# Alphabetical Index

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## A

- abline - Draws a line on the current axes with a given slope and intercept.
- alignmat - Alignment of matrices and N-way arrays.
- alignpeaks - Calibrates wavelength scale using standard peaks.
- alignspectra - Calibrates wavelength scale using standard spectrum.
- als - Alternating Least Squares computational engine.
- analysis - Graphical user interface for data analysis.
- analyzeparticles - Analyze particles (blobs, connected regions) in image.
- anglemapper - Classification based on angle measures between signals.
- ann - Artificial Neural Network regression models.
- anova1w - One-way analysis of variance.
- anova2w - Two-way analysis of variance.
- anovadoe - Function to perform ANOVA for 2^k factorial model X, Y data.
- areadr - Reads ascii data and strips header.
- arithmetic - Apply simple arithmetic operations to all or part of dataset.
- asca - Apply ANOVA Simultaneous Component Analysis to a crossed DOE dataset.
- asdreadr - Imports data from Analytical Spectral Devices (ASD) Indico (Versions 6 and 7) data files.
- asfreadr - Reads AIT ASF files.
- auto - Autoscales matrix to mean zero unit variance.
- autocor - Auto-correlation function for time series data.
- autoset - GUI used to modfiy settings of
`auto`. - autoexport - Exports a DataSet object to a file of the specified format.
- autoimport - Automatically reads specified file. Handles all standard filetypes.

## B

- b3spline - Univariate spline fit and prediction.
- baseline - Subtracts a polynomial baseline offset from spectra.
- baselinew - Baseline using windowed polynomial filter.
- besttime - Returns a string describing the time interval provided (in seconds).
- batchalign - Convert data columns based on matching ref col to target vector.
- batchdigester - Parse wafer or batch data into MPCA or Summary PCA form.
- batchfold - Transform batch data into dataset for analysis.
- batchmaturity - Batch process model and monitoring.
- boxbehnken - Create a Box-Behnken Design of Experiments.
- browse - PLS_Toolbox Toolbar and Workspace browser.
- brukerxrpdreadr - Reads Bruker XRPD RAW files into a DataSet object.
- builddbstr - Builds a database connection string.

## C

- calccvbias - Calculate the Cross-Validation Bias from a cross-validated model.

- calcdifference - Calculate normalized difference between two datasets.
- calibsel - Statistical procedure for variable selection.
- caltransfer - Create or apply calibration and instrument transfer models.
- ccdface - Create a Face-Centered Central Composite Design of Experiments.
- ccdsphere - Create a Spherical Central Composite Design of Experiments.
- cellne - Compares two cells for inequality in size and/or values.
- centerfigure - Places a given figure into a centered default position.
- chilimit - Chi-squared confidence limits from sum-of-squares residuals.
- choosecomp - Automatic selection of components for various model types.
- choosencomp - GUI to select number of components from SSQ table.
- class2logical - Create a PLSDA logical block from class assignments.
- classcenter - Centers classes in data to the mean of each class.
- classcentroid - Centers data to the centroid of all classes.
- classcolors - Defines the colors to be used for classes in plots.
- classsummary - List class and axisscale distributions for a DataSet.
- cluster - KNN and K-means cluster analysis with dendrograms.
- cls - Classical Least Squares regression for multivariate Y.
- coadd - Reduce resolution through combination of adjacent variables or samples.
- coda_dw - Calculates values for the Durbin_Watson criterion of columns of data set.
- coda_dw_interactive - Interactive version of CODA_DW.
- comparelcms_sim_interactive - Interactive interface for COMPARELCMS.
- comparelcms_simengine - Calculational Engine for comparelcms.
- comparemodels - Create summary table of models' performance statistics.
- comparevars - Compares two variables of any type and returns differences.
- compressmodel - Remove references to unused variables from a model.
- confusionmatrix - Create confusion matrix.
- confusiontable - Create confusion table.
- conload - Congruence loadings for PARAFAC, TUCKER and NPLS.
- constrainfit - Finds A minimizing ||X-A*B'|| subject to constraints, given XtB and BtB.
- cooksd - Calculates Cooks Distance based on regression model.
- copycvfields - Copy cross-validation results into model from structure.
- copydsfields - Copies informational fields between datasets and/or models.
- corcondia - Evaluates consistency of PARAFAC model.
- coreanal - Analysis of the core array of a Tucker model.
- corecalc - Calculate the Tucker3 core given the data array and loadings.
- correctbias - Adjusts a regression model for bias and slope errors.
- corrmap - Correlation map with variable grouping.
- corrspec - Resolves correlation spectroscopy maps.
- cov_cv - Estimation of a regularized inverse covariance matrix.
- cow - Correlation Optimized Warping function with linear interpolation.
- cr - Continuum Regression for multivariate y.
- crcvrnd - Cross-validation for continuum regression.
- crosscor - Cross-correlation function for time series data.
- crossval - Cross-validation for decomposition and linear regression.

