seriation: Infrastructure for Ordering Objects Using Seriation

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).

AuthorMichael 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 publication2016-08-07 16:00:55
MaintainerMichael Hahsler <mhahsler@lyle.smu.edu>
LicenseGPL-3
Version1.2-1
http://lyle.smu.edu/IDA/seriation

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

Functions

bertin_cut_line Man page
bertinplot Man page
bluered Man page
chameleon Man page
Chameleon Man page
chameleon_ds4 Man page
chameleon_ds5 Man page
chameleon_ds7 Man page
chameleon_ds8 Man page
create_lines_data Man page
create_ordered_data Man page
criterion Man page
criterion.array Man page
criterion.dist Man page
criterion.matrix Man page
c.ser_permutation Man page
dendser Man page
DendSer Man page
dissplot Man page
dist Man page
ga Man page
GA Man page
gaperm_mixedMutation Man page
get_criterion_method Man page
get_method Man page
get_order Man page
get_order.hclust Man page
get_order.integer Man page
get_order.ser_permutation Man page
get_order.ser_permutation_vector Man page
get_permutation_matrix Man page
get_rank Man page
get_seriation_method Man page
grays Man page
greenred Man page
greys Man page
hmap Man page
Irish Man page
is.robinson Man page
iVAT Man page
length.ser_permutation_vector Man page
list_criterion_methods Man page
list_seriation_methods Man page
Munsingen Man page
panel.bars Man page
panel.blocks Man page
panel.circles Man page
panel.lines Man page
panel.squares Man page
path_dist Man page
permutation Man page
permutation_matrix2vector Man page
permutation_vector Man page
permutation_vector2matrix Man page
permute Man page
permute.array Man page
permute.data.frame Man page
permute.dendrogram Man page
permute.dist Man page
permute.hclust Man page
permute.list Man page
permute.matrix Man page
permute.numeric Man page
pimage Man page
pimage.dist Man page
pimage.matrix Man page
plot.reordered_cluster_dissimilarity_matrix Man page
print.reordered_cluster_dissimilarity_matrix Man page
print.ser_permutation Man page
print.ser_permutation_vector Man page
Psych24 Man page
random.robinson Man page
register_DendSer Man page
register_GA Man page
registry_criterion Man page
registry_seriate Man page
reorder Man page
reorder.hclust Man page
rev.ser_permutation_vector Man page
Robinson Man page
ser_align Man page
ser_cor Man page
ser_dist Man page
seriate Man page
seriate.array Man page
seriate.dist Man page
seriate.matrix Man page
"[.ser_permutation" Man page
ser_permutation Man page
ser_permutation_vector Man page
set_criterion_method Man page
set_seriation_method Man page
show_criterion_methods Man page
show_seriation_methods Man page
Townships Man page
VAT Man page
Wood Man page
Zoo Man page

Files

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

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.