## Algorithms

**IMPORTANT***all downloadable material listed on these pages – appended by specifics mentioned under the individual headers/chapters – is available for public use. Please note that while great care has been taken, the software, code and data are provided “as is” and that Q&T, LIFE, KU does not accept any responsibility or liability.*

The following software are …..

Name | Description | Download |
---|---|---|

Simulated GC-MS | GC-MS datasets are simulated over short retention-time intervals | Get the data |

AHIMBU | Automatic hierarchical classification model builder (AHIMBU). An automated tool for complex classification. Check the paper heremodels. | Check the paper - check the code (requires PLS_Toolbox) |

Multiblock Toolbox | M-files for various PCA- and PLS-like multiblock algorithms in MATLAB | Get the code |

PARADISe | Resolving untargeted GC-MS data | Get the code |

Routine for calculating normalized 2D radial pair distributions | Calculations used in paper "The mean hydration of carbohydrates as studied by normalized 2-D radial pair distributions" in Journal of Molecular Graphics and Modeling | Get the code |

Uni-modality (and monotonic) constrained least squares regression | M-files for unimodality constrained least squares regression. | Get the code |

PARAFAC for complex-valued problems | Useful e.g. for problems in tele communication | |

Non-negativity constrained least squares regression | M-files for non-negativity constrained least squares regression. | Get the code |

The Missing Toolbox | Simple functions for handling missing values. | Get the code |

GEMANOVA model for MATLAB 5/6 | Model for fitting multi-linear ANOVA models in MATLAB. | Get the code |

MILES for MATLAB 5/6 | Algorithm for fitting maximum likelihood models through least squares algorithms | Get the code |

Jackknifed PARAFAC | Jackknifing of PARAFAC models - Version 2.03 - self-contained (no need for the Nway Toolbox) | Get the code |

PARAFAC2 model for MATLAB 5.2 | Save the file and type - help parafac2 - in MATLAB (Updated Jan 2003). | Get the code |

Low-field NMR toolbox | (Version 3.0 including simplified use by Power-SLICING) Contains algorithms for exponential fitting, phase correction of quadrature data and SLICING | Get the code |

INCA | Imports and prepares fluorometric data from the PE-FLDM for use in MATLAB, e.g., The N-way Toolbox for MATLAB. | Get the code |

The N-way Toolbox for MATLAB | (matlab 7.3) Procedures for fitting PARAFAC, Tucker, N-PLS and other N-way models. | Get the code |

Extended Multiplicative Signal Correction (EMSC) for MATLAB | EMSC/EISC signal correction | Get the code |

SENSABLE | GUI for processing of sensor based data | Get the code |

DTW and COW | Code for signal alignment by Dynamic Time Warping and/or Correlation Optimized Warping for Matlab | Get the code |

iToolbox | (updated, extended version of the iPLS toolset) Set of interval-based PLS and PCA routines for exploratory investigations. | Get the code |

PARALIND | (aka restricted PARATUCk2) for modeling multi-way data with linear dependencies | Get the code |

INDAFAC | sparse implementation of Levenberg Marquadt algorithm for PARAFAC in Matlab | Get the code |

Rayleigh scatter correcting PARAFAC of EEM data | From "First order Rayleigh scatter as a separate component in the decomposition of fluorescence landscapes", Rinnan, Booksh, Bro Analytica Chimica Acta, Volume 537, Issues 1-2, 29 April 2005, Pages 349-358 | |

Extended Canonical Variates Analysis | a discrimination method for collinear data by Lars Nørgaard, Rasmus Bro, Frank Westad, Søren Balling Engelsen | |

CuBatch | is a graphical user interface based on the Matlab environment that can be employed for the analysis and the handling of the most disparate types of data. | Get the code |

EEMSCAT | is a tool for removing scatter from EEMs and for interpolating values in the removed areas. | |

Clustering | is a tool for performing interactive two- and multi-way clustering. | Get the code |

CONLOAD | for calculating correlation loadings and congruence loadings for two-way and multi-way models | Get the code |

iCDF | a freeware function to import netCDF files from GC-MS, LC-MS etc. software in MATLAB | Get the code |

Signflip | a freeware function to correct for sign ambiguity in SVD/PCA (MATLAB) | |

Rotation of PCA models | a freeware function to rotate and counterotate scores or loadings (MATLAB - uses PLS_Toolbox) | Get the code |

DOMFluor | Characterizing dissolved organic matter fluorescence with parallel factor analysis. | Get the code |

icoshift | An ultra rapid and versatile tool for the alignment of spectral datasets | Get the code |

EEMizer | automatically determine the appropriate PARAFAC model for EEM data | Get the code |

SMR | Sparse matrix regression for coclustering | Get the code |

FDOMFLuor | FDOMcorr Toolbox by Kate Murphy. Simplify and automate correction of DOM EEM data | Get the code |

Loads2Chrom | identify modelled peaks from GC-MS datasets. | Get the code |

FastChrom | Processing of chromatographic data | Get the code |

NSIMCA | Multi-way classification | Get the code |

CMTF Toolbox | Coupled Matrix and Tensor Factorization for Matlab | Get the code |

PCA bootstrap | Bootstrap based Confidence Limits in Principal Component Analysis | Get the code |

POLYS 2.0 | An open source software package for building 3D structures of polysaccharides | Get the code |

Chromatric Spatial Variance Toolbox | Matlab toolbox for RGB image analysis | |

drEEM | Matlab toolbox supporting visualisation and PARAFAC of excitation emission matrices (EEMs) | Get the code |

AutoChrome | Matlab toolbox for automatically finding the right PARAFAC2 model of e.g. GCMS data | Get the code |

SCREAM | A novel method for multi-way regression problems with shifts and shape changes in one mode | Get the code |

rPLS | Recursive weighted Partial least Squares for variable selection | Get the code |

Spiderplots | Visual presentation of factor loadings | Get the code |

SPCA | Sparse Principal Component Analysis | Get the code |

SPARAFAC | Sparse (non-negative) PARAFAC | Get the code |

HYPERTOOLS | Tools for hyperspectral analysis |

This software are form other researchers

Name | Code by | Download |
---|---|---|

MVACDF, a multivariate data format standard | Get the code | |

The Standard Dataset Object for Matlab | Eigenvector | |

Image Analysis Toolbox IMAT | courtesy of Sensory Science, Department of Food Science, KVL | Get the code |

The PLS-Genetic Algorithm Toolbox | courtesy of Riccardo Leardi - University of Genoa, Italy | Get the code |

MATLAB Tensor Classes for Fast Algorithm Prototyping | B. Bader & T. Kolda | |

iToolbox GUI 1.01 | Dr. Giorgio Luciano | Get the code |

Multi-way VIP for multi-way variable selection | M. Cocchi and coworkers | |

FPDC Probabilistic clustering. | Cristina Torora | Get the code |

Multi-way PLS regression for R. | Casey Kneale |

This software are some old stuff

Name | Description | Download |
---|---|---|

PARAFAC | Models for estimating PARAFAC (old version now covered by the N-way Toolbox) | Get the code |

GUI iPLS | (independent of Command Line iPLS) Interval PLS for variable selection with optimization of interval width. | Get the code |

Multi-way PLS | Standalone M-files for multi-linear partial least squares regression (old version now covered by the N-way Toolbox) | Get the code |

Three-way Procedures with a three-way dataset | Tucker, PARAFAC, GRAM, RAFA and misc. 2nd order models with a test data set (old version now covered by the N-way Toolbox) | Get the code |