Release Notes Version 7 8: Difference between revisions
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Version 7.8 of PLS_Toolbox and Solo was released in June, 2014. | |||
For general product information, see [http://www.eigenvector.com/software/pls_toolbox.htm PLS_Toolbox Product Page]. For information on Solo, see [http://www.eigenvector.com/software/solo.htm Solo Product Page]. | |||
(back to [[Release Notes PLS Toolbox and Solo]]) | |||
==New Features in Solo and PLS_Toolbox== | ==New Features in Solo and PLS_Toolbox== | ||
===[[asca| ASCA (Analysis of Variance Simultaneous Component Analysis)]]=== | ===[[asca| ASCA (Analysis of Variance Simultaneous Component Analysis)]]=== | ||
* Add new command-line and Analysis Window-based access to ASCA method | * Add new command-line and Analysis Window-based access to ASCA method | ||
* | * Allows multivariate analysis of designed experiments by creating a PCA model for each of the ANOVA-calculated effect matrices. | ||
* In the Analysis window, user can navigate through each factor's PCA model investigating the magnitude and influenced variables. | |||
* Effect of each factor are reported in the Effects column and in the scores for the PCA model for the particular factor. | |||
* The variable(s) which are significantly influenced by the factor are given by the loadings for the PCA model on that factor. | |||
* Includes a permutation calculator which, when enabled, will report the probability that the given effect is significant (based on randomization of samples within each level of each given factor) | |||
===Analysis Interface=== | ===Analysis Interface=== | ||
* Add ASCA (ANOVA Simultaneous Component Analysis) analysis method | * Add ASCA (ANOVA Simultaneous Component Analysis) analysis method | ||
* Add support for "wide" (thick) venetian blinds | * Add support for "wide" (thick) venetian blinds | ||
* Give advice when current cross-validation conditions are non-optimal | * SVM-R / SVM-C: Support all cross-validation methods (not just random) | ||
* Show visual display of cross-validation sample splitting | |||
* Give advice when current cross-validation conditions are non-optimal | |||
* Improve cross-validation speed | * Improve cross-validation speed | ||
* | * Add "weights" option to PLS and PLSDA to weight samples | ||
* Add showyinbiplot option which allows hiding y-loadings in the Biplot | * Add showyinbiplot option which allows hiding y-loadings in the Biplot | ||
* Speed improvements for iPLS, iPLSDA, Stepwise MLR | |||
* For two-class PLSDA models, include the average number of samples CORRECT as additional column (translation of fractional error into actual number of samples) | |||
* Add sorting option for dates in cache. | * Add sorting option for dates in cache. | ||
* Allow drag/drop of exported model cache model+data format file into Analysis | |||
* Add "rebuild model" to menu context menu (clear + build) | |||
* Add Matthew's Correlation Coefficient to the output from confusionmatrix (two classes only) | |||
* Calculate and show area under the curve (AUC) for ROC curves | |||
* Calculate and display the min/max/ave percentage of samples left out per cross-validation cycle | |||
* Add ability to automatically create plots when creating a report | |||
* Better exporting of text-based information in Report Writer (e.g. Confusion tables and matrices) | |||
* Always reconcile variables in test set with model, even when the NUMBER of variables matches | |||
* ANN: fix for wrong CV predicted values shown for models with > 1 Node (RMSECV was correct) | |||
* Fix for pointer not always getting set back to arrow | * Fix for pointer not always getting set back to arrow | ||
===Preprocessing=== | ===Preprocessing=== | ||
* Log10: Use an offset AND ignore negative values | * Log10: Use an offset AND ignore negative values | ||
* Normalize: Allow normalization with multi-way data | * Normalize: Allow normalization with multi-way data | ||
* Arithmetic: Add visual variable selection | * Arithmetic: Add visual variable selection and clarify other options | ||
* GLSW: Make sure data .include field is applied to external data | |||
===Browse=== | ===Browse=== | ||
Line 28: | Line 48: | ||
* Add new drag drop behavior for datasets onto datasets, datasets onto preprocessing, and datasets onto models. | * Add new drag drop behavior for datasets onto datasets, datasets onto preprocessing, and datasets onto models. | ||
* Add support for F2 = rename selected variable | * Add support for F2 = rename selected variable | ||
* Easier to navigate EigenGuide video list and improved handling when new list can't be obtained | |||
