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