Release Notes Version 6 5

Version 6.5 of PLS_Toolbox and Solo was released in October, 2011.

For general product information, see PLS_Toolbox Product Page. For information on Solo, see Solo Product Page.

(back to Release Notes PLS Toolbox and Solo)

NEW FEATURES

Classification Methods

• Total flexibility in choosing class sets to model (through class groups interfaces or Edit > Options > Method Options menu)
• Confusion table and matrix tools added
• Unified reporting of classification results for SIMCA, KNN, PLSDA, and SVMDA including:

• all class probabilities
• most probable assignment
• strict in-class assignment
• strict multi-class assignments

• KNN Cross-validation fully supported

Design Of Experients (DOE) Tools

• Significant addition of tools for DOE generation and testing
• Experiement Designer tool added to create, examine, and print run sheets for designed experiments
• DOE Anova tool added to calculate significance of factors and interactions
• Added support tools to: scale factors, calculate interactions, identify confused factors and interactions
• Design generation tools included for:

• Mixed-level Full Factorial Designs (factdes)
• Fractional Factorial Designs (ffacdes1)
• Face and Spherical Central Composite Designs (ccdface, ccdsphere)
• Box-Behnken Designs (boxbehnken)

Other Method Improvements

• Permutation testing of regression and classification models greatly improved with probabilities of model significance and plots
• Support Vector Machine One-Class support added (svmoc; command-line only)
• MCR/ALS contrast algorithm improved providing better handling of low signal cases.
• MLR support for studentized residuals, T^2 and limits added
• MODELSELECTOR trigger can now use of any classification model or a simple logical test on predictions from a regression or PCA model.

Preprocessing

• Variable Alignment method added (using either peak alignment using registerspec or Correlation Optimized Warping (COW))
• Correlation Optimized Warping (COW) and Dynamic Time Warping (DTW) added (from http://www.models.kvl.dk/DTW_COW )
• Poisson scaling offset support added
• Class centering method added for Multilevel PLS models and other clutter-correction methods
• "Transform" options for data blocks in Analysis window. Context menu gives quick access to:

• Batch Digestion (MPCA, Summary PCA)
• Calibration Transfer
• Polynomial Augmentation (Non-linear modeling)
• Coadd Data Reduction (Down-sampling)
• Calibration Sample Selection (redundant sample exclusion, re Westerhuis method)

• Baseline removal improved with manual entry of baseline points and easier graphical selection.
• GLSW improved to work with multi-class PLSDA classification models (multivariate logical y-blocks)
• Help and technical details easy-access links added to Preprocessing Window
• Descriptions automatically update to show current settings for adjustable methods

Import / Export

• Omnic SPA file importer added
• Galactic DHB file importer added (support in SPC reader)
• 3-way data importing from multiple files or multiple Excel spreadsheets added
• Excel multi-sheet document importing improved (better labeling and concatenation options)
• XML format, improved importing of objects and image DataSets
• System clipboard importing improved
• Importer list easier to navigate
• Autoexport tool added for easy saving of data to external formats

DataSet Editor

• Summary statistics for all or part of the given data (View > Summary Statistics, context menu access) added
• Access to all classes, labels, and axisscales on data table view (pull-down menus on Data tab)
• Date stamps as axisscales improved. Dates are displayed as text dates and not datestamp values
• Selection of data improved with easier selection full integration with plots of data
• Data exchange between interfaces improved (File > Send To menu)
• Quick access to commonly used operations (via toolbar buttons)

Plot Controls

• "Stacked" plots (automatic y-scale toolbar button cycles through scaled data, stacked data, normal view)
• "Color by" any related data or user-selected data
• "Invert selection" toolbar button added
• Improved access to data in table format
• Persistent selection capability. Selection mode stays activated after a selection. (Optional - disable through settings)
• Customizable line widths (context menu on the plot)
• Customizable figure toolbar to choose which toolbar buttons are shown.
• Time-based axes have improved automatic update after a zoom or pan

Analysis Window

• Automatic data augmentation by simply importing / loading new data
• Easier to read format for main table with improved information
• Model Cache speed improvements

Workspace Browser

• DOE Experiment Designer and easy Calibration Transfer model application added
• Drag/drop of multiple items improved

NEW FUNCTIONS AND FILES

• Full Support for Matlab R2011b

Misc New Functions

autoexport - Exports a DataSet object to a file of the specified format.

classcenter - Centers classes in data to the mean of each class.

flucut - Remove scatter from fluorescence EEM data.

permutetest - Permutation testing for regression and classification models.

permuteplot - Create plot of permutation test results.

permuteprobs - Display probabilities derived from permutation testing.

poissonscale - Perform Poisson scaling with scaling offset.

spareadr - Reads Thermo Fisher SPA files.

specalignset - Settings used to modify variable alignment preprocessing.

svmoc - Support Vector Machine for one-class analysis.

Distribution Fitting Toolbox Tools

randomttest - Randomization t-test for evaluating residuals from two models.

signtest - Pairwise sign test for evaluating residuals from two models.

wilcoxon - Pairwise Wilcoxon signed rank test for evaluating residuals from two models.

Design of Analysis Tools

anovadoe - Function to perform ANOVA for 2^k factorial model X, Y data

boxbehnken - Create a Box-Behnken Design of Experiments.

ccdface - Create a Face-Centered Central Composite Design of Experiments.

ccdsphere - Create a Spherical Central Composite Design of Experiments.

doegen - Generate a Design of Experiments (DOE) DataSet object.

doegui - Design of Experiments tool.

doeeffectsplot - Main & Interaction Effects plots.

doeinteractions - Calculates interaction terms of a raw DOE matrix.

doescale - Convert coded DOE to scaled DOE or scaled back to coded.

factdes - Full factorial design of experiments.

ffacconfusion - DOECONFUSION Generates confusion table for a fractional factorial DOE.

ffacdes1 - FACTDES Fractional factorial 2-level design of experiments.

Other Changes

crossval - improved display of classification results, improved integration with model input

excludemissing - improved handling of unusual missing data patterns

fasternnls - improved performance for large numbers of factors and for low signal problems

parafac2 - improved memory efficiency and missing data support

residuallimit - add support for calculating confidence level from given Q value and a model

stdgen - tuned performance

summary - improved output and display options. Now outputs DSO or displays more useful data.

svmda - improved parameter selection for special cases

wlsbaseline - added variable weights as output (weighting used on each variable in spectrum)