline.Rd fpc/man/confusion.Rd fpc/man/sseg.Rd fpc/man/distancefactor.Rd fpc/man/mergenormals.Rd fpc/man/concomp.Rd fpc/man/rFace.Rd fpc/man/mixpredictive.Rd fpc/man/discrproj.Rd fpc/man/dbscan.Rd fpc/man/cat2bin.Rd fpc/man/fixreg.Rd fpc/man/adcoord.Rd fpc/man/tonedata.Rd fpc/man/wfu.Rd fpc/man/discrete.recode.Rd fpc/man/calinhara.Rd fpc/man/tdecomp.Rd fpc/man/cweight.Rd fpc/man/localshape.Rd fpc/man/batcoord.Rd fpc/man/lcmixed.Rd fpc/man/mahalconf.Rd fpc/man/clusterboot.Rd fpc/man/piridge.zeroes.Rd fpc/man/kmeansruns.Rd fpc/man/fixmahal.Rd fpc/man/minsize.Rd fpc/man/bhattacharyya.dist.Rd fpc/man/pamk.Rd fpc/man/weightplots.Rd fpc/man/cov.wml.Rd fpc/man/simmatrix.Rd fpc/man/randcmatrix.Rd fpc/man/piridge.Rd fpc/man/diptest.multi.Rd fpc/man/ancoord.Rd fpc/man/mahalanofix.Rd fpc/man/distcritmulti.Rd fpc/man/jittervar.Rd fpc/man/clujaccard.Rd fpc/man/fpclusters.Rd fpc/man/prediction.strength.Rd fpc/man/fpc-package.Rd fpc/man/mixdens.Rd fpc/man/cluster.stats.Rd fpc/man/mergeparameters.Rd fpc/man/mahalanodisc.Rd fpc/man/can.Rd fpc/man/clusexpect.Rd fpc/man/cmahal.Rd fpc/man/itnumber.Rd fpc/man/mvdcoord.Rd fpc/man/solvecov.Rd fpc/man/awcoord.Rd fpc/man/regmix.Rd

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