seriation: Infrastructure for Ordering Objects Using Seriation

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Infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).

Author
Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Kurt Hornik [aut, cph], Fionn Murtagh [ctb, cph], Michael Brusco [ctb, cph], Stephanie Stahl [ctb, cph], Hans-Friedrich Koehn [ctb, cph]
Date of publication
2016-08-07 16:00:55
Maintainer
Michael Hahsler <mhahsler@lyle.smu.edu>
License
GPL-3
Version
1.2-1
URLs

View on CRAN

Man pages

bertinplot
Plot a Bertin Matrix
Chameleon
2D Data Sets used for the CHAMELEON Clustering Algorithm
col
Different Useful Color Palettes
criterion
Criterion for a Loss/Merit Function for Data Given a...
criterion_methods
Registry for Criterion Methods
data
Create Simulated Data for Seriation Evaluation
dissimilarity
Dissimilarities and Correlations Between Seriation Orders
dissplot
Dissimilarity Plot
get_order
Extracting Order Information from a Permutation Object
hmap
Plot Heat Map Reordered Using Seriation
Irish
Irish Referendum Data Set
Munsingen
Hodson's Munsingen Data Set
permutation
Class ser_permutation - A Collection of Permutation Vectors...
permutation_matrix
Conversion Between Permutation Vector and Permutation Matrix
permutation_vector
Class ser_permutation_vector - A Single Permutation Vector...
permute
Permute the Order in Various Objects
pimage
Permutation Image Plot
Psych24
Results of 24 Psychological Test for 8th Grade Students
register_DendSer
Register Seriation Methods from Package DendSer
register_GA
Register a Genetic Algorithm Seriation Method
reorder_hclust
Reorder Dendrograms using Optimal Leaf Ordering
robinson
Create and Recognize Robinson and Pre-Robinson Matrices
seriate
Seriate Dissimilarity Matrices, Matrices or Arrays
seriation_methods
Registry for Seriation Methods
Townships
Bertin's Characteristics of Townships
VAT
Visual Analysis for Cluster Tendency Assessment (VAT/iVAT)
Wood
Gene Expression Data for Wood Formation in Poplar Trees
Zoo
Zoo Data Set

Files in this package

seriation
seriation/inst
seriation/inst/CITATION
seriation/inst/doc
seriation/inst/doc/seriation.pdf
seriation/inst/doc/seriation.Rnw
seriation/inst/doc/seriation.R
seriation/tests
seriation/tests/testthat.R
seriation/tests/testthat
seriation/tests/testthat/test-permuation_vector.R
seriation/tests/testthat/test-criterion.R
seriation/tests/testthat/test-dissimilarity.R
seriation/tests/testthat/test-DendSer_GA.R
seriation/tests/testthat/test-seriate.R
seriation/src
seriation/src/lt.h
seriation/src/stress.c
seriation/src/greedy.c
seriation/src/bbwrcg.f
seriation/src/pathdist.c
seriation/src/criterion.c
seriation/src/arsa.f
seriation/src/bburcg.f
seriation/src/RNG_wrapper.c
seriation/src/fprintf.c
seriation/src/dist.c
seriation/src/bea.f
seriation/src/optimal.c
seriation/NAMESPACE
seriation/data
seriation/data/Wood.rda
seriation/data/Townships.rda
seriation/data/Munsingen.rda
seriation/data/Zoo.rda
seriation/data/Chameleon.rda
seriation/data/Psych24.rda
seriation/data/Irish.rda
seriation/R
seriation/R/seriate.R
seriation/R/criterion.dist.R
seriation/R/pimage.R
seriation/R/bea.R
seriation/R/AAAcolors.R
seriation/R/AAAparameter.R
seriation/R/permutation_vector.R
seriation/R/dissplot.R
seriation/R/seriate.array.R
seriation/R/data.R
seriation/R/seriate.dist.R
seriation/R/AAAregistry.R
seriation/R/hclust_greedy.R
seriation/R/AAAmap.R
seriation/R/robinson.R
seriation/R/criterion.matrix.R
seriation/R/AAAinstalled.R
seriation/R/criterion.array.R
seriation/R/dissimilartiy.R
seriation/R/permutation.R
seriation/R/AAAgrid.R
seriation/R/VAT.R
seriation/R/register_GA.R
seriation/R/register_DendSer.R
seriation/R/permute.R
seriation/R/criterion.R
seriation/R/reorder.hclust.R
seriation/R/bertinplot.R
seriation/R/seriate.matrix.R
seriation/R/hmap.R
seriation/vignettes
seriation/vignettes/seriation.bib
seriation/vignettes/seriation.Rnw
seriation/vignettes/classes.odg
seriation/vignettes/classes.pdf
seriation/README.md
seriation/MD5
seriation/build
seriation/build/vignette.rds
seriation/DESCRIPTION
seriation/man
seriation/man/pimage.Rd
seriation/man/Irish.Rd
seriation/man/seriation_methods.Rd
seriation/man/hmap.Rd
seriation/man/register_GA.Rd
seriation/man/Psych24.Rd
seriation/man/get_order.Rd
seriation/man/dissimilarity.Rd
seriation/man/permutation_matrix.Rd
seriation/man/Chameleon.Rd
seriation/man/col.Rd
seriation/man/VAT.Rd
seriation/man/register_DendSer.Rd
seriation/man/criterion_methods.Rd
seriation/man/Wood.Rd
seriation/man/dissplot.Rd
seriation/man/criterion.Rd
seriation/man/permute.Rd
seriation/man/Townships.Rd
seriation/man/data.Rd
seriation/man/reorder_hclust.Rd
seriation/man/bertinplot.Rd
seriation/man/permutation_vector.Rd
seriation/man/Zoo.Rd
seriation/man/permutation.Rd
seriation/man/robinson.Rd
seriation/man/seriate.Rd
seriation/man/Munsingen.Rd