## D

- datahat - Calculates the model estimate and residuals of the data.
- datasetdemo - Demonstrates use of the dataset object.
- dbscan - Density-based automatic sample clustering.
- delsamps - Deletes samples (rows) or variables (columns) from data matrices.
- demos - Demo list for the PLS_Toolbox.
- deresolv - Changes high resolution spectra to low resolution.
- discrimprob - Discriminate probabilities for continuous predicted values.
- dispmat - Calculates the dispersion matrix of two spectral data sets.
- distslct - Selects samples on outside of data space.
- doeeffectsplot - Create main effect or interaction plot, incl LSD bars.
- doegen - Generate a Design of Experiments (DOE) DataSet object.
- doegui - Design of Experiments tool.
- doeinteractions - Calculates interaction terms of a raw DOE matrix.
- doerunsheet - Create a doe run sheet.
- doescale - Convert coded DOE to scaled DOE or scaled back to coded.
- doptimal - Selects samples based on D-Optimal criteria.
- dp - Draws a diagonal line on an existing figure.
- durbin_watson - Criterion for measure of continuity.

## E

- editds - Editor for DataSet Objects.
- eemoutlier - Automatically remove outliers in PARAFAC models of EEM data.
- ellps - Plots an ellipse on an existing figure.
- encode - Translates a variable into matlab-executable code.
- encodemethod - Create a cross-validation index vector for a given method.
- encodemodelbuilder - Create MATLAB m-code which will regenerate a given model.
- encodexml - Convert standard data types into XML-encoded text.
- erdlgpls - Error dialog.
- estimatefactors - Estimate number of significant factors in multivariate data.
- evolvfa - Evolving factor analysis (forward and reverse).
- evriaddon - Create an Eigenvector Add-On object.
- evriclearlicense - Clears any stored EVRI license information.
- evricompatibility - Tests for inter-product compatibility of Eigenvector toolboxes.
- evridebug - Checks the PLS_Toolbox installation for problems.
- evridir - Locate and or create EVRI home directory.
- evriinstall - Install Eigenvector Research Product.
- evrimovepath - Move all Eigenvector products to the top or bottom of the Matlab path.
- evrirelease - Returns Eigenvector product release number.
- evrireporterror - Gathers error information and optionally reports it.
- evriscript - Create a chain of steps where each step applies a single pls_toolbox function.
- evritraperror - Utility to retrieve error information for debugging purposes.
- evriuninstall - Uninstall an Eigenvector Research toolbox.
- evriupdate - Check Eigenvector.com for available PLS_Toolbox updates.
- ewfa - Evolving window factor analysis.
- excludemissing - Automatically exclude too-much missing data in a matrix.
- explode - Extracts variables from a structure array to the workspace.
- exportfigure - Automatically export figures to an external program.
- exteriorpts - Select samples on the exterior of a data space after normalizing samples.

