optpart: Optimal Partitioning of Similarity Relations
Version 2.3-0

Contains a set of algorithms for creating partitions and coverings of objects largely based on operations on (dis)similarity relations (or matrices). There are several iterative re-assignment algorithms optimizing different goodness-of-clustering criteria. In addition, there are covering algorithms 'clique' which derives maximal cliques, and 'maxpact' which creates a covering of maximally compact sets. Graphical analyses and conversion routines are also included.

Browse man pages Browse package API and functions Browse package files

AuthorDavid W. Roberts <droberts@montana.edu>
Date of publication2016-09-20 18:46:42
MaintainerDavid W. Roberts <droberts@montana.edu>
LicenseGPL (>= 2)
Version2.3-0
URL http://ecology.msu.montana.edu/labdsv/R
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("optpart")

Man pages

archi: Archipelago Analysis
bestfit: Identify the Goodness-of-Fit of Cluster Members
bestopt: Best Of Set Optimal Partitions From Random Starts
classmatch: Classification Matching and Differencing
clique: Maximal Clique Analysis
clique.test: Clique Test
clustering: Clustering Object
compare: Compare Species Constancy for Specified Clusters
confus: Confusion Matrix
consider: Recommendations for Possible Merging of Clusters
disdiam: Dissimilarity Diameters of a Partition
extract: Extract A Specific Cluster Solution From A Stride
fuzconfus: Fuzzy Confusion Matrix
maxpact: Maximally Compact Sets Analysis
mergeclust: Merge Specified Clusters in a Classification
murdoch: Indicator Species Analysis by Murdoch Preference Function
neighbor: Neighbor Analysis of Partitions
optindval: Optimizing Classification by Maximizing Dufrene and...
optpart: Optimal Partitioning of Dissimilarity/Distance Matrices
optpart.internal: Internal Optpart Functions
optsil: Clustering by Optimizing Silhouette Widths
opttdev: Optimizing Classification by Minimizing Table Deviance
partana: Partition Analysis
partition: Convert Object to Partition Object
phi: Calculating the phi Statistic on Taxon Classifications
refine: Refining a Classification by Re-Assigning Memberships
reordclust: Re-order Clusters in a Classification
shoshsite: Site Data for the Shoshone National Forest, Wyoming, USA
shoshveg: Vascular Plant Species Cover for the Shoshone National...
silhouette: Produce a Silhouette Object From a Partana, Clustering, or...
slice: Slice a Hierarchical Clustering Dendrogram with a Mouse
stride: Stride: Producing a Sequence of Clusterings
tabdev: Classification Validity Assessment by Table Deviance
testpart: Identify Misclassified Plots in a Partition
typal: Identification of Typal Samples in a Partition

Functions

archi Man page Source code
bestfit Man page Source code
bestopt Man page Source code
classmatch Man page Source code
clique Man page Source code
clique.test Man page Source code
clustering Man page
clustify Man page Source code
compare Man page Source code
confus Man page Source code
consider Man page Source code
disdiam Man page Source code
disdiam.default Man page Source code
disdiam.stride Man page Source code
extract Man page Source code
extract.mps Source code
extract.stride Man page Source code
fuzconfus Man page Source code
maxpact Man page Source code
mergeclust Man page Source code
mps.test Man page Source code
murdoch Man page Source code
neighbor Man page Source code
opt.core Man page Source code
optindval Man page Source code
optpart Man page Source code
optpart.clustering Man page
optpart.default Man page Source code
optpart.partana Man page
optpart.partition Man page
optpart.stride Man page Source code
opts.core Man page Source code
optsil Man page Source code
optsil.clustering Man page
optsil.default Man page Source code
optsil.partana Man page
optsil.partition Man page
optsil.stride Man page Source code
opttdev Man page Source code
partana Man page Source code
partana.clustering Man page
partana.default Man page Source code
partana.partition Man page Source code
partana.stride Man page Source code
partition Man page Source code
partition.clustering Man page
partition.default Source code
partition.partana Man page
phi Man page Source code
plot.clique Man page Source code
plot.mps Man page Source code
plot.murdoch Man page Source code
plot.partana Man page Source code
plot.stride Man page Source code
print.disdiam Man page Source code
refine Man page Source code
refine.default Man page Source code
refine.nmds Man page Source code
refine.pco Man page Source code
reordclust Man page Source code
shoshsite Man page
shoshveg Man page
silhouette.clustering Man page Source code
silhouette.partana Man page Source code
silhouette.stride Man page Source code
slice Man page Source code
stride Man page Source code
summary.clique Man page Source code
summary.murdoch Man page Source code
summary.partana Man page Source code
summary.tabdev Man page Source code
tabdev Man page Source code
tabdev.default Man page Source code
tabdev.stride Man page Source code
testpart Man page Source code
testsil Man page Source code
typal Man page Source code

Files

inst
inst/ChangeLog
src
src/opttdev.f
src/tabdev.f
src/clcdev.f
src/optsil.f
src/random.c
src/maxpact.f
src/optindval.f
src/optpart.f
src/permute.f
src/archi.f
src/clcdul.f
src/clique.f
NAMESPACE
data
data/shoshveg.rda
data/shoshsite.rda
R
R/phi.R
R/clique.R
R/murdoch.R
R/consider.R
R/typal.R
R/classmatch.R
R/stride.R
R/optsil.R
R/bestfit.R
R/opttdev.R
R/clustify.R
R/testpart.R
R/slice.R
R/reordclust.R
R/partition.R
R/partana.R
R/optindval.R
R/mergeclust.R
R/tabdev.R
R/archi.R
R/disdiam.R
R/silhouette.R
R/optpart.R
R/compare.R
R/refine.R
R/maxpact.R
R/neighbor.R
R/confus.R
MD5
DESCRIPTION
man
man/partana.Rd
man/refine.Rd
man/testpart.Rd
man/bestopt.Rd
man/mergeclust.Rd
man/optsil.Rd
man/maxpact.Rd
man/murdoch.Rd
man/neighbor.Rd
man/tabdev.Rd
man/clique.test.Rd
man/archi.Rd
man/shoshsite.Rd
man/silhouette.Rd
man/bestfit.Rd
man/reordclust.Rd
man/clustering.Rd
man/opttdev.Rd
man/optindval.Rd
man/optpart.internal.Rd
man/compare.Rd
man/consider.Rd
man/shoshveg.Rd
man/clique.Rd
man/partition.Rd
man/typal.Rd
man/fuzconfus.Rd
man/optpart.Rd
man/phi.Rd
man/slice.Rd
man/disdiam.Rd
man/confus.Rd
man/extract.Rd
man/classmatch.Rd
man/stride.Rd
optpart documentation built on May 19, 2017, 2:24 p.m.