imported>Neal |
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| ===Purpose===
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| Alternating Least Squares computational engine for multivariate curve resolution (MCR).
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| ===Synopsis===
| | Version 6.7 of PLS_Toolbox and Solo was released in March, 2012. |
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| :[c,s] = als(x,c0,options); | | 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]. |
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| ===Description===
| | (back to [[Release Notes PLS Toolbox and Solo]]) |
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| ALS decomposes a matrix '''X''' as '''CS''' such that '''X''' = '''CS''' + '''E''' where '''E''' is minimized in a least squares sense.
| | ==NEW FEATURES== |
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| Inputs are the matrix to be decomposed (x) (''M'' by ''N''), and the initial guess (c0). If (c0) is size ''M'' by ''K'', where ''K'' is the number of factors, then it is assumed to be the initial guess for '''C'''. If (c0) is size ''K'' by ''N'' then it is assumed to be the initial guess for '''S'''. If ''M'' = ''K'' then, (c0) is assumed to be the initial guess for '''C'''.
| | ===Design Of Experients (DOE) Tools=== |
| | * bla |
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| An optional input (options) is described below.
| | ===Other Method Improvements=== |
| | * bla |
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| | ===Preprocessing=== |
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| | ===Import / Export=== |
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| | ===DataSet Editor=== |
| | * bla |
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| The outputs are the estimated matrices '''C''', (c), (''M'' by ''K'') and '''S''', (s), (''K'' by ''N''). For a typical decomposition, (c) is a matrix of contributions and (s) is a matrix of spectra. The function
| | ===Plot Controls=== |
| | * Selectable plot themes. [[Image:Figbg_color.gif|thumb|| ]] |
| | * bla |
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| :[c,s] = als(x,c0)
| | ===[[AnalysisWindow_Layout|Analysis Window]]=== |
| | * Show CV results for confusion table when available. |
| | * Improved [[modelcache]] performance and string handling. |
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| will decompose (x) using an non-negatively constrained alternating least squares. To include other constraints, use the (options) input described below.
| | ===[[WorkspaceBrowser_Layout|Workspace Browser]] === |
| | * Drag Drop - Enable dragging and dropping of system files onto the Browser window as well as to Analysis window. Enhanced highlighting of drop location. |
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| Note that if no non-zero equality constraints are imposed on a factor the spectra are normalized to unit length. This can lead to significant scaling differences between factors that have non-zero equality constraints and those that do not.
| | ===Command-line Tool Changes=== |
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| ===Options===
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| * '''display''': [ 'off' | {'on'} ] governs level of display to command window.
| | ==NEW FUNCTIONS AND FILES== |
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| * '''plots''': [ 'none' | {'final'} ] governs level of plotting. | | *''Full Support for Matlab R2012a'' |
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| * '''ccon''': [ 'none' | 'reset' | {'fastnnls'} ] non-negativity on contributions. (fastnnls = true least-squares solution)
| | ===Misc New Functions=== |
| | :[[autoexport]] - Exports a DataSet object to a file of the specified format. |
| | :[[classsummary]] - List class and axisscale distributions for a DataSet. |
| | :[[figuretheme]] - Resets a figure background and axes to a specified color. |
| | :[[meantrimmed]] - Trimmed mean. |
| | :[[mediantrimmed]] - Trimmed median. |
| | :[[windowfilter]] - Spectral filtering. |
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| * '''scon''': [ 'none' | 'reset' | {'fastnnls'} ] non-negativity on spectra. (fastnnls = true least-squares solution)
| | ===Design of Analysis Tools=== |
| | :[[anovadoe]] - Function to perform ANOVA for 2^k factorial model X, Y data |
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| * '''cc''': [ ] contributions equality constraints, must be a matrix with ''M'' rows and up to ''K'' columns with NaN where equality constraints are not applied and real value of the constraint where they are applied. If fewer than ''K'' columns are supplied, the missing columns will be filled in as unconstrained,
| | ===Other Changes=== |
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| * '''ccwts''': [inf] a scalar value or a 1x''K'' vector with elements corresponding to weightings on constraints (0, no constraint, 0<wt<inf imposes constraint "softly", and inf is hard constrained). If a scalar value is passed for (ccwts), that value is applied for all ''K'' factors.
| | :[[crossval]] - improved display of classification results, improved integration with model input |
| :Soft constraints are imposed by augmenting an additional column onto '''X''' and a weight of 1 weights a given equality constraint so that it has an equal influence as the average single variable in '''X'''. For additional information see P.J. Gemperline and E. Cash, “Advantages of Soft versus Hard Constraints in Self–Modeling Curve Resolution Problems. Alternating Least Squares with Penalty Functions”, ''Anal. Chem.,'' '''75'''(16), 4236–4243 (2003).
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| * '''sc''': [ ] spectra equality constraints, must be a matrix with ''N'' columns and up to ''K'' rows with NaN where equality contraints are not applied and real value of the constraint where they are applied. If fewer than ''K'' rows are supplied, the missing rows will be filled in as unconstrained.
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| * '''scwts''': [inf] weighting for spectral equality constraints (see ccwts) above.
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| * '''sclc''': [ ] contributions scale axis, vector with ''M'' elements otherwise 1:M is used.
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| * '''scls''': [ ] spectra scale axis, vector with ''N'' elements otherwise 1:N is used.
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| * '''condition''': [{'none'}| 'norm' ] type of conditioning to perform on '''S''' and '''C''' before each regression step. 'norm' uses conditioning which can help stabilize the regression when factors are significantly different in magnitude.
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| * '''tolc''': [ {1e-5} ] tolerance on non-negativity for contributions.
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| * '''tols''': [ {1e-5} ] tolerance on non-negativity for spectra.
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| * '''ittol''': [ {1e-8} ] convergence tolerance.
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| * '''itmax''': [ {100} ] maximum number of iterations.
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| * '''timemax''': [ {3600} ] maximum time for iterations.
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| * '''rankfail''': [ 'drop' |{'reset'}| 'random' | 'fail' ] how are rank deficiencies handled:
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| * '''drop''' - drop deficient components from model,
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| * '''reset''' - reset deficient components to initial guess,
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| * '''random''' - replace deficient components with random vector,
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| * '''fail''' - stop analysis, give error.
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| ===Examples===
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| To decompose a matrix (x) without non-negativity constraints use:
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| :options = als('options');
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| :options.ccon = 'none';
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| :options.scon = 'none';
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| :[c,s] = als(x,c0,options);
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| The following shows an example of using soft-constraints on the second spectral component of a three-component solution assuming that the variable softs contains the spectrum to which component two should be constrained.
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| :[m,n] = size(x);
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| :options = als('options');
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| :options.sc = NaN\*ones(3,n); %all 3 unconstrained
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| :options.sc(2,:) = softs; %constrain component 2
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| :options.scwts = 0.5; %consider as 1/2 of total signal in X
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| :[c,s] = als(x,c0,options);
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| ===See Also===
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| [[mcr]], [[parafac]], [[pca]]
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