* Give option to clear data from base workspace if large data is pushed into Analysis or Image Manager | * Give option to clear data from base workspace if large data is pushed into Analysis or Image Manager | ||
Line 35: | Line 56: | ||
===Importers=== | ===Importers=== | ||
* Add new Bruker XRPD importer (.raw file format) | |||
* Improved handling of imports when multiple importers match the file type | |||
* Text graphical import tool - improved support for ignoring data, automatically detecting types, and visibility | * Text graphical import tool - improved support for ignoring data, automatically detecting types, and visibility | ||
* Streamlined importing from GUIs- no longer necessary to select file type first, simply locate and load the file(s) of interest | * Streamlined importing from GUIs- no longer necessary to select file type first, simply locate and load the file(s) of interest | ||
* Automatically sort filenames into alphabetical order when importing | * Automatically sort filenames into alphabetical order when importing | ||
* Horiba importer ([[hjyreadr]]) automatically transpose image so that it matches Horiba's image mode | * Horiba importer ([[hjyreadr]]) automatically transpose image so that it matches Horiba's image mode | ||
* Text importer ([[textreadr]]): | * Text importer ([[textreadr]]): | ||
** | ** Date format yyyymmddTHHMMSS (datestr format 30) is now recognized automatically | ||
** Fix | ** Improved handling of small data tables | ||
** Fix handling of double-quoted label that looks numeric | |||
** Recognize dates which use spelled out month names | ** Recognize dates which use spelled out month names | ||
** Add improved auto-detection of XLS (look for binary file) | ** Add improved auto-detection of XLS (look for binary file) | ||
* SPC importer ([[spcreadr]]): | * SPC importer ([[spcreadr]]): | ||
** Fix for bug reading files with negative scaling exponents (fexp<0) | ** Fix for bug reading files with negative scaling exponents (fexp<0) | ||
Line 55: | Line 75: | ||
===Plot Controls=== | ===Plot Controls=== | ||
* Add scroll-wheel functionality (zoom plot, combine with shift or control to zoom one axes, click and move to pan) | * Add scroll-wheel functionality (zoom plot, combine with shift or control to zoom one axes, click and move to pan) | ||
* Add click-to-highlight feature to move a line or class set to the front of the plot | * Add click-to-highlight feature to move a line or class set to the front of the plot | ||
* Add class connect methods "spider" and "means" (connect means of each x) | |||
* Significant improvement to speed of updating when plot control listbox does not need to be repopulated | * Significant improvement to speed of updating when plot control listbox does not need to be repopulated | ||
* Add logic to bring target figure back to focus after docking controls (avoids issue that clicking on figure looses focus on figure) | * Add logic to bring target figure back to focus after docking controls (avoids issue that clicking on figure looses focus on figure) | ||
* Add "automonotonic" flag to plotgui to avoid use of monotonic in "auto" mode unless allowed | |||
* Add density-plot replot on zoom functionality | |||
* Allow ALL options to be seen in settings | * Allow ALL options to be seen in settings | ||
* Change connect class toolbar button into a popup menu | * Change connect class toolbar button into a popup menu | ||
* Convert Axis Settings from instant-pop-up to context-menu-based command | * Convert Axis Settings from instant-pop-up to context-menu-based command | ||
Line 82: | Line 102: | ||
* Add "copy image to clipboard" functionality. | * Add "copy image to clipboard" functionality. | ||
===[[ | ===[[Modeloptimizergui|Model Optimizer]]=== | ||
* | * Add R2C, R2CV, and compression information (from ANN and SVM models) to displayed fields | ||
===[[mpca]] / [[parafac]]=== | ===[[mpca|MPCA]] / [[parafac|PARAFAC]]=== | ||
* Allow for single slab input for prediction if sizes of two existing modes match variables for n-way array | * Allow for single slab input for prediction if sizes of two existing modes match variables for n-way array | ||
===[[bspcgui|Batch Processor]]=== | |||
* Fix for manually selecting batch steps. | |||
==New Command-line Features and Functions== | ==New Command-line Features and Functions== | ||
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**Fix for bug when converting multiple inputs to options structure when one of those inputs was a cell array | **Fix for bug when converting multiple inputs to options structure when one of those inputs was a cell array | ||
