NEWS

---

ropls 1.37.6

• minor vignette update

ropls 1.37.4

• plot_score new name of the previous gg_scoreplot method

ropls 1.37.2

• gg_scoreplot: now handling the 1D or empty models

ropls 1.35.4

• gg_scoreplot: minor update

ropls 1.35.2

• gg_scoreplot: update to handle OPLS models

ropls 1.29.32

• view: minor modification

ropls 1.29.30

• view: minor modification

ropls 1.29.28

• view: minor modification

ropls 1.29.26

• gg_scoreplot: minor modification

ropls 1.29.24

• gg_scoreplot: minor modification

ropls 1.29.22

• gg_scoreplot: generic method to be applied either to a SummarizedExperiment or an opls object

ropls 1.29.20

• gg_scoreplot: modification of the info to display with plotly

ropls 1.29.18

MINOR MODIFICATION

• minor documentation update

ropls 1.29.16

MINOR MODIFICATION

• minor documentation update

ropls 1.29.14

NEW FEATURE

• NCI60 dataset from omicade4 available in MultiAssayExperiment and MultiDataSet

ropls 1.29.12

MINOR MODIFICATION

• minor documentation update

ropls 1.29.10

MINOR MODIFICATION

• minor documentation update

ropls 1.29.8

NEW FEATURE

• 'opls' method now handles MultiAssayExperiment

ropls 1.29.6

NEW FEATURE

• 'opls' method now handles SummarizedExperiment

ropls 1.29.4

NEW FEATURE

• 'view' method now handles SummarizedExperiment
• 'sacurine' dataset includes the ExpressionSet and SummarizedExperiment formats

ropls 1.29.2

MINOR MODIFICATION

• new bioc release

ropls 1.27.8

MINOR MODIFICATION

• minor vignette correction

ropls 1.27.6

MINOR MODIFICATION

• minor vignette correction

ropls 1.27.4

MINOR MODIFICATION

• minor vignette update

ropls 1.27.2

MINOR MODIFICATION

• minor documentation update

ropls 1.23.12

MINOR MODIFICATION

• minor documentation update

ropls 1.23.8

MINOR MODIFICATION

• vignette: minor update

ropls 1.23.6

MINOR MODIFICATION

• 'view' method: minor update of documentation

ropls 1.23.4

BUG FIXED

• 'view' method: display of row names

ropls 1.23.2

BUG FIXED

• 'view' method: display of row names (reversed in the previous versions)

ropls 1.19.16

INTERNAL MODIFICATION

• '.header' function: 'class(x) == ' removed from code to take into account the R 4.0 changes

ropls 1.19.14

INTERNAL MODIFICATION

• 'strF' function: use of is.array instead of is.matrix to take into account the R 4.0 changes

ropls 1.19.12

INTERNAL MODIFICATION

• 'strF' function: replacement by 'is(x, )': cont'd

ropls 1.19.10

INTERNAL MODIFICATION

• 'strF' function: 'class(x) ==' replaced by 'is(x, )' as required by R/Bioconductor

ropls 1.19.8

NEW FEATURE

• 'view' method: 'standardizeL' argument for the standardization of column values for display

ropls 1.19.6

BUG FIXED

• 'view' method: ExpressionSet with empty metadata

ropls 1.19.4

NEW FEATURE

• 'view' method: plot extended to data.frames and ExpressionSet

ropls 1.19.2

BUG FIXED

• 'view' method: in case the matrix has no row nor column names

ropls 1.17.34

NEW FEATURE

• 'view' method (wrapper of the imageF and strF functions)

ropls 1.17.32

BUG FIXED

• plot.oplsMultiDataSet correction to include all plots in the .pdf file

ropls 1.17.30

MINOR MODIFICATION

• Additional correction in getMset documentation (example)

ropls 1.17.28

MINOR MODIFICATION

• Correcting typo in getMset documentation (example)

ropls 1.17.26

MINOR MODIFICATION

• Including the set name in the figure of MultiDataSet models

ropls 1.17.24

MINOR MODIFICATION

• Correction of the documentation for 'residuals' and 'plot-oplsMultidDataSet'

