Alphabetical Index

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.

asinhx - Arcsinh transform.

asinsqrt - Arcsin square root transformation.

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.

dataset2table - Convert DatasetObject to Matlab Table Object.

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.

fitcircle - Fits circles (and spheres) to x,y (and z) data.

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.

grootmanager - Manage and update MATLAB graphics root object properties.

grooteditor - Interactively edit graphics root properties and property sets.

grootmanager - Manage and update MATLAB graphics root object properties.

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.

pr_entropy - Pattern recognition entropy (PRE), Shannon entropy, transform.

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)