fpc v2.2-7

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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.

Functions in fpc

Name Description
ancoord Asymmetric neighborhood based discriminant coordinates
calinhara Calinski-Harabasz index
can Generation of the tuning constant for regression fixed point clusters
bhattacharyya.dist Bhattacharyya distance between Gaussian distributions
bhattacharyya.matrix Matrix of pairwise Bhattacharyya distances
adcoord Asymmetric discriminant coordinates
awcoord Asymmetric weighted discriminant coordinates
batcoord Bhattacharyya discriminant projection
cdbw CDbw-index for cluster validation
cat2bin Recode nominal variables to binary variables
clusexpect Expected value of the number of times a fixed point cluster is found
cluster.varstats Variablewise statistics for clusters
classifdist Classification of unclustered points
cluster.magazine Run many clustering methods on many numbers of clusters
cluster.stats Cluster validation statistics
clusterbenchstats Run and validate many clusterings
clustatsum Compute and format cluster validation statistics
cgrestandard Standardise cluster validation statistics by random clustering results
cqcluster.stats Cluster validation statistics (version for use with clusterbenchstats
cmahal Generation of tuning constant for Mahalanobis fixed point clusters.
cov.wml Weighted Covariance Matrices (Maximum Likelihood)
clusterboot Clusterwise cluster stability assessment by resampling
diptest.multi Diptest for discriminant coordinate projection
dipp.tantrum Simulates p-value for dip test
dbscan DBSCAN density reachability and connectivity clustering
clucols Sets of colours and symbols for cluster plotting
cweight Weight function for AWC
cvnn Cluster validation based on nearest neighbours
con.comp Connectivity components of an undirected graph
distancefactor Factor for dissimilarity of mixed type data
discrete.recode Recodes mixed variables dataset
confusion Misclassification probabilities in mixtures
discrproj Linear dimension reduction for classification
discrcoord Discriminant coordinates/canonical variates
distcritmulti Distance based validity criteria for large data sets
findrep Finding representatives for cluster border
fixmahal Mahalanobis Fixed Point Clusters
fpc-package fpc package overview
clujaccard Jaccard similarity between logical vectors
fpclusters Extracting clusters from fixed point cluster objects
distrsimilarity Similarity of within-cluster distributions to normal and uniform
dridgeline Density along the ridgeline
lcmixed flexmix method for mixed Gaussian/multinomial mixtures
localshape Local shape matrix
flexmixedruns Fitting mixed Gaussian/multinomial mixtures with flexmix
mahalconf Mahalanobis fixed point clusters initial configuration
fixreg Linear Regression Fixed Point Clusters
dudahart2 Duda-Hart test for splitting
mergenormals Clustering by merging Gaussian mixture components
kmeansruns k-means with estimating k and initialisations
extract.mixturepars Extract parameters for certain components from mclust
mahalanofix Mahalanobis distances from center of indexed points
itnumber Number of regression fixed point cluster iterations
mahalanodisc Mahalanobis for AWC
kmeansCBI Interface functions for clustering methods
piridge.zeroes Extrema of two-component Gaussian mixture
plotcluster Discriminant projection plot.
mvdcoord Mean/variance differences discriminant coordinates
ridgeline Ridgeline computation
jittervar Jitter variables in a data matrix
mixdens Density of multivariate Gaussian mixture, mclust parameterisation
prediction.strength Prediction strength for estimating number of clusters
ncoord Neighborhood based discriminant coordinates
valstat.object Cluster validation statistics - object
pamk Partitioning around medoids with estimation of number of clusters
regmix Mixture Model ML for Clusterwise Linear Regression
unimodal.ind Is a fitted denisity unimodal or not?
zmisclassification.matrix Matrix of misclassification probabilities between mixture components
mergeparameters New parameters from merging two Gaussian mixture components
mixpredictive Prediction strength of merged Gaussian mixture
xtable Partition crosstable with empty clusters
randconf Generate a sample indicator vector
plot.valstat Simulation-standardised plot and print of cluster validation statistics
piridge Ridgeline Pi-function
solvecov Inversion of (possibly singular) symmetric matrices
neginc Neg-entropy normality index for cluster validation
minsize Minimum size of regression fixed point cluster
randomclustersim Simulation of validity indexes based on random clusterings
tdecomp Root of singularity-corrected eigenvalue decomposition
sseg Position in a similarity vector
stupidkcentroids Stupid k-centroids random clustering
stupidkaven Stupid average dissimilarity random clustering
rFace "Face-shaped" clustered benchmark datasets
randcmatrix Random partition matrix
weightplots Ordered posterior plots
nselectboot Selection of the number of clusters via bootstrap
stupidknn Stupid nearest neighbour random clustering
tonedata Tone perception data
ridgeline.diagnosis Ridgeline plots, ratios and unimodality
simmatrix Extracting intersections between clusters from fpc-object
stupidkfn Stupid farthest neighbour random clustering
wfu Weight function (for Mahalabobis distances)
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Date 2020-06-25
License GPL
URL https://www.unibo.it/sitoweb/christian.hennig/en/
NeedsCompilation no
Packaged 2020-06-25 10:36:21 UTC; chrish
Repository CRAN
Date/Publication 2020-06-26 06:10:17 UTC

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