seriation - Infrastructure for Ordering Objects Using Seriation - R package

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This package provides the infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms (see below for a full list). Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).

Installation

Stable CRAN version: install from within R with

install.packages("seriation")

Current development version: Download package from AppVeyor or install from GitHub (needs devtools).

install_git("mhahsler/seriation")

Usage

Load library, read data and calculate distances. Then use default seriation.

library(seriation)
data("iris")
x <- as.matrix(iris[-5])
x <- x[sample(1:nrow(x)),]

d <- dist(x)
order <- seriate(d)
order
object of class ‘ser_permutation’, ‘list’
contains permutation vectors for 1-mode data

  vector length seriation method
1           150             ARSA

Compare quality.

rbind(
 random = criterion(d),
 reordered = criterion(d, order)
)
          AR_events AR_deviations       RGAR Gradient_raw Gradient_weighted Path_length
random       550620    948833.712 0.49938328          741         -1759.954   392.77766
reordered     54846      9426.094 0.04974243       992214       1772123.418    83.95758
            Inertia Least_squares       ME Moore_stress Neumann_stress     2SUM      LS
random    214602194      78852819 291618.0    927570.00     461133.357 29954845 5669489
reordered 356945979      76487641 402332.1     13593.32       5274.093 17810802 4486900

Available Seriation Methods

For dissimilarity data:

For matrices:

References