## F

- factdes - Full factorial design of experiments.
- fastnnls - Fast non-negative least squares.
- fasternnls - Fast non-negative least squares.
- ffacconfusion - Generates confusion table for a fractional factorial DOE.
- ffacdes1 - Fractional factorial design of experiments.
- figbrowser - Browser with icons of all Matlab figures.
- figmerit - Analytical figures of merit for multivariate calibration.
- figuretheme - Resets a figure background and axes to a specified color.
- filtering_and_despiking_settings_gui - Settings GUI for filtering and despiking preprocessing method
- findindx - Finds the index of the array element closest to value r.
- fir2ss - Transform FIR model into equivalent state space model.
- fitpeaks - Peak fitting routine.
- flucut - Remove scatter from fluorescence EEM data.
- frpcr - Full-ratio PCR calibration and prediction.
- frpcrengine - Engine for full-ratio PCR regression.
- ftest - F test and inverse F test statistic.
- fullsearch - Exhaustive Search Algorithm for small problems.

## G

- gaselctr - Genetic algorithm for variable selection with PLS.
- genalg - Genetic Algorithm for Variable Selection.
- genalgplot - Plot GA results using selected variable plot, color-coded by RMSECV.
- gapsegment - Provides Gap-Segment derivatives.
- getdatasource - Extract summary dataset info.
- getmlversion - Returns current Matlab version as an integer.
- getpidata - Uses the current PI connection to construct a DSO from 'taglist'.
- getplspref - Get overriding options (preferences) for PLS_Toolbox functions.
- glog - Generalized log transform.
- glsw - Generalized least-squares weighting/preprocessing.
- gram - Generalized rank annihilation method.
- gscale - Group/block scaling for a single or multiple blocks.
- gscaler - Applies group/block scaling to submatrices of a single matrix.
- gselect - Selects objects in a figure (various selection styles).

## H-L

- helppls - Context related help on the PLS_Toolbox.
- hitachieemreadr - Reads Hitachi EEM files with Rayleigh removal.
- horibamultimodelapply - Apply multiple models to Horiba Aqualog samples.
- hjyreadr - Reads HORIBA Jobin Yvon files (Windows Only).
- hline - Adds horizontal lines to figure at specified locations.
- importtool - GUI for designating column/row data types in incoming data.
- infobox - Display a string in an information box.
- ils_esterror - Estimation error for ILS models.
- ipls - Interval PLS variable selection.
- ismac - Overload of ISMAC for backward compatibility.
- ismodel - Returns boolean TRUE if input object is a standard model structure.
- jcampreadr - Reads a JCAMP file into a DataSet object.
- jmlimit - Confidence limits for Q residuals via Jackson-Mudholkar.
- kennardstone - Select a subset of samples from a data set by the Kennard-Stone algorithm.
- knn - K-nearest neighbor classifier.
- knnscoredistance - Calculate the average distance to the k-Nearest Neighbors in score space.
- kurtosis - Returns the kurtosis statistic for a vector or matrix.
- lamsel - Determines indices of wavelength axes in specified ranges.
- lddlgpls - Dialog to load variable from workspace or MAT file.
- leverag - Calculate sample leverages.
- line_filter - Spectral filtering.
- lmoptimize - Levenberg-Marquardt non-linear optimization.
- lmoptimizebnd - Levenberg-Marquardt bounded non-linear optimization.
- localmaxima - Automated identification of local maxima.
- logdecay - Mean centers and variance scales a matrix using the log decay of the variable axis.
- loopfilereadr - An example function for reading files in a loop from a directory.
- lreg - Predictions based on softmax multinomial logistic regression model.
- lregda - Predictions based on Logistic Regression (LREGDA) classification models.
- lsq2top - Fits a polynomial to the top/(bottom) of data.
- lwr - Locally weighted regression for univariate Y.
- lwrpred - Engine for locally weighted regression models.

