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fpc (version 2.2-13)

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

19,713

Version

2.2-13

License

GPL

Last Published

September 24th, 2024

Functions in fpc (2.2-13)

clucols

Sets of colours and symbols for cluster plotting
cgrestandard

Standardise cluster validation statistics by random clustering results
cluster.varstats

Variablewise statistics for clusters
clusterbenchstats

Run and validate many clusterings
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
classifdist

Classification of unclustered points
cov.wml

Weighted Covariance Matrices (Maximum Likelihood)
cmahal

Generation of tuning constant for Mahalanobis fixed point clusters.
cvnn

Cluster validation based on nearest neighbours
cweight

Weight function for AWC
con.comp

Connectivity components of an undirected graph
cqcluster.stats

Cluster validation statistics (version for use with clusterbenchstats
clusterboot

Clusterwise cluster stability assessment by resampling
confusion

Misclassification probabilities in mixtures
dbscan

DBSCAN density reachability and connectivity clustering
dipp.tantrum

Simulates p-value for dip test
distancefactor

Factor for dissimilarity of mixed type data
dudahart2

Duda-Hart test for splitting
distcritmulti

Distance based validity criteria for large data sets
distrsimilarity

Similarity of within-cluster distributions to normal and uniform
discrcoord

Discriminant coordinates/canonical variates
extract.mixturepars

Extract parameters for certain components from mclust
diptest.multi

Diptest for discriminant coordinate projection
discrete.recode

Recodes mixed variables dataset
dridgeline

Density along the ridgeline
discrproj

Linear dimension reduction for classification
itnumber

Number of regression fixed point cluster iterations
fpc-package

fpc package overview
fpclusters

Extracting clusters from fixed point cluster objects
fixreg

Linear Regression Fixed Point Clusters
kmeansCBI

Interface functions for clustering methods
findrep

Finding representatives for cluster border
jittervar

Jitter variables in a data matrix
fixmahal

Mahalanobis Fixed Point Clusters
flexmixedruns

Fitting mixed Gaussian/multinomial mixtures with flexmix
kmeansruns

k-means with estimating k and initialisations
lcmixed

flexmix method for mixed Gaussian/multinomial mixtures
mahalanodisc

Mahalanobis for AWC
localshape

Local shape matrix
mahalanofix

Mahalanobis distances from center of indexed points
mergeparameters

New parameters from merging two Gaussian mixture components
mahalconf

Mahalanobis fixed point clusters initial configuration
mergenormals

Clustering by merging Gaussian mixture components
minsize

Minimum size of regression fixed point cluster
mixdens

Density of multivariate Gaussian mixture, mclust parameterisation
mixpredictive

Prediction strength of merged Gaussian mixture
plotcluster

Discriminant projection plot.
pamk

Partitioning around medoids with estimation of number of clusters
prediction.strength

Prediction strength for estimating number of clusters
piridge

Ridgeline Pi-function
neginc

Neg-entropy normality index for cluster validation
randconf

Generate a sample indicator vector
mvdcoord

Mean/variance differences discriminant coordinates
ncoord

Neighborhood based discriminant coordinates
nselectboot

Selection of the number of clusters via bootstrap
piridge.zeroes

Extrema of two-component Gaussian mixture
rFace

"Face-shaped" clustered benchmark datasets
randomclustersim

Simulation of validity indexes based on random clusterings
regmix

Mixture Model ML for Clusterwise Linear Regression
unimodal.ind

Is a fitted denisity unimodal or not?
tdecomp

Root of singularity-corrected eigenvalue decomposition
randcmatrix

Random partition matrix
tonedata

Tone perception data
solvecov

Inversion of (possibly singular) symmetric matrices
sseg

Position in a similarity vector
ridgeline

Ridgeline computation
weightplots

Ordered posterior plots
wfu

Weight function (for Mahalabobis distances)
valstat.object

Cluster validation statistics - object
plot.valstat

Simulation-standardised plot and print of cluster validation statistics
ridgeline.diagnosis

Ridgeline plots, ratios and unimodality
simmatrix

Extracting intersections between clusters from fpc-object
stupidkfn

Stupid farthest neighbour random clustering
stupidkaven

Stupid average dissimilarity random clustering
stupidkcentroids

Stupid k-centroids random clustering
xtable

Partition crosstable with empty clusters
stupidknn

Stupid nearest neighbour random clustering
zmisclassification.matrix

Matrix of misclassification probabilities between mixture components
cat2bin

Recode nominal variables to binary variables
can

Generation of the tuning constant for regression fixed point clusters
calinhara

Calinski-Harabasz index
cdbw

CDbw-index for cluster validation
bhattacharyya.dist

Bhattacharyya distance between Gaussian distributions
bhattacharyya.matrix

Matrix of pairwise Bhattacharyya distances
awcoord

Asymmetric weighted discriminant coordinates
ancoord

Asymmetric neighborhood based discriminant coordinates
batcoord

Bhattacharyya discriminant projection
adcoord

Asymmetric discriminant coordinates