# Release Notes Version 6 5

From Eigenvector Documentation Wiki

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)

## Contents

## 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

### Command-line Tool Changes

## 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)