## M

- madc - Function that is a scale estimator given by the Median Absolute Deviation.
- matchrows - Matches up rows from two DataSet objects using labels or sizes.
- matchvars - Align variables of a dataset to allow prediction with a model.
- manrotate - Graphical interface to manually rotate model loadings.
- MCCT_Object - Class for modelcentric calibration transfer.
- mcr - Multivariate curve resolution with constraints.
- mdcheck - Missing Data Checker and infiller.
- med2top - Fits a constant to top/(bottom) of data.
- medcn - Median center scales matrix to median zero.
- minimizemodel - Shrinks model by removing non-critical information.
- minmax - min-max scaling, scales each row or column to have a minimum of 0 and a maximum of 1
- mlpca - Maximum likelihood principal components analysis.
- mlr - Multiple Linear Regression for multivariate Y.
- mlrengine - Multiple Linear Regression computational engine.
- mlsca - Apply Multi-level Simultaneous Component Analysis to a nested DOE dataset.
- mncn - Scale matrix to mean zero.
- modelcache - Stores and retrieves models in the model cache.
- modeloptimizer - Create model for iterating over analysis models.
- modeloptimizergui - GUI for modeloptimizer.
- modelselector - Create or apply a model selector model.
- modelstatssummary - Generate a succinct list of descriptive model statistics.
- modelstruct - Constructs an empty model structure.
- modelviewer - Visualization tool for multi-way models.
- modlpred - Predictions using standard model structures.
- modlrder - Displays model info for standard model structures.
- moveobj - Interactively reposition graphics objects.
- mpca - Multi-way (unfold) principal components analysis.
- mplot - Automatic creation of subplots and plotting.
- mscorr - Multiplicative scatter/signal correction (MSC).
- msc_settings_gui - GUI for MSC Preprocessing.
- ms_bin - Bins Mass Spectral data into user-defined bins.
- mtfreadr - Read AdventaCT Multi-Trace Format (MTF) files.
- multiblock - Create or apply a multiblock model for joining data.

## N-O

- netcdfreadr - Reads in netCDF files and outputs a DataSet and or structure.
- newtondf - Newton's root finder.
- nippls - NIPALS Partial Least Squares computational engine.
- normaliz - Normalize rows of matrix.
- npls - Multilinear-PLS (N-PLS) for true multi-way regression.
- npreprocess - Preprocessing of multi-way arrays.
- nvalidate - Validate the number PARAFAC or Tucker components.
- omnicreadr - Reads OMNICix HDF5 image files.
- opcclient - Creates an object which allows access to OPC servers.
- openfluor - Write a PARAFAC model output to text file ready for importing in OpenFluor.
- oplecorr - Optical Pathlength Estimation and Correction.
- opusreadr - Reads Bruker OPUS files.
- oscapp - Applies OSC model to new data.
- osccalc - Calculates orthogonal signal correction (OSC).
- outerm - Computes outer product of any number of vectors.

## P

- parafac - Parallel factor analysis for n-way arrays.
- parafac2 - Parallel factor analysis for unevenly sized n-way arrays.
- parafacforopenfluor - Exports data/dso and parafac model as a openfluor .txt file
- parsemixed - Parse numerical and text data into a DataSet Object.
- parsexml - Convert XML file to a MATLAB structure.
- pca - Principal components analysis.
- pcaengine - Principal Components Analysis computational engine.
- pcapro - Projects new data on old principal components model.
- pcolormap - Pseudocolor plot with labels and colorbar.
- pcr - Principal components regression for multivariate Y.
- pcrengine - Principal Component Regression computational engine.
- peakfind - Automated identification of peaks.
- peakfunction - Outputs the estimated peaks from parameters in PEAKDEF.
- peakstruct - Makes an empty peak definition structure.
- peaksigmoid - Outputs a sigmoid function.
- percentile - Finds percentile point (similar to MEDIAN).
- pereadr - Reads PerkinElmer format files.
- permutetest - Permutation testing for regression and classification models.
- permuteplot - Create plot of permutation test results.
- permuteprobs - Display probabilities derrived from permutation testing.
- ploteigen - Builds dataset object of eigenvalues/RMSECV information.
- plotgui - Interactive data viewer.
- plotloads - Extract and display loadings information from a model structure.
- plotmonotonic - Plot lines with breaks when the x-value "doubles-back" on itself.
- plotscores - Extract and display score information from a model.
- pls - Partial least squares regression for multivariate Y.
- plsda - Partial least squares discriminant analysis.
- plsdaroc - Calculate and display ROC curves for PLSDA model.
- plsdthres - Bayesian threshold determination for PLS Discriminate Analysis.
- plslogo - Generates PLS_Toolbox CR surface logo.
- plsnipal - NIPALS algorithm for one PLS latent variable.
- plspulsm - Identifies FIR dynamics models for MISO systems.
- plsrsgcv - Generate PLS models for MSPC with cross-validation.
- plsrsgn - Generates a matrix of PLS models for MSPC.
- plsver - Displays version information.
- pltreadr – Reads a Vision Air PLT model file as an EVRI model structure.
- plttern - Plots a 2D ternary diagram.
- pltternf - Plots a 3D ternary diagram with frequency of occurrence.
- poissonscale - Perform Poisson scaling with scaling offset.
- polyinterp - Polynomial interpolation, smoothing, and differentiation.
- polytransform - Add polynomial and cross terms to data matrix or dataset.
- polypls - PLS regression with polynomial inner-relation.
- pqnorm - Probabilistic Quotient Normalization for rows of a matrix.
- preprocess - Selection and application of standard preprocessing structures.
- preprocessiterator - Create array of preprocessing combinations.
- preprouser - User-defined preprocessing methods.
- projdemo - Demo of the MLR, PCR, and PLS regression vectors.
- purity - Self-modeling mixture analysis method based on purity of variables or spectra.
- purityengine - calculates purity values of columns of data set.

