CHANGES IN VERSION 1.37.6 ------------------------------ o minor vignette update CHANGES IN VERSION 1.37.4 ------------------------------ o plot_score new name of the previous gg_scoreplot method CHANGES IN VERSION 1.37.2 ------------------------------ o gg_scoreplot: now handling the 1D or empty models CHANGES IN VERSION 1.35.4 ------------------------------ o gg_scoreplot: minor update CHANGES IN VERSION 1.35.2 ------------------------------ o gg_scoreplot: update to handle OPLS models CHANGES IN VERSION 1.29.32 ------------------------------ o view: minor modification CHANGES IN VERSION 1.29.30 ------------------------------ o view: minor modification CHANGES IN VERSION 1.29.28 ------------------------------ o view: minor modification CHANGES IN VERSION 1.29.26 ------------------------------ o gg_scoreplot: minor modification CHANGES IN VERSION 1.29.24 ------------------------------ o gg_scoreplot: minor modification CHANGES IN VERSION 1.29.22 ------------------------------ o gg_scoreplot: generic method to be applied either to a SummarizedExperiment or an opls object CHANGES IN VERSION 1.29.20 ------------------------------ o gg_scoreplot: modification of the info to display with plotly CHANGES IN VERSION 1.29.18 ------------------------------ MINOR MODIFICATION o minor documentation update CHANGES IN VERSION 1.29.16 ------------------------------ MINOR MODIFICATION o minor documentation update CHANGES IN VERSION 1.29.14 ------------------------------ NEW FEATURE o NCI60 dataset from omicade4 available in MultiAssayExperiment and MultiDataSet CHANGES IN VERSION 1.29.12 ------------------------------ MINOR MODIFICATION o minor documentation update CHANGES IN VERSION 1.29.10 ------------------------------ MINOR MODIFICATION o minor documentation update CHANGES IN VERSION 1.29.8 ------------------------------ NEW FEATURE o 'opls' method now handles MultiAssayExperiment CHANGES IN VERSION 1.29.6 ------------------------------ NEW FEATURE o 'opls' method now handles SummarizedExperiment CHANGES IN VERSION 1.29.4 ------------------------------ NEW FEATURE o 'view' method now handles SummarizedExperiment o 'sacurine' dataset includes the ExpressionSet and SummarizedExperiment formats CHANGES IN VERSION 1.29.2 ------------------------------ MINOR MODIFICATION o new bioc release CHANGES IN VERSION 1.27.8 ------------------------------ MINOR MODIFICATION o minor vignette correction CHANGES IN VERSION 1.27.6 ------------------------------ MINOR MODIFICATION o minor vignette correction CHANGES IN VERSION 1.27.4 ------------------------------ MINOR MODIFICATION o minor vignette update CHANGES IN VERSION 1.27.2 ------------------------------ MINOR MODIFICATION o minor documentation update CHANGES IN VERSION 1.23.12 ------------------------------ MINOR MODIFICATION o minor documentation update CHANGES IN VERSION 1.23.8 ------------------------------ MINOR MODIFICATION o vignette: minor update CHANGES IN VERSION 1.23.6 ------------------------------ MINOR MODIFICATION o 'view' method: minor update of documentation CHANGES IN VERSION 1.23.4 ------------------------------ BUG FIXED o 'view' method: display of row names CHANGES IN VERSION 1.23.2 ------------------------------ BUG FIXED o 'view' method: display of row names (reversed in the previous versions) CHANGES IN VERSION 1.19.16 ------------------------------ INTERNAL MODIFICATION o '.header' function: 'class(x) == ' removed from code to take into account the R 4.0 changes CHANGES IN VERSION 1.19.14 ------------------------------ INTERNAL MODIFICATION o 'strF' function: use of is.array instead of is.matrix to take into account the R 4.0 changes CHANGES IN VERSION 1.19.12 ------------------------------ INTERNAL MODIFICATION o 'strF' function: replacement by 'is(x, )': cont'd CHANGES IN VERSION 1.19.10 ------------------------------ INTERNAL MODIFICATION o 'strF' function: 'class(x) ==' replaced by 'is(x, )' as required by R/Bioconductor CHANGES IN VERSION 1.19.8 ------------------------------ NEW FEATURE o 'view' method: 'standardizeL' argument for the standardization of column values for display CHANGES IN VERSION 1.19.6 ------------------------------ BUG FIXED o 'view' method: ExpressionSet with empty metadata CHANGES IN VERSION 1.19.4 ------------------------------ NEW FEATURE o 'view' method: plot extended to data.frames and ExpressionSet CHANGES IN VERSION 1.19.2 ------------------------------ BUG FIXED o 'view' method: in case the matrix has no row nor column names CHANGES IN VERSION 1.17.34 ------------------------------ NEW FEATURE o 'view' method (wrapper of the imageF and strF functions) CHANGES IN VERSION 1.17.32 ------------------------------ BUG FIXED o plot.oplsMultiDataSet correction to include all plots in the .pdf file CHANGES IN VERSION 1.17.30 ------------------------------ MINOR MODIFICATION o Additional correction in getMset documentation (example) CHANGES IN VERSION 1.17.28 ------------------------------ MINOR MODIFICATION o Correcting typo in getMset documentation (example) CHANGES IN VERSION 1.17.26 ------------------------------ MINOR MODIFICATION o Including the set name in the figure of MultiDataSet models CHANGES IN VERSION 1.17.24 ------------------------------ MINOR MODIFICATION o Correction of the documentation for 'residuals' and 'plot-oplsMultidDataSet' CHANGES IN VERSION 1.17.22 ------------------------------ INTERNAL MODIFICATION o Correction of the example in the oplsMultiDataSet class documentation CHANGES IN VERSION 1.17.20 ------------------------------ NEW FEATURE o plotPhenoDataC parameter for coloring (score plots) according to one column from the pData data frame when the opls method has been applied to an ExpresssionSet CHANGES IN VERSION 1.17.18 ------------------------------ INTERNAL MODIFICATION o Minor internal modification CHANGES IN VERSION 1.17.16 ------------------------------ INTERNAL MODIFICATION o Minor internal modification CHANGES IN VERSION 1.17.14 ------------------------------ NEW FEATURE o Example of the analyis of a MultiDataSet ('NCI60_4arrays' from the 'omicade4' package) CHANGES IN VERSION 1.17.12 ------------------------------ NEW FEATURE o Multi data set names display on graphics CHANGES IN VERSION 1.17.10 ------------------------------ NEW FEATURE o plot method for oplsMultiDataSet objects CHANGES IN VERSION 1.17.8 ------------------------------ NEW FEATURE o opls can now be applied to MultiDataSet objects; getMset method to extract the complemented MultiDataSet CHANGES IN VERSION 1.17.6 ------------------------------ INTERNAL MODIFICATION o minor internal modification CHANGES IN VERSION 1.17.4 ------------------------------ INTERNAL MODIFICATION o minor internal modification CHANGES IN VERSION 1.17.2 ------------------------------ NEW FEATURE o info.txtC and fig.pdfC argument values NULL and NA replaced by 'none' and 'interactive', respectively CHANGES IN VERSION 1.15.26 ------------------------------ NEW FEATURE o plot method: dev.new() is not called internally any more; consequently the 'parDevNewL' argument has been removed; layout can be either 1x1 or 2x2, depending on the length of the 'typeVc' argument; 'fig.pdfC' and 'info.txtC' arguments have been added for compatibility reasons with other packages; they have the same role as 'file.pdfC' and '.sinkC' which now generate a deprecated warning. CHANGES IN VERSION 1.15.24 ------------------------------ MINOR MODIFICATION o plot method: turning off ellipse display in case of a single sample the class CHANGES IN VERSION 1.15.22 ------------------------------ INTERNAL MODIFICATION o imageF function: minor modification of the log parameter CHANGES IN VERSION 1.15.20 ------------------------------ NEW FEATURE o imageF function to visualize a numerical matrix CHANGES IN VERSION 1.15.18 ------------------------------ INTERNAL MODIFICATION o minor internal modification CHANGES IN VERSION 1.15.16 ------------------------------ INTERNAL MODIFICATION o modification of the way additional columns are added to the pData and fData of an ExpressionSet instance o 'Biobase' package now as 'depends' (not 'import') CHANGES IN VERSION 1.15.14 ------------------------------ INTERNAL MODIFICATION o minor internal modification CHANGES IN VERSION 1.15.12 ------------------------------ INTERNAL MODIFICATION o minor modification in examples defining ExpressionSet instances CHANGES IN VERSION 1.15.10 ------------------------------ INTERNAL MODIFICATION o 'eset' is now a slot of the 'opls' class (used when the 'opls' method is applied to an ExpressionSet instance) CHANGES IN VERSION 1.15.8 ------------------------------ NEW FEATURE o 'plot' method: parPaletteVc argument to specify colors CHANGES IN VERSION 1.15.6 ------------------------------ NEW FEATURE o Application to ExpressionSet: first 2 scores and loadings, as well as fitted values and VIP now returned in the pData and fData INTERNAL MODIFICATION o Unit testing switched from 'RUnit' to 'testthat' CHANGES IN VERSION 1.15.4 ------------------------------ INTERNAL MODIFICATION o Checking that the data matrix does not contain any infinite or NaN value CHANGES IN VERSION 1.15.2 ------------------------------ INTERNAL MODIFICATION o ImmunoOncology tag added to biocViews o minor correction in the diagnostics graph labeling 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