CHANGES IN VERSION 1.36.4

MINOR MODIFICATION

    o minor documentation update

CHANGES IN VERSION 1.36.2

MINOR MODIFICATION

    o SpikePos dataset from the BioMark package now included in biosigner

CHANGES IN VERSION 1.29.2
------------------------------

MINOR MODIFICATION

    o minor update of the 'show' method

CHANGES IN VERSION 1.25.6
------------------------------

MINOR MODIFICATION

    o minor modification update

CHANGES IN VERSION 1.25.4
------------------------------

MINOR MODIFICATION

    o biosigner.Rmd vignette: update

CHANGES IN VERSION 1.25.2
------------------------------

NEW FEATURE

    o biosign: now handles SummarizedExperiment and MultiAssayExperiment instances

CHANGES IN VERSION 1.19.2
------------------------------

MINOR MODIFICATION

    o getMset: minor correction in documentation

CHANGES IN VERSION 1.17.2
------------------------------

MINOR MODIFICATION

    o getMset: minor correction in documentation

CHANGES IN VERSION 1.15.4
------------------------------

MINOR MODIFICATION

    o biosigner.Rmd vignette: minor update

CHANGES IN VERSION 1.15.2
------------------------------

NEW FEATURE

    o biosigner.Rmd vignette: ropls::view method replaces ropls::strF (deprecated)

CHANGES IN VERSION 1.13.20
------------------------------

BUG FIXED

    o plot.biosignMultiDataSet correction to include all plots in the .pdf file

CHANGES IN VERSION 1.13.18
------------------------------

MINOR MODIFICATION

    o Minor correction in the plot.biosignMultiDataSet documentation
    
CHANGES IN VERSION 1.13.16
------------------------------

MINOR MODIFICATION

    o Minor correction in the biosignMultiDataSet class documentation
    
CHANGES IN VERSION 1.13.14
------------------------------

MINOR MODIFICATION

    o Minor correction in the biosignMultiDataSet class documentation

CHANGES IN VERSION 1.13.12
------------------------------

INTERNAL MODIFICATION

    o Minor internal modification

CHANGES IN VERSION 1.13.10
------------------------------

INTERNAL MODIFICATION

    o Minor internal modification

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

NEW FEATURE

    o final call to warnings() omitted

CHANGES IN VERSION 1.13.6
------------------------------

NEW FEATURES

    o seedI argument now available (set to 123 by default)
    o biosign can now be applied to MultiDataSet objects (getMset method to get the updated MultiDataSet back)

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

MINOR MODIFICATION

    o minor internal modification

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

NEW FEATURE

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

CHANGES IN VERSION 1.11.26
------------------------------

NEW FEATURE

    o biosign and plot methods: '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 1.11.24
------------------------------

MINOR MODIFICATION

    o minor internal modification

CHANGES IN VERSION 1.11.22
------------------------------

MINOR MODIFICATION

    o minor internal modification

CHANGES IN VERSION 1.11.20
------------------------------

MINOR MODIFICATION

    o minor internal modification

CHANGES IN VERSION 1.11.18
------------------------------

MINOR MODIFICATION

    o minor internal modification

CHANGES IN VERSION 1.11.16
------------------------------

MINOR MODIFICATION

    o minor internal modification for the handling of ExpressionSet instances

CHANGES IN VERSION 1.11.14
------------------------------

MINOR MODIFICATION

    o minor internal modification

CHANGES IN VERSION 1.11.12
------------------------------

MINOR MODIFICATION

    o minor modification in the example of application to ExpressionSet instances
    
CHANGES IN VERSION 1.11.10
------------------------------

MINOR MODIFICATION

    o minor update of example
    
CHANGES IN VERSION 1.11.8
------------------------------

MINOR MODIFICATION

    o vignette minor modification

CHANGES IN VERSION 1.11.6
------------------------------

MINOR MODIFICATION

    o dev.new() is no more called by the plot method

CHANGES IN VERSION 1.11.4
------------------------------

BUG FIXED

    o error message when y is a character but not a factor is now fixed

CHANGES IN VERSION 1.11.2
------------------------------

NEW FEATURES

    o Application to ExpressionSet: tiers now returned in the fData

CHANGES IN VERSION 1.7.4
------------------------------

INTERNAL MODIFICATIONS

    o unit testing on Windows 32 bits disabled
    
CHANGES IN VERSION 1.7.2
------------------------------

INTERNAL MODIFICATIONS

    o modification in unit testing

CHANGES IN VERSION 1.3.6
------------------------------

INTERNAL MODIFICATIONS

    o minor internal modification for compatibility with the Galaxy module

CHANGES IN VERSION 1.3.4
------------------------------

MINOR MODIFICATIONS

    o minor modification in vignette

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

MINOR MODIFICATIONS

    o vignette now in pdf format

CHANGES IN VERSION 1.1.14
------------------------------

INTERNAL MODIFICATIONS

    o Biobase import restricted to ExpressionSet, exprs, and pData
    function/methods to avoid warning (conflict on 'combine' with randomForest)

