Evrimodel and Release Notes Version 8 5: Difference between pages

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===purpose===
Build an EVRI Model Object.


===Synopsis===
==Version 8.5==
Version 8.5 of PLS_Toolbox and Solo was released in September, 2017.


:model = evrimodel(modeltype); %creates a model object of type (modeltype)
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].
:model = evrimodel; %creates a generic model object


===Description===
(back to [[Release Notes PLS Toolbox and Solo]])


An [[EVRIModel_Objects|EVRIModel object]] is a generic object that contains a standard Eigenvector model object. The model can be either "empty" (uncalibrated), "calibrated", or "applied" (prediction on new data). The examples below show building and applying a model using the object's built-in methods.
==Overview==


Model objects are also output from numerous PLS_Toolbox functions (in the calibrated or applied state.) The content of these models can be interrogated through the model properties (the object fields available depend on the model type and can be accessed through the "fieldnames" method).
* The primary focus of version 8.5 has been in Calibration Transfer and additional importers.


The models can also be used through the standard methods as described below.
* PLS_Toolbox/Solo 8.5 has been tested extensively with Matlab 2017b prerelease and should be compatible with the coming release.


For details on how to work with the objects, the the [[EVRIModel Objects|EVRIModel Objects page]].
* Simplified interface design changes. Various controls have been moved to simplify interfaces. Seldom used settings have been moved to options in several cases (e.g., simplified [[Svm|SVM]] panel).


====Optional Input====
* The Analysis window's confusion matrix and table toolbar icon now returns classification results for both [http://wiki.eigenvector.com/index.php?title=Sample_Classification_Predictions#Class_Pred_Most_Probable 'most probable'] and [http://wiki.eigenvector.com/index.php?title=Sample_Classification_Predictions#Class_Pred_Strict  'strict'] classifications. In the 'strict' case it also lists the 'strictthreshold' value used.
* '''modeltype''' = standard model object type to create. E.g. 'pls','pca'.


====Output====
==Calibration Transfer==
* '''model''' = standard model object of type (modeltype)
* [[MCCTTool | New Model-centric Calibration Transfer]] - Interface to develop instrument specific models with calibration transfer.


====Examples====
* [[nlstd| NLSTD]] - Create or apply non-linear instrument transfer models (PLS_Toolbox only).
* '''BUILD MODEL'''
  m = evrimodel('pls'); %creates an empty PLS model object
  m.x = x;              %assigns data to the X-block (predictor)
  m.y = y;              %assigns data to the Y-block (predictand)
  m.ncomp = ncomp;      %sets the number of components in the model
  m.options = options;  %assigns model options with a standard options structure
  m.calibrate;          %performs calibration method


* '''CROSS-VALIDATE MODEL'''
* [[sstcal| SST]] - Spectral Subspace Transformation calibration transfer.
  m.crossvalidate(x,cvi)


* '''APPLY MODEL'''
* [[Demonstration_Datasets|Corn DSO]] - New calibration transfer demonstration data set added. 80 samples of corn measured on 3 different NIR spectrometers with moisture, oil, protein and starch values for each of the samples is also included.
  p = m.apply(data)


* '''PLOT CONTENTS'''
==Importers==
  m.plotscores
  m.plotloads
  m.ploteigen


===Properties===
* [[shimadzueemreadr]] - Imports Shimadzu EEM formatted text files.
The following properties can be modified through SETPLSPREF using
* [[visionairxmlreadr]] - Imports Vision Air formatted XML files (X- & Y-Blocks).
  setplspref('evrimodel','property',value)
* [[pltreadr]] - Imports Vision Air model files (.plt).
The properties govern model method behavior and include the following:
 
====General options====
* [[aqualogreadr]] - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
* '''noobject''': [ {false} | true ] Disables object use altogether.
 
* '''usecache''': [ {false} | true ] Governs use of model cache when models are calibrated or applied using object methods.
* [[jascoeemreadr]] - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
====Type and class testing options====
 
* '''stricttesting''': [ false | {true} ] Give warning/error when code tests a model by using "isstruct" or "isfield(...,'modeltype'). Best practices are to avoid these methods and use ismodel() instead. This option helps detect code where the poor practices are used.
* [[hitachieemreadr]] - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
* '''strictmodeltype''': [ false | {true} ] Give warning/error when a model type is changed to either an undefined model  type or from one model type to an incompatible model type.
 
