Three-mode software

(Other suppliers)

Introduction

Please contact the authors mentioned to get the latest and most accurate information. Note also that the addresses/links were correct at the time they were entered but most likely have changed after that date.

Contents

• Three-mode mixture method of clustering
• R-Package -CA3variants - Three-way variants of correspondence analysis
• MATLAB Toolbox for three-mode analysis: Various
• Common Principal Component Analysis - CPC
• DATAN - Trilinear modelling for fluorescence and NMR data
• MATLAB program for the Tucker3 model
• R-Package - ThreeWay
• Parallel factor analysis - PARAFAC
• Computation of core for PARAFAC Three-way procedures; PARAFAC; Multiway-PLS
• R-Package -multiway Multiway proceduresS
• Tucker3 model with missing data - GEPCAM
• MATLAB Library for three-mode programs including rotations for Tucker3 core arrays
• Parallel factor analysis with constraints/MATLAB/PASCAL
• STATIS
• R-Rackage - rTensor - Manipulating n-waytensor>
• MR/3 - Multiresolution Software for Three-Mode Analysis
• NewMDSX - A multidimensional scaling package including three-way scaling methods
• SUMMAX
• PARDEC - A package with several Three-Mode Models
• PTAk - Principal Tensor Analysis on k-modes
• SAS-CALIS - Multimode Factor Analysis
• Simultaneous Components Analysis
• MATLAB programs for Parafac models in signal processing
• R-Package - rrcov3way. Includes robust procedures

R-Package -CA3variants - Three-way variants of correspondence analysis

• Description
  Three-way symmetric and non-symmtrical correspondence analysis
• Language/Operating systems
  R-Package - code in E. J. Beh, and R. Lombardo (2014). Correspondence analysis. Theory, practice and new strategies , Chapter 11. Wiley, Chichester, UK.
• Author(s)
  Eric J. Beh, Rosaria Lombardo

MATLAB Toolbox for three-mode analysis

• Description
  MATLAB toolboxes for data analysis: multi-way analysis, missing data, NMR modeling, PLS variable selection, PARAFAC2, numerical analysis (e.g. nonnegative, unimodal least squares regression), maximum likelihood fitting, multi-block modeling etc.
• Language/Operating systems
  Implemented in MATLAB under DOS; distribution on special request.
• Author(s)
  Rasmus Bro & Claus A. Andersson
  [ Home Page Bro]
  [ N-way toolbox for Matlab: PARAFAC, Tucker, N-PLS, fast NNLS, unimodality, etc.] [ Application of multi-way partial least squares regression]  [PARAFAC tutorial]

MATLAB Library for three-mode programs

• Description
  MATLAB programs for performing three-mode data analysis and especially for rotating three-way core matrices
• Language/Operating systems
  Implemented in MATLAB; distribution on special request.
• Author(s)
  Henk A.L. Kiers

MATLAB program for the Tucker3 model

• Description
  Three-mode principal component analysis, using Kroonenberg and De Leeuw's algorithm
• Language/Operating systems
  Implemented in MATLAB; distribution on special request only.
• Author(s)
  Paul J. Gemperline

R-Package ThreeWay

• Description
  The R package ThreeWay is presented and its main features are illustrated. The aim of ThreeWay is to offer a suit of functions for handling three-way arrays. In particular, the most relevant available functions are T3 and CP, which implement, respectively, the Tucker3 and Candecomp/Parafac methods.
• Language/Operating systems
  R- package - ThreeWay
• Author(s)
  Paolo Giordani
  Henk A. L.Kiers
  Maria A. Del Ferraro

R-Package multiway

• Description
  Fits multi-way component models via alternating least squares algorithms with optional constraints. Fit models include N-way Canonical Polyadic Decomposition, Individual Differences Scaling, Multiway Covariates Regression, Parallel Factor Analysis, Simultaneous Component Analysis, and Tucker Factor Analysis.
• Language/Operating systems
  R-Package - multiway
• Author(s)
  Nathan E. Helwig

