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fpc (version 2.2-3)

Flexible Procedures for Clustering

Description

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.

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Version

Install

install.packages('fpc')

Monthly Downloads

19,476

Version

2.2-3

License

GPL

Maintainer

Christian Hennig

Last Published

June 28th, 2019

Functions in fpc (2.2-3)

batcoord

Bhattacharyya discriminant projection
bhattacharyya.matrix

Matrix of pairwise Bhattacharyya distances
can

Generation of the tuning constant for regression fixed point clusters
ancoord

Asymmetric neighborhood based discriminant coordinates
adcoord

Asymmetric discriminant coordinates
awcoord

Asymmetric weighted discriminant coordinates
calinhara

Calinski-Harabasz index
cat2bin

Recode nominal variables to binary variables
bhattacharyya.dist

Bhattacharyya distance between Gaussian distributions
cdbw

CDbw-index for cluster validation
clucols

Sets of colours and symbols for cluster plotting
clusterbenchstats

Run and validate many clusterings
cluster.varstats

Variablewise statistics for clusters
cluster.stats

Cluster validation statistics
cluster.magazine

Run many clustering methods on many numbers of clusters
clujaccard

Jaccard similarity between logical vectors
clusexpect

Expected value of the number of times a fixed point cluster is found
clustatsum

Compute and format cluster validation statistics
cgrestandard

Standardise cluster validation statistics by random clustering results
classifdist

Classification of unclustered points
dbscan

DBSCAN density reachability and connectivity clustering
dipp.tantrum

Simulates p-value for dip test
cweight

Weight function for AWC
cvnn

Cluster validation based on nearest neighbours
cov.wml

Weighted Covariance Matrices (Maximum Likelihood)
cqcluster.stats

Cluster validation statistics (version for use with clusterbenchstats
confusion

Misclassification probabilities in mixtures
con.comp

Connectivity components of an undirected graph
discrete.recode

Recodes mixed variables dataset
discrproj

Linear dimension reduction for classification
distrsimilarity

Similarity of within-cluster distributions to normal and uniform
dridgeline

Density along the ridgeline
distcritmulti

Distance based validity criteria for large data sets
distancefactor

Factor for dissimilarity of mixed type data
clusterboot

Clusterwise cluster stability assessment by resampling
discrcoord

Discriminant coordinates/canonical variates
diptest.multi

Diptest for discriminant coordinate projection
fixreg

Linear Regression Fixed Point Clusters
flexmixedruns

Fitting mixed Gaussian/multinomial mixtures with flexmix
fpc-package

fpc package overview
fpclusters

Extracting clusters from fixed point cluster objects
findrep

Finding representatives for cluster border
fixmahal

Mahalanobis Fixed Point Clusters
mahalanofix

Mahalanobis distances from center of indexed points
dudahart2

Duda-Hart test for splitting
cmahal

Generation of tuning constant for Mahalanobis fixed point clusters.
extract.mixturepars

Extract parameters for certain components from mclust
mahalanodisc

Mahalanobis for AWC
neginc

Neg-entropy normality index for cluster validation
kmeansCBI

Interface functions for clustering methods
nselectboot

Selection of the number of clusters via bootstrap
ridgeline.diagnosis

Ridgeline plots, ratios and unimodality
mvdcoord

Mean/variance differences discriminant coordinates
mixdens

Density of multivariate Gaussian mixture, mclust parameterisation
ncoord

Neighborhood based discriminant coordinates
kmeansruns

k-means with estimating k and initialisations
mixpredictive

Prediction strength of merged Gaussian mixture
weightplots

Ordered posterior plots
minsize

Minimum size of regression fixed point cluster
mergeparameters

New parameters from merging two Gaussian mixture components
solvecov

Inversion of (possibly singular) symmetric matrices
plotcluster

Discriminant projection plot.
wfu

Weight function (for Mahalabobis distances)
rFace

"Face-shaped" clustered benchmark datasets
tdecomp

Root of singularity-corrected eigenvalue decomposition
tonedata

Tone perception data
randcmatrix

Random partition matrix
prediction.strength

Prediction strength for estimating number of clusters
mahalconf

Mahalanobis fixed point clusters initial configuration
mergenormals

Clustering by merging Gaussian mixture components
piridge.zeroes

Extrema of two-component Gaussian mixture
simmatrix

Extracting intersections between clusters from fpc-object
sseg

Position in a similarity vector
itnumber

Number of regression fixed point cluster iterations
plot.valstat

Simulation-standardised plot and print of cluster validation statistics
jittervar

Jitter variables in a data matrix
unimodal.ind

Is a fitted denisity unimodal or not?
randomclustersim

Simulation of validity indexes based on random clusterings
piridge

Ridgeline Pi-function
localshape

Local shape matrix
randconf

Generate a sample indicator vector
lcmixed

flexmix method for mixed Gaussian/multinomial mixtures
pamk

Partitioning around medoids with estimation of number of clusters
regmix

Mixture Model ML for Clusterwise Linear Regression
ridgeline

Ridgeline computation
stupidkcentroids

Stupid k-centroids random clustering
zmisclassification.matrix

Matrix of misclassification probabilities between mixture components
xtable

Partition crosstable with empty clusters
stupidknn

Stupid nearest neighbour random clustering
valstat.object

Cluster validation statistics - object