CHANGES IN VERSION 1.13.8
------------------------------

INTERNAL MODIFICATION

    o minor correction in the documentation
    
CHANGES IN VERSION 1.13.6
------------------------------

INTERNAL MODIFICATION

    o update of package vignette

CHANGES IN VERSION 1.13.4
------------------------------

INTERNAL MODIFICATION

    o fixed bug in unit test

CHANGES IN VERSION 1.13.2
------------------------------

BUG CORRECTION

    o predict method: naming of the predicted Y matrix output columns in case of PLS modeling of multiple responses
    
INTERNAL MODIFICATION

    o ropls.Rproj file added for package management with RStudio

CHANGES IN VERSION 1.7.2
------------------------------

INTERNAL MODIFICATION

    o vignette now in pdf format

CHANGES IN VERSION 1.5.22
------------------------------

INTERNAL MODIFICATION

    o minor code formatting

CHANGES IN VERSION 1.5.20
------------------------------

BUG CORRECTION

    o PCA: correction in the computation of variance and R2X (svd), and the determination of the optimal number of components

CHANGES IN VERSION 1.5.18
------------------------------

INTERNAL MODIFICATION

    o correction in the vignette (determination of optimal number of components in PCA)

CHANGES IN VERSION 1.5.16
------------------------------

INTERNAL MODIFICATION

    o minor vignette formatting

CHANGES IN VERSION 1.5.14
------------------------------

NEW FEATURE

    o 'fromW4M' function and 'toW4M' method to import preprocessed tables
    generated by the online Workflow4metabolomics infrastructure into an
    ExpressionSet bioconductor object (and vice versa)

CHANGES IN VERSION 1.5.12
------------------------------

INTERNAL MODIFICATION

    o minor vignette formatting

CHANGES IN VERSION 1.5.10
------------------------------

INTERNAL MODIFICATION

    o checking automated documentation with the 'roxygen2' package; automated vignette with rmarkdown and knitr

CHANGES IN VERSION 1.5.8
------------------------------

INTERNAL MODIFICATION

    o deleting missing files from svn repository

CHANGES IN VERSION 1.5.6
------------------------------

NEW FEATURE

    o opls can now be applied to ExpressionSet instances
    o vignette is now in html format
    o automated documentation with the 'roxygen2' package; automated vignette with rmarkdown and knitr

CHANGES IN VERSION 1.5.4
------------------------------

NEW FEATURE

    o package documentation now available with ?ropls, help("ropls"), or help("ropls-package")

CHANGES IN VERSION 1.5.2
------------------------------

BUG FIXED

    o stop messages generated when non-significant predictive or first orthogonal components are obtained

CHANGES IN VERSION 1.5.0
------------------------------

NEW FEATURES

    o 'opls' is now an S4 class: please use the accessors e.g. 'getScoreMN(oplsModel)' instead of 'oplsModel$scoreMN', or 'getScoreMN(oplsModel, orthoL = TRUE)' instead of 'oplsModel$orthoScoreMN'
    o The full list of accessors is: getLoadingMN, getScoreMN, getVipVn, getWeightMN (all with the orthoL argument), in addition to getSummaryDF, getPcaVarVn, getSubsetVi
    o Please see the vignette and documentation for examples    
    

CHANGES IN VERSION 1.3.19
------------------------------

BUG FIXED

    o Committing the new files

CHANGES IN VERSION 1.3.18
------------------------------

NEW FEATURE

    o 'coefficients' method renamed as 'coef'
    
BUG FIXED

    o 'methods-opls_class.R' file renamed as 'opls-methods.R' to ensure 'opls' class is defined before the methods

CHANGES IN VERSION 1.3.17
------------------------------

BUG FIXED

    o Committing the new files

CHANGES IN VERSION 1.3.16
------------------------------

BUG FIXED

    o Committing the new files

CHANGES IN VERSION 1.3.15
------------------------------

NEW FEATURES

    o Switching to S4 class
    o Evaluating the metabolomics workflow in the vignette    