MATLAB programs for Parafac models in signal processing

• Description
  The suite consists of a collection of MatLab M-files to perform Parafac analysis with various degrees of sophistication.
  • TALS.m
    "Plain-vanilla" Matlab implementation of the PARAFAC 3-way alternating least squares algorithm. Works with real or complex-valued data. Very robust, but memory-intensive. Initialization provided by the user, or else random.
  • COMFAC.m
    This is a "loaded" Matlab implementation of 3-way PARAFAC fitting that incorporates various options and speed-ups. In particular, it performs Tucker3-compression of large arrays, followed by algebraic initialization in compressed space when appropriate, alternating least squares refinement in compressed space, decompression of the compressed solution, and final alternating least squares refinement in the original space. Works with real or complex data, but specifically designed to handle complex data. Gauss-Newton is also an option, instead of alternating least squares.
  • Also programs for Least Absolute Error (L₁ norm) PARAFAC fitting are available, but these have not been posted yet - please contact the author if you need this
• Language/Operating systems
  Implemented in MATLAB; downloadable from
  Please refer to the Triple SPICE website
• Author(s)
  Nikos Sidiropoulos

Common Principal Components Analysis

• Description
  Programs to perform Flury's Common Principal Components analysis. Common Principal Components (CPC) is a data analysis technique created by Bernhard Flury that allows two or more matrices to be compared in a hierarchical fashion. The ideas are most completely presented in Flury, B. (1988), Common Principal Components and Related Multivariate Methods. NewYork: Wiley. Please refer to the the Web site of the author of the software Patrick Phillips.
• Language/Operating systems
  Available for a large number of operating sytems, such as DOS, Windows 3.1/95/NT, UNIX, Macintish, etc.
• Author(s)
  Patrick Phillips (pphil at darkwing.uoregon.edu)

GEPCAM - GEneralized Principal Components Analysis with Missing data

• Description
  Three-mode principal component analysis with a regression-based alternating least squares algorithm and special missing data handling.
• Language/Operating systems
  FORTRAN source file, includes two IMSL routines
• Author(s)
  Johannes(Hans) .C. van Houwelingen, Vakgroep Medische Statistiek en Informatica, Leiden Universiteit, The Netherlands.
  

PARAFAC

• Description
  Parallel factor analysis for three-way data; includes among others missing data handling, data synthesization, split-half analyses.
• Language/Operating systems
  FORTRAN program (Windows XP and earlier)
• Author(s)
  Richard A. Harshman †

PFCORE

• Description
  Computes core matrices for solutions from a parallel factor analysis for three-way data.
• Language/Operating systems
  FORTRAN source; DOS executable.
• Author(s)
  Richard .A. Harshman (deceased)

PARAFAC with constraints/MATLAB/Pascal

• Description
  Parallel factor analysis for three-way data; also includes clustered variables.
• Language/Operating systems
  MATLAB implementation of PARAFAC; distribution upon special request only.
• Author(s)
  Wim P. Krijnen

ACT (STATIS)

• Description
  Three-mode analysis of three-way data (tables) using three steps
  (1) an analysis of the elements of the third mode (interstructure)
  (2) the derivation of a summary of the frontal planes (compromise)
  (3) an analysis within each level of the third mode (intrastructure).
• Language/Operating systems
  Windows version is included in the SPAD-TM unit of the SPAD software system SPAD distributed by DECISIA.
  The website is in French.
• Author(s)
  Christine Lavit

R-package - rTensor

• Description
  A set of tools for creation, manipulation, and modeling of tensors with arbitrary number of modes. rTensor provides common tensor operations as methods, including matrix unfolding, summing/averaging across modes, calculating the Frobenius norm, and taking the inner product between two tensors. rTensor implements various tensor decomposition, including CP, GLRAM, MPCA, PVD, and Tucker. Some auxiliary functions are included.
• Language/Operating systems
  R-Package - rtensor
• Author(s)
  James Li, Jacob Bien, Martin Wells, and Koki Tsuyuzaki

SCA - Simultaneous Component Analysis

• Description
  Perfect congruence analysis and target rotations for sets of covariance (or correlation) matrices.
• Language/Operating systems
  Pascal; DOS executable.
• Author
  Henk A.L. Kiers)

MIXCLUS3 - MIXture method of CLUStering for three-mode data

• Description
  Maximum-likelihood based clustering procedure using mixtures of normal distributions as its basic model.
• Language/Operating systems
  FORTRAN source file, or DOS executable.
• Author(s)
  Kaye E. Basford
  

SUMMAX

• Description
  A three-mode generalization of Thurstone's centroid factor analysis, in which the components (initially) have only elements 1, 0, and -1. Also handles a variant of the Parafac model.
• Language/Operating systems
  FORTRAN source; further details unknown
• Author(s)
  Peter Orlik, Department of Psychology, Universität Saarbrücken, Saar, Germany.

