# 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.

- Author
- Christian Hennig <c.hennig@ucl.ac.uk>
- Date of publication
- 2015-08-14 08:27:19
- Maintainer
- Christian Hennig <c.hennig@ucl.ac.uk>
- License
- GPL
- Version
- 2.1-10
- URLs

## Man pages

- adcoord
- Asymmetric discriminant coordinates
- adcoord
- Asymmetric discriminant coordinates
- ancoord
- Asymmetric neighborhood based discriminant coordinates
- ancoord
- Asymmetric neighborhood based discriminant coordinates
- awcoord
- Asymmetric weighted discriminant coordinates
- awcoord
- Asymmetric weighted discriminant coordinates
- batcoord
- Bhattacharyya discriminant projection
- batcoord
- Bhattacharyya discriminant projection
- bhattacharyya.dist
- Bhattacharyya distance between Gaussian distributions
- bhattacharyya.dist
- Bhattacharyya distance between Gaussian distributions
- bhattacharyya.matrix
- Matrix of pairwise Bhattacharyya distances
- bhattacharyya.matrix
- Matrix of pairwise Bhattacharyya distances
- calinhara
- Calinski-Harabasz index
- calinhara
- Calinski-Harabasz index
- can
- Generation of the tuning constant for regression fixed point...
- can
- Generation of the tuning constant for regression fixed point...
- cat2bin
- Recode nominal variables to binary variables
- cat2bin
- Recode nominal variables to binary variables
- classifdist
- Classification of unclustered points
- classifdist
- Classification of unclustered points
- clucols
- Sets of colours and symbols for cluster plotting
- clucols
- Sets of colours and symbols for cluster plotting
- clujaccard
- Jaccard similarity between logical vectors
- clujaccard
- Jaccard similarity between logical vectors
- clusexpect
- Expected value of the number of times a fixed point cluster...
- clusexpect
- Expected value of the number of times a fixed point cluster...
- clusterboot
- Clusterwise cluster stability assessment by resampling
- clusterboot
- Clusterwise cluster stability assessment by resampling
- cluster.stats
- Cluster validation statistics
- cluster.stats
- Cluster validation statistics
- cluster.varstats
- Variablewise statistics for clusters
- cluster.varstats
- Variablewise statistics for clusters
- cmahal
- Generation of tuning constant for Mahalanobis fixed point...
- cmahal
- Generation of tuning constant for Mahalanobis fixed point...
- concomp
- Connectivity components of an undirected graph
- concomp
- Connectivity components of an undirected graph
- confusion
- Misclassification probabilities in mixtures
- confusion
- Misclassification probabilities in mixtures
- cov.wml
- Weighted Covariance Matrices (Maximum Likelihood)
- cov.wml
- Weighted Covariance Matrices (Maximum Likelihood)
- cweight
- Weight function for AWC
- cweight
- Weight function for AWC
- dbscan
- DBSCAN density reachability and connectivity clustering
- dbscan
- DBSCAN density reachability and connectivity clustering
- dipp.tantrum
- Simulates p-value for dip test
- dipp.tantrum
- Simulates p-value for dip test
- diptest.multi
- Diptest for discriminant coordinate projection
- diptest.multi
- Diptest for discriminant coordinate projection
- discrcoord
- Discriminant coordinates/canonical variates
- discrcoord
- Discriminant coordinates/canonical variates
- discrete.recode
- Recodes mixed variables dataset
- discrete.recode
- Recodes mixed variables dataset
- discrproj
- Linear dimension reduction for classification
- discrproj
- Linear dimension reduction for classification
- distancefactor
- Factor for dissimilarity of mixed type data
- distancefactor
- Factor for dissimilarity of mixed type data
- distcritmulti
- Distance based validity criteria for large data sets
- distcritmulti
- Distance based validity criteria for large data sets
- dridgeline
- Density along the ridgeline
- dridgeline
- Density along the ridgeline
- dudahart2
- Duda-Hart test for splitting
- dudahart2
- Duda-Hart test for splitting
- extract.mixturepars
- Extract parameters for certain components from mclust
- extract.mixturepars
- Extract parameters for certain components from mclust
- fixmahal
- Mahalanobis Fixed Point Clusters
- fixmahal
- Mahalanobis Fixed Point Clusters
- fixreg
- Linear Regression Fixed Point Clusters
- fixreg
- Linear Regression Fixed Point Clusters
- flexmixedruns
- Fitting mixed Gaussian/multinomial mixtures with flexmix
- flexmixedruns
- Fitting mixed Gaussian/multinomial mixtures with flexmix
- fpclusters
- Extracting clusters from fixed point cluster objects
- fpclusters
- Extracting clusters from fixed point cluster objects
- fpc-package
- fpc package overview
- fpc-package
- fpc package overview
- itnumber