**Revision to logic - give preference to classes in DSO when grouping (if no classes passed) THEN use labels (if no classes present in DSO) | **Revision to logic - give preference to classes in DSO when grouping (if no classes passed) THEN use labels (if no classes present in DSO) | ||
* [[brukerxrpdreadr]] -add new Bruker XRPD importer (.raw file format) | |||
*[[confusionmatrix]] / [[confusiontable]] | *[[confusionmatrix]] / [[confusiontable]] | ||
**Handle excluded samples in simca case. | **Handle excluded samples in simca case. | ||
**Allow cell array of strings to be passed as trueClass and predClass | **Allow cell array of strings to be passed as trueClass and predClass | ||
**Fix for bug in texttable output when no y is present | **Fix for bug in texttable output when no y is present | ||
* [[dataset]] -Add augment | * [[dataset]] | ||
** -Add augment method, will create class that tracks augmented dataSets after a concatenation | |||
** -Add table method, gets text table with labels from DataSet | |||
* [[doegui|Experiment Designer]] -Add randomize menu item, overhaul options usage, and fix a few bugs with loading a DOE dataset. | * [[doegui|Experiment Designer]] -Add randomize menu item, overhaul options usage, and fix a few bugs with loading a DOE dataset. | ||
* [[oplecorr]] -Add new "Optical Path-Length Estimation and Correction" preprocessing (command-line only) | |||
* [[reviewcrossval]] - Examines cross-validation settings for typical problems. | |||
* [[textreadr]] -Add "catdim" and "autopermute" options to manually control concatenation of multiple files |
Latest revision as of 16:33, 10 June 2014
Version 7.8 of PLS_Toolbox and Solo was released in June, 2014.
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 in Solo and PLS_Toolbox
ASCA (Analysis of Variance Simultaneous Component Analysis)
- Add new command-line and Analysis Window-based access to ASCA method
- Allows multivariate analysis of designed experiments by creating a PCA model for each of the ANOVA-calculated effect matrices.
- In the Analysis window, user can navigate through each factor's PCA model investigating the magnitude and influenced variables.
- Effect of each factor are reported in the Effects column and in the scores for the PCA model for the particular factor.
- The variable(s) which are significantly influenced by the factor are given by the loadings for the PCA model on that factor.
- Includes a permutation calculator which, when enabled, will report the probability that the given effect is significant (based on randomization of samples within each level of each given factor)
Analysis Interface
- Add ASCA (ANOVA Simultaneous Component Analysis) analysis method
- Add support for "wide" (thick) venetian blinds
- SVM-R / SVM-C: Support all cross-validation methods (not just random)
- Show visual display of cross-validation sample splitting
- Give advice when current cross-validation conditions are non-optimal
- Improve cross-validation speed
- Add "weights" option to PLS and PLSDA to weight samples
- Add showyinbiplot option which allows hiding y-loadings in the Biplot
- Speed improvements for iPLS, iPLSDA, Stepwise MLR
- For two-class PLSDA models, include the average number of samples CORRECT as additional column (translation of fractional error into actual number of samples)
- Add sorting option for dates in cache.
- Allow drag/drop of exported model cache model+data format file into Analysis
- Add "rebuild model" to menu context menu (clear + build)
- Add Matthew's Correlation Coefficient to the output from confusionmatrix (two classes only)
- Calculate and show area under the curve (AUC) for ROC curves
- Calculate and display the min/max/ave percentage of samples left out per cross-validation cycle
- Add ability to automatically create plots when creating a report
- Better exporting of text-based information in Report Writer (e.g. Confusion tables and matrices)
- Always reconcile variables in test set with model, even when the NUMBER of variables matches
- ANN: fix for wrong CV predicted values shown for models with > 1 Node (RMSECV was correct)
- Fix for pointer not always getting set back to arrow
Preprocessing
- Log10: Use an offset AND ignore negative values
- Normalize: Allow normalization with multi-way data
- Arithmetic: Add visual variable selection and clarify other options
- GLSW: Make sure data .include field is applied to external data
Browse
- Align variables (if possible) when joining two datasets in the samples dimension
- Add new drag drop behavior for datasets onto datasets, datasets onto preprocessing, and datasets onto models.