## Q-R

- querydb - Executes a query on a database defined by connection string.
- qconcalc - Calculate Q residuals contributions for predictions on a model.
- randomttest - Randomization t-test for evaluating residuals from two models.
- range - Calculates the range of the values.
- readme - Release notes for Version 5.0 of PLS_Toolbox.
- reducennsamples - Selects a subset of samples by removing nearest neighbors.
- regcon - Converts regression model to y = ax + b form.
- registerspec - Shift spectra based on expected peak locations.
- replace - Replaces variables based on PCA or PLS models.
- reportwriter - Write a summary of the analysis including associated figures to html/word/powerpoint.
- rescale - Scales data back to original scaling.
- residuallimit - Esitmates confidence limits for the sum of squared residuals.
- resize - Resizes arguments to same length.
- reversebytes - Flips order of bytes in a word.
- reviewcrossval - Examines cross-validation settings for typical problems.
- reviewmodel - Examines a standard model structure for typical problems.
- ridge - Ridge regression by Hoerl-Kennard-Baldwin.
- ridgecv - Ridge regression by cross validation.
- rinverse - Calculate pseudo inverse for PLS, PCR and RR models.
- rmse - Calculate Root Mean Square Error.
- roccurve - Calculate and display ROC curve(s) for yknown and ypred.
- rwb - Red white and blue color map.

## S

- sammon - Sammon projection for data.
- savgol - Savitzky-Golay smoothing and differentiation.
- savgolcv - Cross-validation for Savitzky-Golay smoothing and differentiation.
- scale - Scales data using specified means and std. devs.
- setpath - Modifies and saves current directory to the MATLAB search path.
- setplspref - Set overriding options (preferences) for PLS_Toolbox functions.
- shimadzueemreadr – Reads Shimadzu EEM files with Rayleigh removal.
- shuffle - Randomly re-orders matrix and multiple blocks rows.
- signtest - Pairwise sign test for evaluating residuals from two models.
- simca - Soft Independent Method of Class Analogy.
- simpls - Partial Least Squares computational engine using SIMPLS algorithm.
- skewness: Returns the skewness statistic for a vector or matrix.
- snabsreadr - Reads Stellarnet ABS XY files.
- snv - Standard normal variate scaling.
- spareadr - Reads Thermo Fisher SPA files.
- spcreadr - Reads a Galactic SPC file.
- specalignset - Settings used to modfiy spectral alignment.
- specedit - GUI for selecting spectral regions on a plot.
- spereadr - Reads Princeton Instruments SPE file.
- spgreadr - Reads Thermo Fischer SPG files.
- splitcaltest - Splits randomly ordered data into calibration and test sets.
- splitds - Splits a DSO based on unique values in field, mode (dim), and set.