ropls 1.17.22

INTERNAL MODIFICATION

• Correction of the example in the oplsMultiDataSet class documentation

ropls 1.17.20

NEW FEATURE

• 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

ropls 1.17.18

INTERNAL MODIFICATION

• Minor internal modification

ropls 1.17.16

INTERNAL MODIFICATION

• Minor internal modification

ropls 1.17.14

NEW FEATURE

• Example of the analyis of a MultiDataSet ('NCI60_4arrays' from the 'omicade4' package)

ropls 1.17.12

NEW FEATURE

• Multi data set names display on graphics

ropls 1.17.10

NEW FEATURE

• plot method for oplsMultiDataSet objects

ropls 1.17.8

NEW FEATURE

• opls can now be applied to MultiDataSet objects; getMset method to extract the complemented MultiDataSet

ropls 1.17.6

INTERNAL MODIFICATION

• minor internal modification

ropls 1.17.4

INTERNAL MODIFICATION

• minor internal modification

ropls 1.17.2

NEW FEATURE

• info.txtC and fig.pdfC argument values NULL and NA replaced by 'none' and 'interactive', respectively

ropls 1.15.26

NEW FEATURE

• 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.

ropls 1.15.24

MINOR MODIFICATION

• plot method: turning off ellipse display in case of a single sample the class

ropls 1.15.22

INTERNAL MODIFICATION

• imageF function: minor modification of the log parameter

ropls 1.15.20

NEW FEATURE

• imageF function to visualize a numerical matrix

ropls 1.15.18

INTERNAL MODIFICATION

• minor internal modification

ropls 1.15.16

INTERNAL MODIFICATION

• modification of the way additional columns are added to the pData and fData of an ExpressionSet instance
• 'Biobase' package now as 'depends' (not 'import')

ropls 1.15.14

INTERNAL MODIFICATION

• minor internal modification

ropls 1.15.12

INTERNAL MODIFICATION

• minor modification in examples defining ExpressionSet instances

ropls 1.15.10

INTERNAL MODIFICATION

• 'eset' is now a slot of the 'opls' class (used when the 'opls' method is applied to an ExpressionSet instance)

ropls 1.15.8

NEW FEATURE

• 'plot' method: parPaletteVc argument to specify colors

ropls 1.15.6

NEW FEATURE

• Application to ExpressionSet: first 2 scores and loadings, as well as fitted values and VIP now returned in the pData and fData

INTERNAL MODIFICATION

• Unit testing switched from 'RUnit' to 'testthat'

ropls 1.15.4

INTERNAL MODIFICATION

• Checking that the data matrix does not contain any infinite or NaN value

ropls 1.15.2

INTERNAL MODIFICATION

• ImmunoOncology tag added to biocViews
• minor correction in the diagnostics graph labeling

ropls 1.13.8

INTERNAL MODIFICATION

• minor correction in the documentation

ropls 1.13.6

INTERNAL MODIFICATION

• update of package vignette

ropls 1.13.4

INTERNAL MODIFICATION

• fixed bug in unit test

ropls 1.13.2

BUG CORRECTION

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

INTERNAL MODIFICATION

• ropls.Rproj file added for package management with RStudio

ropls 1.7.2

INTERNAL MODIFICATION

• vignette now in pdf format

ropls 1.5.22

INTERNAL MODIFICATION

• minor code formatting

ropls 1.5.20

BUG CORRECTION

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

ropls 1.5.18

INTERNAL MODIFICATION

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

ropls 1.5.16

INTERNAL MODIFICATION

• minor vignette formatting

ropls 1.5.14

NEW FEATURE

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

ropls 1.5.12

INTERNAL MODIFICATION

• minor vignette formatting

ropls 1.5.10

INTERNAL MODIFICATION

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

ropls 1.5.8

INTERNAL MODIFICATION

• deleting missing files from svn repository

ropls 1.5.6

NEW FEATURE

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

ropls 1.5.4

NEW FEATURE

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

ropls 1.5.2

BUG FIXED

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

ropls 1.5.0

NEW FEATURES

• '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'
• The full list of accessors is: getLoadingMN, getScoreMN, getVipVn, getWeightMN (all with the orthoL argument), in addition to getSummaryDF, getPcaVarVn, getSubsetVi
• Please see the vignette and documentation for examples

ropls 1.3.19

BUG FIXED

• Committing the new files

ropls 1.3.18

NEW FEATURE

• 'coefficients' method renamed as 'coef'