CHANGES IN VERSION 1.3.14
------------------------------

NEW FEATURES

    o plot.opls: when 'parAsColFcVn' is a character vector, it is converted to a factor (thus drawing ellipses by default)
            
BUG FIXED

    o plot.opls: handling of ellipse display when parEllipseL parameter set to NA (default)

CHANGES IN VERSION 1.3.13
------------------------------

NEW FEATURES

    o opls: no scaling option now available
            
BUG FIXED

    o opls: computation of the matrix of correlations (when the number of features is <= 100)

CHANGES IN VERSION 1.3.12
------------------------------

NEW FEATURES

    o opls: multiclass PLS-DA implemented (PLS2 approach; comments added in the vignette)
            default number of permutations set to 20 (instead of 10)
            predictive components denoted in the tables by 'p' (instead of 'h' previously)
            OPLS(-DA): simplified "modelDF" data frame ('rotation' row has been suppressed)
            
BUG FIXED

    o opls: PCA model with 'svd' and a single component
            

CHANGES IN VERSION 1.3.11
------------------------------

NEW FEATURES

    o opls: for OPLS(-DA), vipVn and orthoVipVn are now computed as the VIP4,p and VIP4,o described in Galindo-Prieto et al (2014)
    o plot.opls: changes in palette: black/grey colors for diagnostics and other colors for scores    

CHANGES IN VERSION 1.3.10
------------------------------

BUG FIXED

    o plot.opls: minor bug fixed ('x-score' label and color display of test samples when 'subset' is not NULL)

CHANGES IN VERSION 1.3.9
------------------------------

NEW FEATURES

    o vignette: minor update

CHANGES IN VERSION 1.3.8
------------------------------

NEW FEATURES

    o vignette: "some words of warning" section added

CHANGES IN VERSION 1.3.7
------------------------------

NEW FEATURES

    o vignette: default figures from plot.opls included
    
CHANGES IN VERSION 1.3.6
------------------------------

NEW FEATURES

    o strF: object size now displayed in Mb (instead of bytes); minor corrections to handle all matrices and data frames (whatever the dimensions, mode, row and column names)
    o unit tests: new tests added to increase test coverage

CHANGES IN VERSION 1.3.5
------------------------------

NEW FEATURES

    o unit tests: warning message corrected in order to allow test coverage display on the Bioconductor page
    
CHANGES IN VERSION 1.3.4
------------------------------

NEW FEATURES

    o vignette: minor correction in the default number of permutations for single response (O)PLS(-DA) models

CHANGES IN VERSION 1.3.3
------------------------------

NEW FEATURES

    o vignette: detailed explanations of Q2Y computation 


CHANGES IN VERSION 1.3.2
------------------------------

NEW FEATURES

    o plot.opls: 'plotVc' argument renamed 'typeVc' similarly to the default 'plot' function

CHANGES IN VERSION 1.3.1
------------------------------

NEW FEATURES

    o opls: now takes either a (numeric) data frame or matrix as 'x' input (instead of matrix only)   
    o predict: now takes either a (numeric) data frame or matrix as 'newdata' input (instead of matrix only) 

CHANGES IN VERSION 1.1.11
------------------------------

NEW FEATURES

    o NEWS format updated

CHANGES IN VERSION 1.1.10
------------------------------

NEW FEATURES

    o opls: PLS models can now be built for 'x' data with a single variable
        
CHANGES IN VERSION 1.1.9
------------------------------

NEW FEATURES

    o opls: default number of permutations set to 10 (instead of 100) as a compromise to enable both quick computation and a first hint at model significance

    o opls: maximum number of components in automated mode (predI = NA or orthoI = NA) set to 10 (instead of 15)

    o plot.opls: bug corrected in case of single component model without permutation testing

CHANGES IN VERSION 1.1.8
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o sacurine dataset name simplification: names of sample metadata are now 'age', 'bmi', and 'gender' instead of 'ageVn', 'bmiVn', and 'genderFc'; names of variableMetadata are now 'msiLevel', 'hmdb', 'chemicalClass' instead of 'msiLevelVn', 'hmdbVc', 'chemicalClassVc'