- splithalf - performs splithalf validation of PARAFAC and PARAFAC2 models.

- ssqtable - Displays variance captured table for model.
- statdemo - Elementary stats, t test, F test and AVOVA.
- stddemo - Demo of the STDSSLCT, STDGEN, and OSCCALC functions.
- stdfir - Standardization based on FIR modelling.
- stdgen - Piecewise and direct standardization transform generator.
- stdize - Applies transform from STDGEN to new spectra.
- stdsslct - Selects data subsets (often for use in standardization).
- stepwise_regrcls - Step-wise regression for CLS models.
- string_x - Add backslash before troublesome TeX characters.
- subgroupcl - Displays a confidence ellipse for points in a two-dimensional plot.
- summary - Summarizing statistics for sample data.
- super_reduce - Eliminates highly correlated variables.
- svdlgpls - Dialog to save variable to workspace or MAT file.
- svm - SVM Support Vector Machine for regression.
- svmda - SVM Support Vector Machine for classification.
- svmoc - Support Vector Machine for one-class analysis.

## T-V

- table2dataset - Convert Matlab Table Object to DatasetObject.
- tconcalc - Calculate Hotellings T2 contributions for predictions on a model.
- testrobustness - Test regression model for robustness to various effects.
- testfitpeaks - Demo calls to the FITPEAKS function.
- testpeakdefs - Checks peak parameters in a peak definition structure.
- tld - Trilinear decomposition.
- trendtool - Univariate trend analysis tool.
- tsqlim - Confidence limits for Hotelling's T^2.
- tsqmtx - Calculates matrix for T^2 contributions for PCA.
- tsqqmtx - Calculates matrix for T^2+Q contributions for PCA and MPCA.
- ttestp - Evaluates t-distribution and its inverse.
- tucker - Analysis for n-way arrays.
- unfoldm - Rearranges (unfolds) an augmented matrix to row vectors.
- unfoldmw - Unfolds multiway arrays along specified order.
- unhist - Create a vector whose values follow an empirical distribution.
- updatemod - Update model structure to be compatible with the current version.
- varcap - Variance captured for each variable in PCA model.
- varcapy - Calculate percent y-block variance captured by a PLS regression model.
- varimax - Orthogonal rotation of loadings.
- vip - Calculate Variable Importance in Projection from regression model.
- visionairxmlreadr – Reads Vision Air formatted XML files in as X-block and Y-block DataSet Objects.
- vline - Adds vertical lines to figure at specified locations.

## W-Z

- wilcoxon - Pairwise Wilcoxon signed rank test for evaluating residuals from two models.
- windowfilter - Spectral filtering.
- wlsbaseline - Weighted least squares baseline function.
- writeasf - Writes AIT ASF files from a dataset object.
- writecsv - Export a DataSet object to a comma-separated values (CSV) file.
- wrtpulse - Create input/output matrices for dynamic model identification.
- writeplt – Exports an EVRI model structure as a Vision Air PLT model file.
- writespc - Write a DataSet object to a Galactic SPC file.
- wtfa - Window target factor analysis.
- xclgetdata - Extracts matrix from an Excel spreadsheet.
- xclputdata - Write matrix to an Excel spreadsheet.
- xclreadr - Reads an ASCII or .XLS file in as a DataSet Object.
- xgb - Gradient Boosted Tree (XGBoost) for regression or classification.
- xgbda - Gradient Boosted Tree Ensemble for classification (Discriminant Analysis) using XGBoost.
- xlsreadr - Reads .XLS files from MS Excel and other spreadsheets.
- xycorrcoef - Calculates the correlation coefficients between variables in X-block and variables in Y-block.
- xyreadr - Reads one or more ASCII XY or XY... files into a DataSet object.
- yscale - Rescales the y-axis limits on each subplot in a figure.
- zline - Adds vertical lines to 3D figure at specified locations.

(Sub topic of PLS_Toolbox_Topics)