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fpc (version 2.2-9)

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

13,898

Version

2.2-9

License

GPL

Last Published

December 6th, 2020

Functions in fpc (2.2-9)

cdbw

CDbw-index for cluster validation
adcoord

Asymmetric discriminant coordinates
cat2bin

Recode nominal variables to binary variables
bhattacharyya.matrix

Matrix of pairwise Bhattacharyya distances
awcoord

Asymmetric weighted discriminant coordinates
batcoord

Bhattacharyya discriminant projection
bhattacharyya.dist

Bhattacharyya distance between Gaussian distributions
calinhara

Calinski-Harabasz index
can

Generation of the tuning constant for regression fixed point clusters
ancoord

Asymmetric neighborhood based discriminant coordinates
clusexpect

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

Run many clustering methods on many numbers of clusters
cluster.stats

Cluster validation statistics
clucols

Sets of colours and symbols for cluster plotting
clujaccard

Jaccard similarity between logical vectors
clustatsum

Compute and format cluster validation statistics
classifdist

Classification of unclustered points
cgrestandard

Standardise cluster validation statistics by random clustering results
cvnn

Cluster validation based on nearest neighbours
cweight

Weight function for AWC
cluster.varstats

Variablewise statistics for clusters
confusion

Misclassification probabilities in mixtures
con.comp

Connectivity components of an undirected graph
clusterbenchstats

Run and validate many clusterings
cov.wml

Weighted Covariance Matrices (Maximum Likelihood)
cqcluster.stats

Cluster validation statistics (version for use with clusterbenchstats
clusterboot

Clusterwise cluster stability assessment by resampling
dbscan

DBSCAN density reachability and connectivity clustering
dipp.tantrum

Simulates p-value for dip test
dudahart2

Duda-Hart test for splitting
cmahal

Generation of tuning constant for Mahalanobis fixed point clusters.
discrete.recode

Recodes mixed variables dataset
diptest.multi

Diptest for discriminant coordinate projection
distrsimilarity

Similarity of within-cluster distributions to normal and uniform
findrep

Finding representatives for cluster border
dridgeline

Density along the ridgeline
fpc-package

fpc package overview
discrcoord

Discriminant coordinates/canonical variates
fixmahal

Mahalanobis Fixed Point Clusters
flexmixedruns

Fitting mixed Gaussian/multinomial mixtures with flexmix
mahalanodisc

Mahalanobis for AWC
distancefactor

Factor for dissimilarity of mixed type data
distcritmulti

Distance based validity criteria for large data sets
fixreg

Linear Regression Fixed Point Clusters
mahalanofix

Mahalanobis distances from center of indexed points
extract.mixturepars

Extract parameters for certain components from mclust
itnumber

Number of regression fixed point cluster iterations
kmeansCBI

Interface functions for clustering methods
discrproj

Linear dimension reduction for classification
jittervar

Jitter variables in a data matrix
mergenormals

Clustering by merging Gaussian mixture components
plotcluster

Discriminant projection plot.
mahalconf

Mahalanobis fixed point clusters initial configuration
pamk

Partitioning around medoids with estimation of number of clusters
fpclusters

Extracting clusters from fixed point cluster objects
piridge

Ridgeline Pi-function
mvdcoord

Mean/variance differences discriminant coordinates
ncoord

Neighborhood based discriminant coordinates
simmatrix

Extracting intersections between clusters from fpc-object
regmix

Mixture Model ML for Clusterwise Linear Regression
ridgeline

Ridgeline computation
prediction.strength

Prediction strength for estimating number of clusters
minsize

Minimum size of regression fixed point cluster
ridgeline.diagnosis

Ridgeline plots, ratios and unimodality
plot.valstat

Simulation-standardised plot and print of cluster validation statistics
mergeparameters

New parameters from merging two Gaussian mixture components
piridge.zeroes

Extrema of two-component Gaussian mixture
randconf

Generate a sample indicator vector
rFace

"Face-shaped" clustered benchmark datasets
weightplots

Ordered posterior plots
randomclustersim

Simulation of validity indexes based on random clusterings
mixpredictive

Prediction strength of merged Gaussian mixture
mixdens

Density of multivariate Gaussian mixture, mclust parameterisation
xtable

Partition crosstable with empty clusters
randcmatrix

Random partition matrix
stupidkaven

Stupid average dissimilarity random clustering
localshape

Local shape matrix
wfu

Weight function (for Mahalabobis distances)
neginc

Neg-entropy normality index for cluster validation
kmeansruns

k-means with estimating k and initialisations
lcmixed

flexmix method for mixed Gaussian/multinomial mixtures
tdecomp

Root of singularity-corrected eigenvalue decomposition
tonedata

Tone perception data
nselectboot

Selection of the number of clusters via bootstrap
zmisclassification.matrix

Matrix of misclassification probabilities between mixture components
solvecov

Inversion of (possibly singular) symmetric matrices
stupidkcentroids

Stupid k-centroids random clustering
sseg

Position in a similarity vector
unimodal.ind

Is a fitted denisity unimodal or not?
valstat.object

Cluster validation statistics - object
stupidkfn

Stupid farthest neighbour random clustering
stupidknn

Stupid nearest neighbour random clustering