- Add support for F2 = rename selected variable
- Easier to navigate EigenGuide video list and improved handling when new list can't be obtained
- Give option to clear data from base workspace if large data is pushed into Analysis or Image Manager
Dataset Editor
- Add View > Class and Axisscale Summary menu to EditDS (views Class Summary table)
- Add View Boxplot to menus (simple boxplot call)
Importers
- Add new Bruker XRPD importer (.raw file format)
- Improved handling of imports when multiple importers match the file type
- Text graphical import tool - improved support for ignoring data, automatically detecting types, and visibility
- Streamlined importing from GUIs- no longer necessary to select file type first, simply locate and load the file(s) of interest
- Automatically sort filenames into alphabetical order when importing
- Horiba importer (hjyreadr) automatically transpose image so that it matches Horiba's image mode
- Text importer (textreadr):
- Date format yyyymmddTHHMMSS (datestr format 30) is now recognized automatically
- Improved handling of small data tables
- Fix handling of double-quoted label that looks numeric
- Recognize dates which use spelled out month names
- Add improved auto-detection of XLS (look for binary file)
- SPC importer (spcreadr):
- Fix for bug reading files with negative scaling exponents (fexp<0)
- Fix to better handle files that have binary logs as well as text audit logs
- Add ability to specify data is an image by including "imagesize=..." and "imageorder=..." in audit log
- Add ability to specify author and name to be used by including them as key=value pairs in audit log
Plot Controls
- Add scroll-wheel functionality (zoom plot, combine with shift or control to zoom one axes, click and move to pan)
- Add click-to-highlight feature to move a line or class set to the front of the plot
- Add class connect methods "spider" and "means" (connect means of each x)
- Significant improvement to speed of updating when plot control listbox does not need to be repopulated
- Add logic to bring target figure back to focus after docking controls (avoids issue that clicking on figure looses focus on figure)
- Add "automonotonic" flag to plotgui to avoid use of monotonic in "auto" mode unless allowed
- Add density-plot replot on zoom functionality
- Allow ALL options to be seen in settings
- Change connect class toolbar button into a popup menu
- Convert Axis Settings from instant-pop-up to context-menu-based command
- Axis Settings "all fonts" option now changes axes fonts too
- Change class colors base to improve visibility
- Move axis lines and class outlines to bottom of plot order so that right-click controls are not inaccessible
- Exporting figure: add new "resizemode" option to control resizing behavior
- Revise classmarkers to improve speed and automatically tie colors to classcolors
Hierarchical Model Builder
- Add ability to set preferences including whether Q and T2 tests are based on reduced statistics and what thresholds should be used to trigger "otherwise" in PLSDA-based rule nodes
- Add scores as ouptut option for regression models
- Add "on-canvas" display of numerics, strings, errors, and model types
- Added ability to set condition on end points before the content of the end point has been defined
- Improve behavior when overwriting nodes with similar node type
- Allow drag/drop of models onto nodes to overwrite existing rule node WITHOUT changing branches (if possible)
- Allow double-click of model-based rule nodes to open model in Analysis
- Fix for error using "load" toolbar button or menu option
- Add "copy image to clipboard" functionality.
Model Optimizer
- Add R2C, R2CV, and compression information (from ANN and SVM models) to displayed fields
MPCA / PARAFAC
- Allow for single slab input for prediction if sizes of two existing modes match variables for n-way array
Batch Processor
- Fix for manually selecting batch steps.
New Command-line Features and Functions
Misc New Functions
Command-Line Changes
- anovadoe
- Fix to force use of center points
- Use design information to identify center points ONLY (don't infer based on values)
- Allow input of matrix for y (squelches statistical tests - only reports coefficients)
- Add calculation of 3-way interactions
- Calculate the ANOVA decomposition column/matrices as needed for ASCA
- boxplot
- Fix for bug which would truncate labels to a single character
- Fix for bug when converting multiple inputs to options structure when one of those inputs was a cell array
- Revision to logic - give preference to classes in DSO when grouping (if no classes passed) THEN use labels (if no classes present in DSO)
- brukerxrpdreadr -add new Bruker XRPD importer (.raw file format)
- confusionmatrix / confusiontable
- Handle excluded samples in simca case.
- Allow cell array of strings to be passed as trueClass and predClass
- Fix for bug in texttable output when no y is present
- dataset
- -Add augment method, will create class that tracks augmented dataSets after a concatenation
- -Add table method, gets text table with labels from DataSet
- Experiment Designer -Add randomize menu item, overhaul options usage, and fix a few bugs with loading a DOE dataset.
- oplecorr -Add new "Optical Path-Length Estimation and Correction" preprocessing (command-line only)
- reviewcrossval - Examines cross-validation settings for typical problems.
- textreadr -Add "catdim" and "autopermute" options to manually control concatenation of multiple files