BUG FIXED

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

ropls 1.3.17

BUG FIXED

• Committing the new files

ropls 1.3.16

BUG FIXED

• Committing the new files

ropls 1.3.15

NEW FEATURES

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

ropls 1.3.14

NEW FEATURES

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

BUG FIXED

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

ropls 1.3.13

NEW FEATURES

• opls: no scaling option now available

BUG FIXED

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

ropls 1.3.12

NEW FEATURES

• 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

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

ropls 1.3.11

NEW FEATURES

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

ropls 1.3.10

BUG FIXED

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

ropls 1.3.9

NEW FEATURES

• vignette: minor update

ropls 1.3.8

NEW FEATURES

• vignette: "some words of warning" section added

ropls 1.3.7

NEW FEATURES

• vignette: default figures from plot.opls included

ropls 1.3.6

NEW FEATURES

• 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)
• unit tests: new tests added to increase test coverage

ropls 1.3.5

NEW FEATURES

• unit tests: warning message corrected in order to allow test coverage display on the Bioconductor page

ropls 1.3.4

NEW FEATURES

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

ropls 1.3.3

NEW FEATURES

• vignette: detailed explanations of Q2Y computation

ropls 1.3.2

NEW FEATURES

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

ropls 1.3.1

NEW FEATURES

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

ropls 1.1.11

NEW FEATURES

• NEWS format updated

ropls 1.1.10

NEW FEATURES

• opls: PLS models can now be built for 'x' data with a single variable

ropls 1.1.9

NEW FEATURES

• 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
• opls: maximum number of components in automated mode (predI = NA or orthoI = NA) set to 10 (instead of 15)
• plot.opls: bug corrected in case of single component model without permutation testing

ropls 1.1.8

SIGNIFICANT USER-VISIBLE CHANGES

• 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'

ropls 1.1.7

NEW FEATURES

• 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

ropls 1.1.6

NEW FEATURES

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

ropls 1.1.5

NEW FEATURES

• current implementation supports two-class only classification

ropls 1.1.4

NEW FEATURES

• renamed slot of opls object: rotationMN -> weightStarMN

ropls 1.1.3

NEW FEATURES

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

ropls 1.1.2

BUG FIXES

• Minor internal changes

ropls 1.1.1

SIGNIFICANT USER-VISIBLE CHANGES

• 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)
• renamed method: roplsF -> opls
• renamed arguments testVi -> now 'subset' which indicates the indices of the training (instead of the testing) observations
• values: tMN -> scoreMN pMN -> loadingMN wMN -> weightMN bMN -> coefficients rMN -> rotationMN varVn -> pcaVarVn tOrthoMN -> orthoScoreMN pOrthoMN -> orthoLoadingMN wOrthoMN -> orthoWeightMN
• new (S3) methods for objects of class 'opls' print summary plot predict fitted coefficients residuals

ropls 1.0.2

NEW FEATURES

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

ropls 1.0.1

SIGNIFICANT USER-VISIBLE CHANGES

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

ropls 0.99.7

SIGNIFICANT USER-VISIBLE CHANGES

• rename ('sacurine' data set) for compatibility with 'Workflow4Metabolomics.org': 'profileMN' -> dataMatrix 'sampleDF' -> sampleMetadata 'variableDF' -> variableMetadata

ropls 0.99.6

SIGNIFICANT USER-VISIBLE CHANGES

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

ropls 0.99.4

SIGNIFICANT USER-VISIBLE CHANGES

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

ropls 0.99.2

SIGNIFICANT USER-VISIBLE CHANGES

• rename: ropF -> roplsF ropStrF -> strF
• depreacated roplsF arguments: parObsColLabVcn: now available through the parLabVc and parAsColVcn arguments parObsLegVc: not useful
• 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

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