CHANGES IN VERSION 1.1.12
------------------------------

INTERNAL MODIFICATIONS

    o minor modification in unit tests

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

NEW FEATURE

    o biosign can now be applied to an ExpressionSet object
    o vignette in html format
    
INTERNAL MODIFICATIONS

    o documentation generated with roxygen2 and vignette with rmarkdown

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

INTERNAL MODIFICATIONS

    o error message fixed when missing values in the accuracy vector obtained by the bootstrap step

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

INTERNAL MODIFICATIONS

    o versioning update
    o unit tests silenced on windows platforms because of errors on the moscato2 bioc platform running on windows 8

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

INTERNAL MODIFICATIONS

    o bug fixed (when tierMN contains 0 only)
    o 'show' method: better handling of messages when no signature is found

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

INTERNAL MODIFICATIONS

    o unit tests: test_biosign_diaplasma and test_biosign_sacurine added
    o internal renaming of variables (to indicate their type) and functions (to facilitate their understanding)
    o PLS-DA: to avoid errors during generation of models, the number of predictive components is at least 1   

CHANGES IN VERSION 1.1.0
------------------------------

PACKAGE MODIFICATION

    o Wellcome to the biosigner package for feature selection from omics datasets
    o The package implements a new wrapper method detecting the features which are important for PLS-DA, Random Forest, or SVM binary classification    
    o The package contains the 'diaplasma' LC-MS metabolomics real dataset (plasma samples from diabetic type 1 and 2 patients)    
    o Please see the vignette for details about the approach and package use
    o The corresponding publication is currently under review.   

CHANGES IN VERSION 0.99.11
------------------------------

BUG FIXED

    o in vignette (due to switch in S4 methods for ropls)

CHANGES IN VERSION 0.99.10
------------------------------

PACKAGE MODIFICATION

    o grDevices, graphics, stats, utils imported in DESCRIPTION

CHANGES IN VERSION 0.99.9
------------------------------

PACKAGE MODIFICATION

    o vignette update

CHANGES IN VERSION 0.99.8
------------------------------

PACKAGE MODIFICATION

    o adding the import of the following function in NAMESPACE: abline arrows axis box boxplot dev.new dev.off head image layout median mtext par pdf rect tail title var
    o defining the getAccuracyMN and getSignatureLs accessors

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

PACKAGE MODIFICATION

    o additional unit test silenced in test_biosign_randomforest (because of errors on the moscato2 Windows 2008 platform)

CHANGES IN VERSION 0.99.6
------------------------------

PACKAGE MODIFICATION

    o unit tests silenced in test_biosign_randomforest and test_biosign_predict (because of errors on the moscato2 Windows 2008 platform)

CHANGES IN VERSION 0.99.5
------------------------------

PACKAGE MODIFICATION

    o importing of packages in NAMESPACE fixed
    o use of S4 methods (instead of S3)

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

PACKAGE MODIFICATION

    o correction of a bug in the test_biosign_plsdaF test function

CHANGES IN VERSION 0.99.0
------------------------------

PACKAGE MODIFICATION

    o set version number to 0.99.0 for Bioconductor

CHANGES IN VERSION 0.5.13
------------------------------

NEW FEATURES

    o biosign: printing messages (for development purpose) removed

CHANGES IN VERSION 0.5.12
------------------------------

NEW FEATURES

    o biosign: new ordering of tierMC (previsously by decreasing row sums): now rows containing maximum tier are first grouped, before being ordered by decreasing row sums within each group
    o biosign: remove deprecated CV functions and their calls; remove deprecated arguments

CHANGES IN VERSION 0.5.11
------------------------------

NEW FEATURES

    o diaplasma dataset: minor changes in variable names (column names of dataMatrix and row names of variableMetadata)

CHANGES IN VERSION 0.5.10
------------------------------

NEW FEATURES

    o unit tests: now run on 'diaplasma' dataset (instead of 'sacurine' from the 'ropls' package)

CHANGES IN VERSION 0.5.9
------------------------------

NEW FEATURES

    o predict.biosign: predictions on 'S+A' signatures now possible

BUG FIXES

    o diaplasma dataset: formatting of dataMatrix column names (and variableMetadata row names)

CHANGES IN VERSION 0.5.8
------------------------------

NEW FEATURES

    o diaplasma dataset: annotations (when available) annotated to column names of dataMatrix (and row names of variableMetadata)

CHANGES IN VERSION 0.5.7
------------------------------
    
BUG FIXES
  
    o biosign: now correctly attribute grade from score when one or more methods has no S variables
    o plot.biosign: management of errors when signatures are empty

CHANGES IN VERSION 0.5.6
------------------------------

NEW FEATURES

    o biosign: now call itself on the best half variables when no significant variables are found
    o biosign: now produce grade A and less when no S are produced
    