MR/3 - Multiresolution Software for Three-Mode Analysis

• Description
  3D wavelet transforms, and combined wavelet transforms and principal components analysis (Karhunen-Loeve transform). Suitable for image sequences, color (RGB or other) images, time series of matrices, multi-channel and multi-band data, hyperspectral data, and video (if formatted as an image sequence).
• Language/Operating systems
  Available as executables (originally C++) for Windows 95/98/ME/2000/NT, Linux, and Solaris.
• Author(s)
  Jean-Luc Starck, CEA, Saclay, France, and Fionn Murtagh,
  

DATAN - Trilinear modelling for fluorescence and NMR data

• Description
  Program for analyses of multidimensional spectroscopic measurements based trilinear decomposition that is particularly designed for fluorescence and nuclear magnetic resonance data.
• Language/Operating systems
  Windows 98/NT and UNIX.
• Author(s)
  Mikael Kubista (mikael.kubista at multid.se)
  Bjorn Sjogreen (bjorn.sjogreen at multid.se)
  Amin Forootan (amin.forootan at multid.se)
  

SAS/CALIS - Multmode Factor Analysis

• Description
  Program for structural equation models in which both Lisrel, EQS and COSAN or RAM model formulations can be used. Also three-mode factor analysis on multimode covariance matrices can be carried out.
• Language/Operating systems
  Many operating systems (see SAS information).
• Author(s)
  Wolfgang Hartmann
  

PARDEC - Package of Three-Mode Programs

• Description
  This package contains the following collection of algorithms: Tucker, PARAFAC, PARDEC, ORTDEC and some minor algorithms for computing initial approximation for PARAFAC algorithm and calculation of condition number of the solution.
• Language/Operating systems
  This package works on different platforms: Windows (95/98/NT/2000), Linux, SGI UNIX, DEC ALPHA and probably in others. You need Tcl/Tk and if you want (need) to compile the sources you need LAPACK and BLAS libraries. We strongly recommend to use the optimized BLAS library that can be provided with your operating system or use the public domain ATLASpackage because of 5-10 times improvement in speed.
• Author(s)
  Ilghiz Ibraghimov. His Ilghiz Research is a company suggesting the three-way related software packages for scientific research developed in past few years for public domain. You can download it for free and use it with the restrictions written in corresponding agreement.

PTAk - Principal Tensor Analysis on k-modes

• Description
  A multiway method to decompose a tensor (array) of any order, as a generalisation of SVD also supporting non-identity metrics and penalisations. 2-way SVD with these extensions is also available. The package includes also some other multiway methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP with these extensions.
• Language/Operating systems
  R PTAk
• Author(s)
  Didier Leibovici
  

rrcov3way - R-Package. Includes robust procedures

• Description
  The R package rrcov3way provides a set of tools for fitting the Tucker3 and PARAFAC models to multidimensional arrays by use of classical, robust and compositional estimating procedures. It includes other options to the standard least squares algorithm in case of data with outliers and/or characterized by a biased covariance structure. A comprehensive collection of three-way plots, diagnostics and data processing functions is also included. Other R-packages are mentioned.
• Language/Operating systems
  R-package
• Author(s)
  Valentin Todorov, Violetta Simonacci, Maria Anna Di Palma, Michele Gallo
  

NewMDSX - Library of multidimensional scaling programs

• Description
  NewMDSX is a library of multidimensional scaling programs, with associated documentation & test input/output.
  • The MS-DOS version is available free.
  • The re-written NewMDSX for Windows (with graphics, data input wizards and other improvements) is currently available as a free 3-month beta-version, and will later be available at low cost as a supported package.
  • Programs are primarily drawn from Bell Labs and Guttman-Lingoes-Roskam sources, but also include MDSORT (Takane), CORRESP(ondence analysis), PRINCOMP as well as HICLUS and WOMBATS -- a general purpose program for manipulating data input and calculating measures of dis/similarity.
• Language/Operating systems
  MS-DOS and Windows
• Contact
  Sigma Essex Research & Consultancy
  

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