optpart: Optimal Partitioning of Similarity Relations

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.

Install the latest version of this package by entering the following in R:
install.packages("optpart")
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
http://ecology.msu.montana.edu/labdsv/R

View on CRAN

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.