October 12, 2022
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- Extreme gradient boosting wrapper added in interfaceXGB.R. - crossValidate gains performanceType parameter that defaults to "auto" which chooses depending on classification or survival task or can be set to any user-specified performance metric. - SelectParams default performanceType is now balanced accuracy, for consistency with other functions. - Vignette text updated to refer to balanced accuracy and to add k-NN and XGB classifiers to classifier table. - NEWS file updated for upcoming Bioconductor release.

Dario Strbenac authored on 12/10/2022 13:05:23
September 28, 2022
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- Tweaks to colCoxTests documentation to fix the last couple of warnings.

Dario Strbenac authored on 28/09/2022 12:10:03
September 27, 2022
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- crossValidate works with selectionMehod being none.

Dario Strbenac authored on 27/09/2022 01:26:02
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- plotFeatureClasses now works if classes is column name of data frame. - prepareData warning for variable name conversion for modelling.

Dario Strbenac authored on 27/09/2022 00:50:16
September 21, 2022
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- Fixed a couple of variable name typos. - Previous commit did not do variable name extraction correctly when getFeatures was not being used. Now it is done correctly regardless whether the variables are extracted from trained model (possibly already subsetted) or from feature selection (corresponding to original set of features).

Dario Strbenac authored on 21/09/2022 07:00:05
September 15, 2022
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- finalModel accessor added for getting final model properly. - Conversion back into selected features' original names fixed if feature selection does subsetting after the features are selected.

Dario Strbenac authored on 15/09/2022 04:30:03
September 13, 2022
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- Provide a convenience S4 method for ClassifyResult input object for ROCplot, so that users don't need to put their result into a list, like performancePlot, rankingPlot, selectionPlot already provide.

Dario Strbenac authored on 13/09/2022 02:00:04
September 12, 2022
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- Accessors for metadata columns changed to be robust in situtations when the column doesn't exist by using $column rather than [, "column"] access style.

Dario Strbenac authored on 12/09/2022 05:00:05
September 7, 2022
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Update interfacePrevalidation.R

Ellis Patrick authored on 07/09/2022 11:55:12 • GitHub committed on 07/09/2022 11:55:12
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Update interfacePrevalidation.R

Ellis Patrick authored on 07/09/2022 05:37:55 • GitHub committed on 07/09/2022 05:37:55
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Update rankingCoxPH.R

Ellis Patrick authored on 07/09/2022 03:08:03 • GitHub committed on 07/09/2022 03:08:03
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Update runTest.R

Ellis Patrick authored on 07/09/2022 02:45:27 • GitHub committed on 07/09/2022 02:45:27
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- Restored utilities.R.

Dario Strbenac authored on 07/09/2022 00:48:49
September 6, 2022
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Allow mix of categorical and numeric variables in coxPH

Ellis Patrick authored on 06/09/2022 23:36:21
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export colCoxTests

Ellis Patrick authored on 06/09/2022 22:57:36