BUG FIXES
  
    o biosign: remove an unnecessary test in the 'translate' code

CHANGES IN VERSION 0.5.5
------------------------------

NEW FEATURES

    o biosign: now correctly handle non significant rank/results for one or two methods when at least one other is significant
    
BUG FIXES
  
    o now ensure 20% of out of the bag samples in the bootstrap extraction
    o predict: handling void signatures in predictions

CHANGES IN VERSION 0.5.4
------------------------------

NEW FEATURES

    o minor modifications

CHANGES IN VERSION 0.5.3
------------------------------

NEW FEATURES

    o minor modifications


CHANGES IN VERSION 0.5.2
------------------------------

NEW FEATURES

    o first complete version of the package (including the vignette)


CHANGES IN VERSION 0.5.1
------------------------------

NEW FEATURES

    o diaplasma dataset added
    
CHANGES IN VERSION 0.4.13
------------------------------

NEW FEATURES

    o plot: new typeC = "boxplot" argument for plotting the individual features from the signature    
    o first draft of vignette

CHANGES IN VERSION 0.4.12
------------------------------

NEW FEATURES
    
    o 'predict' method now available

CHANGES IN VERSION 0.4.11
------------------------------

NEW FEATURES
    
    o 'AS' model and signature returned as outputs from 'biosign'
    o variables with NA are removed from the 'x' matrix prior to Random Forest and SVM modeling
    o if missing, 'x' column names are set to 'V1', ..., 'Vp' (where p is the number of variables)
    o 'x' data frame converted to a matrix (generates a warning)
    o 'y' character vector converted to a factor (generates a warning)    

CHANGES IN VERSION 0.4.10
------------------------------

NEW FEATURES
    
    o new argument checks added

CHANGES IN VERSION 0.4.9
------------------------------

NEW FEATURES
    
    o signatures from S and AS models returned by biosign

CHANGES IN VERSION 0.4.8
------------------------------

BUG FIXES
    
    o in case of no significant variable found, a message is returned (instead of an error)

CHANGES IN VERSION 0.4.7
------------------------------

NEW FEATURES
    
    o unit tests updated

CHANGES IN VERSION 0.4.6
------------------------------

BUG FIXES
    
    o minor bug corrections in biosign (accuracy output) and plot.biosign (tiers colors)

CHANGES IN VERSION 0.4.5
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o biosign: accuracy of the 'S+A' model is now computed (in addition to the full and 'S' models)
    
    o plot.biosign: 'S' tiers displayed by default (in addition to 'A' when at least one of the restricted models has an accuracy < 80%

CHANGES IN VERSION 0.4.4
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o plot.biosign: redesigned to display the tiers ('S' and 'A' by default)

CHANGES IN VERSION 0.4.3
------------------------------

NEW FEATURES

    o biosign: binary search implemented to speed up the search for the number of features

CHANGES IN VERSION 0.4.2
------------------------------

NEW FEATURES

    o signatures of only one feature are now possible

CHANGES IN VERSION 0.4.1
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o new names:
        package: 'biosigner' (instead of 'rdiagnosign')
        main method and class: 'biosign' (instead of 'diagnosign')
    
    o biosign:
        new 'recursiveL' argument to obtain shorter and more stable signatures
        
CHANGES IN VERSION 0.3.8
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o diasgnosign: Full and restricted models now available in the outputs

CHANGES IN VERSION 0.3.7
------------------------------

NEW FEATURES

    o Change the evaluation method: now compute the balanced classification rate.

CHANGES IN VERSION 0.3.6
------------------------------

NEW FEATURES

    o unit tests added

CHANGES IN VERSION 0.3.5
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o 'diagnosign'
        'randomforest' method now available

CHANGES IN VERSION 0.3.4
------------------------------

NEW FEATURES

    o Galaxy module for rdiagnosign has been developed
    o ggplot2 removed from dependencies (since it is not used currently)

CHANGES IN VERSION 0.3.3
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    
    o renaming some of the 'dignosign' arguments for simplicity
        crossValI    -> crossvalI
        nbootI       -> bootI
        permutationI -> permI
        pvalThreshN  -> pvalN

CHANGES IN VERSION 0.3.2
------------------------------

NEW FEATURES
    
    o bootstraping included into 'diagnosign' (instead of cross-validation)

CHANGES IN VERSION 0.3.1
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o package renamed: 'rdiagnosign' (instead of 'multimark')
        class 'diagnosign'
        methods 'diagnosign', 'print.diagnosign', 'plot.diagnosign'
    
CHANGES IN VERSION 0.2.3
------------------------------

NEW FEATURES

    o internal parameter 'alpha' set to 0.05 instead of 0

CHANGES IN VERSION 0.2.2
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o 'signastic' function (replaces 'fsi'):
        to compute significant features and corresponding models

CHANGES IN VERSION 0.2.1
------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o rename data set tables
        proMN -> dataMatrix
        obsDF -> sampleMetadata
        feaDF -> variableMetadata

CHANGES IN VERSION 0.2.0
------------------------------

NEW FEATURES

    o 'pls' method available (in addition to 'svm')