* '''fatalalerts''': [ {false} | true ] Governs whether above tests give warnings (false) or throw errors (true).
* [[rawread|RAWREAD]] - Added support for new version format (3 & 4) (See MIA_Toolbox).
====Display options====
 
These settings govern the command-line output for models.
* [[spgreadr|SPGREADR]] Added new feature, options.spectrumindex now can be an integer, an array of integers (indices, & order doesn't matter), or 'all'. When loading multiple files, options.spectrumindex must be either a single value or 'all'.
* '''desc''': [ false | {true} ] Governs display of model summary details (same as model.info).
 
* '''contents''': [ {false} | true ] Governs display of model fields and summary of their contents (old format of display).
==Exporters==
====Model application options====
 
* '''plots''': [ {'none'} | 'final' ] Governs showing of plots when model is calibrated or applied to new data.
* [[writeplt]] - Exports EVRI Model structures to Vision Air PLT files.
* '''display''': [ {'off'} | 'on' ] Governs display of information at the command line when the model is calibrated or applied to new data.  
 
* '''matchvars''': [ 'off' | {'on'} ] Governs use of variable alignment when apply the model to new data (matchvars). When
==Other Features and Improvements==
::When 'on', new data will be aligned to model before application.
* [[Cooksd| Cook's Distance]] - Calculates Cooks Distance for samples in a regression model.
::When 'off', if the new data variables do not match the model's expected variables, an error will be thrown.
 
* '''contributions''': [ {'passed'} | 'used' | 'full' ] Governs detail of returned T^2 and Q contributions. Return contributions for:
* [[rpls| RPLS]] - A recursive PLS and PCR variable selection algorithm.  
::'passed' = only the variables passed by the client in the order passed. This mode allows the client to easily map contributions back to passed data and is the preferred mode.
 
::'used'  = all variables used by the model including even variables which client did not provide. Variable order is that used by model and may not match the order passed by the client.
* [[manhattandist| MANHATTANDIST]] - Calculate Manhattan Distance between rows of a matrix.
::'full'  = all variables used or excluded by the model, including even variables which client did not provide. Variable order is that used by model and may not match the order passed by the client.
 
* '''reducedstats''': [ {'off'} | 'on' ] Governs whether Q and T^2 statistics from models are "reduced" using the confidence limit set in the model.detail.reslim and model.detail.tsqlim fields.
* [[Confusionmatrix]] and [[Confusiontable]] - Classification results formatting options added. Can now specify use of mostprobable or strict classification rule.  
::If 'on', statistics are normalized using the value stored in the appropriate detail sub-field.
* [[calcdifference]] - Calculate difference between two datasets.
::If 'off', statistics are returned as calculated.
* Added GLS Weighting to model optimizer.

Revision as of 09:35, 7 February 2019

Version 8.5

Version 8.5 of PLS_Toolbox and Solo was released in September, 2017.

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)

Overview

  • The primary focus of version 8.5 has been in Calibration Transfer and additional importers.
  • PLS_Toolbox/Solo 8.5 has been tested extensively with Matlab 2017b prerelease and should be compatible with the coming release.
  • Simplified interface design changes. Various controls have been moved to simplify interfaces. Seldom used settings have been moved to options in several cases (e.g., simplified SVM panel).
  • The Analysis window's confusion matrix and table toolbar icon now returns classification results for both 'most probable' and 'strict' classifications. In the 'strict' case it also lists the 'strictthreshold' value used.

Calibration Transfer

  • NLSTD - Create or apply non-linear instrument transfer models (PLS_Toolbox only).
  • SST - Spectral Subspace Transformation calibration transfer.
  • Corn DSO - New calibration transfer demonstration data set added. 80 samples of corn measured on 3 different NIR spectrometers with moisture, oil, protein and starch values for each of the samples is also included.

Importers

  • aqualogreadr - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
  • jascoeemreadr - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
  • hitachieemreadr - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
  • RAWREAD - Added support for new version format (3 & 4) (See MIA_Toolbox).
  • SPGREADR Added new feature, options.spectrumindex now can be an integer, an array of integers (indices, & order doesn't matter), or 'all'. When loading multiple files, options.spectrumindex must be either a single value or 'all'.

Exporters

  • writeplt - Exports EVRI Model structures to Vision Air PLT files.

Other Features and Improvements

  • RPLS - A recursive PLS and PCR variable selection algorithm.
  • MANHATTANDIST - Calculate Manhattan Distance between rows of a matrix.
  • Confusionmatrix and Confusiontable - Classification results formatting options added. Can now specify use of mostprobable or strict classification rule.
  • calcdifference - Calculate difference between two datasets.
  • Added GLS Weighting to model optimizer.