- Number of regression fixed point cluster iterations
- itnumber
- Number of regression fixed point cluster iterations
- jittervar
- Jitter variables in a data matrix
- jittervar
- Jitter variables in a data matrix
- kmeansCBI
- Interface functions for clustering methods
- kmeansCBI
- Interface functions for clustering methods
- kmeansruns
- k-means with estimating k and initialisations
- kmeansruns
- k-means with estimating k and initialisations
- lcmixed
- flexmix method for mixed Gaussian/multinomial mixtures
- lcmixed
- flexmix method for mixed Gaussian/multinomial mixtures
- localshape
- Local shape matrix
- localshape
- Local shape matrix
- mahalanodisc
- Mahalanobis for AWC
- mahalanodisc
- Mahalanobis for AWC
- mahalanofix
- Mahalanobis distances from center of indexed points
- mahalanofix
- Mahalanobis distances from center of indexed points
- mahalconf
- Mahalanobis fixed point clusters initial configuration
- mahalconf
- Mahalanobis fixed point clusters initial configuration
- mergenormals
- Clustering by merging Gaussian mixture components
- mergenormals
- Clustering by merging Gaussian mixture components
- mergeparameters
- New parameters from merging two Gaussian mixture components
- mergeparameters
- New parameters from merging two Gaussian mixture components
- minsize
- Minimum size of regression fixed point cluster
- minsize
- Minimum size of regression fixed point cluster
- mixdens
- Density of multivariate Gaussian mixture, mclust...
- mixdens
- Density of multivariate Gaussian mixture, mclust...
- mixpredictive
- Prediction strength of merged Gaussian mixture
- mixpredictive
- Prediction strength of merged Gaussian mixture
- mvdcoord
- Mean/variance differences discriminant coordinates
- mvdcoord
- Mean/variance differences discriminant coordinates
- ncoord
- Neighborhood based discriminant coordinates
- ncoord
- Neighborhood based discriminant coordinates
- nselectboot
- Selection of the number of clusters via bootstrap
- nselectboot
- Selection of the number of clusters via bootstrap
- pamk
- Partitioning around medoids with estimation of number of...
- pamk
- Partitioning around medoids with estimation of number of...
- piridge
- Ridgeline Pi-function
- piridge
- Ridgeline Pi-function
- piridge.zeroes
- Extrema of two-component Gaussian mixture
- piridge.zeroes
- Extrema of two-component Gaussian mixture
- plotcluster
- Discriminant projection plot.
- plotcluster
- Discriminant projection plot.
- prediction.strength
- Prediction strength for estimating number of clusters
- prediction.strength
- Prediction strength for estimating number of clusters
- randcmatrix
- Random partition matrix
- randcmatrix
- Random partition matrix
- randconf
- Generate a sample indicator vector
- randconf
- Generate a sample indicator vector
- regmix
- Mixture Model ML for Clusterwise Linear Regression
- regmix
- Mixture Model ML for Clusterwise Linear Regression
- rFace
- "Face-shaped" clustered benchmark datasets
- rFace
- "Face-shaped" clustered benchmark datasets
- ridgeline
- Ridgeline computation
- ridgeline
- Ridgeline computation
- ridgeline.diagnosis
- Ridgeline plots, ratios and unimodality
- ridgeline.diagnosis
- Ridgeline plots, ratios and unimodality
- simmatrix
- Extracting intersections between clusters from fpc-object
- simmatrix
- Extracting intersections between clusters from fpc-object
- solvecov
- Inversion of (possibly singular) symmetric matrices
- solvecov
- Inversion of (possibly singular) symmetric matrices
- sseg
- Position in a similarity vector
- sseg
- Position in a similarity vector
- tdecomp
- Root of singularity-corrected eigenvalue decomposition
- tdecomp
- Root of singularity-corrected eigenvalue decomposition
- tonedata
- Tone perception data
- tonedata
- Tone perception data
- unimodal.ind
- Is a fitted denisity unimodal or not?
- unimodal.ind
- Is a fitted denisity unimodal or not?
- weightplots
- Ordered posterior plots
- weightplots
- Ordered posterior plots
- wfu
- Weight function (for Mahalabobis distances)
- wfu
- Weight function (for Mahalabobis distances)
- zmisclassification.matrix
- Matrix of misclassification probabilities between mixture...
- zmisclassification.matrix
- Matrix of misclassification probabilities between mixture...

## Files in this package

fpc |

fpc/tests |

fpc/tests/Examples |

fpc/tests/Examples/fpc-Ex.Rout.save |

fpc/tests/fpctests.Rout.save |

fpc/tests/fpctests.R |

fpc/NAMESPACE |

fpc/data |

fpc/data/tonedata.txt.gz |

fpc/R |

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/MD5 |

fpc/DESCRIPTION |

fpc/man |

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 |