CHANGES IN VERSION 1.1.7
------------------------------

NEW FEATURES

    o Control to avoid overfitting was strenghtened by: i) setting the default number of permutations to 100 (instead of 0) and ii) changing the default plot ("summary") to include both the "permutation" and the "overview" graphics

CHANGES IN VERSION 1.1.6
------------------------------

NEW FEATURES

    o .sinkC argument added in the opls and plot.opls methods: Diversion of messages is required for Galaxy integration

CHANGES IN VERSION 1.1.5
------------------------------

NEW FEATURES

    o current implementation supports two-class only classification

CHANGES IN VERSION 1.1.4
------------------------------

NEW FEATURES

    o renamed slot of opls object: rotationMN -> weightStarMN

CHANGES IN VERSION 1.1.3
------------------------------

NEW FEATURES

    o Minor internal changes regarding default ellipse plotting options and checking the compatibility between the subset size and the cross-validation fold

CHANGES IN VERSION 1.1.2
------------------------------

BUG FIXES

    o Minor internal changes

CHANGES IN VERSION 1.1.1
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The packaging was modified (but not the algorithms) to be consistent with other machine learning packages: 'opls' is now a class and the 'print', 'plot', 'predict', 'summary', 'fitted', 'coefficients' and 'residuals' methods are available (see the vignette)

SIGNIFICANT USER-VISIBLE CHANGES

    o renamed method: roplsF -> opls

    o renamed arguments
        testVi -> now 'subset' which indicates the indices of the training (instead of the testing) observations

    o values:
        tMN -> scoreMN
        pMN -> loadingMN
        wMN -> weightMN
        bMN -> coefficients
        rMN -> rotationMN
        varVn -> pcaVarVn
        tOrthoMN -> orthoScoreMN
        pOrthoMN -> orthoLoadingMN
        wOrthoMN -> orthoWeightMN

    o new (S3) methods for objects of class 'opls'
        print
        summary
        plot
        predict
        fitted
        coefficients
        residuals

CHANGES IN VERSION 1.0.2
------------------------------

NEW FEATURES

    o roplsF outputs: '.char2numF' function (required for class prediction on new datasets); replaces 'c2nLs'

CHANGES IN VERSION 1.0.1
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o renamed roplsF arguments (to indicate integers more explicitly)
        'predN' -> 'predI'
        'orthoN' -> 'orthoI'
        'crossvalN' -> 'crossvalI'
        'permN' -> 'permI'
        'parCompVn' -> 'parCompVi'
        'parTopLoadN' -> 'parTopLoadI'

CHANGES IN VERSION 0.99.7
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o rename ('sacurine' data set) for compatibility with 'Workflow4Metabolomics.org':
        'profileMN'  -> dataMatrix
        'sampleDF'   -> sampleMetadata
        'variableDF' -> variableMetadata
        
CHANGES IN VERSION 0.99.6
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o roplsF:
        handling of PLS models with single predictive component only

CHANGES IN VERSION 0.99.4
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o rename:
        'sacuri' data set -> 'sacurine'

CHANGES IN VERSION 0.99.2
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o rename:
        ropF -> roplsF
        ropStrF -> strF

    o depreacated roplsF arguments:
        parObsColLabVcn: now available through the parLabVc and parAsColVcn arguments
        parObsLegVc: not useful
	
    o rename roplsF arguments:
        ncpN -> predN
        ncoN -> orthoN
        ploVc -> plotVc
        algC -> algoC
        savImg.pdfC -> fileFig.pdfC
        savLog.txtC -> fileInfo.txtC
        logL -> log10L
        perN -> permN
        scaC -> scaleC
        tesVi -> testVi
        vrbC -> verboseC
        parObsColVc -> parAsColVcn
        parPcsVn -> parCompVn
        parMahL -> parEllipsesL
        parObsLabVc -> parLabVc
        parMaiL -> parTitleL
        parNexN -> parTopLoadN		

NEW FEATURES

    o ropColF -> now split between .colorF and .legendF
    o ropMahF -> now .ellipseF