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Viewea07063f
- Typo in train.DataFrame variable fixed. - .predict for DLDA made renamed to DLDA to enable easy dispatch by predict method. - randomForest wrapper now uses ranger as the underlying package instead of randomForest.Dario Strbenac authored on 14/10/2022 00:30:12 |
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Viewed2b7cb5
- 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 |
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View78a4c924
- Restored utilities.R.Dario Strbenac authored on 07/09/2022 00:48:49 |
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View265ed7a5
export colCoxTestsEllis Patrick authored on 06/09/2022 22:57:36 |
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View6e3a76b4
Update utilities.REllis Patrick authored on 05/09/2022 06:03:37 • GitHub committed on 05/09/2022 06:03:37 |
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View69d76269
- train methods now exported and can be used. train generic imported from generics package. - simple params now have performanceType specified. - Fixes to training with multiple views but no aggregation. - Fix to parameter tuning in .doTrain.Dario Strbenac authored on 02/09/2022 06:10:10 |
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Viewba722d29
- train and predict functions created to allow training and prediction to be done independently. But they have the capabilities of crossValidate, such as multi-view methods. Implemented as S3 methods to work well with existing generics defined by R. - runTest, runTests and crossValidate now all utilise prepareData and allow passing in extra parameters for it. - getLocationsAndScales becomes private function. - All reference to targets parameter converted to useFeatures, which allows both the assay and the feature to be specified, rather than only the assay. - .MAEtoWideTable data flattening function is gone. Its functionality is incorporated into prepareData. - Parameter tuning in .doSelection of resubstitution mode now correctly uses training data as the test data instead of accidentally using the testing data.Dario Strbenac authored on 31/08/2022 11:45:02 |
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View127675d5
- getFeatures functions added to simple params settings to extract selected features from within trained model where relevant. - Nearest Shrunken Centroid added as a simple params function and a classifier keyword option.Dario Strbenac authored on 25/08/2022 05:15:03 |
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View86f19320
- Restored runTest, runTests, ModellingParams, CrossValParams as public documented functions. Vignette also restored to explain them. - Constructors for params now expect a character keyword which is then converted into a function internally.Dario Strbenac authored on 21/08/2022 16:07:38 |
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View253c56fc
- All references to runTest and runTests in examples and vignette converted to crossValidate. End users should always use crossValidate from now on. - Minor fixes to code mistakes. - Performance tuning of training method parameters chosen within feature selection is now faithfully used in the model training.Dario Strbenac authored on 17/08/2022 13:55:15 |
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Viewd37fb9c5
- Classifiers and feature selection functions no longer have multiple signaures and are private. - prepareData function to filter and subset input data using common ways, such as missingness and variability. - The variable renaming and storage in Original Feature and Renamed Feature reverted back to column metadata and assay / feature colums. - sampleInfo now reverted back to clinical.Dario Strbenac authored on 14/08/2022 23:45:28 |
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View8fe7aeff
Update utilities.REllis Patrick authored on 09/08/2022 08:21:20 • GitHub committed on 09/08/2022 08:21:20 |
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Viewb964ca82
Update utilities.REllis Patrick authored on 02/08/2022 05:05:50 • GitHub committed on 02/08/2022 05:05:50 |
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Viewcf84dedb
Merge branch 'master' of https://github.com/SydneyBioX/ClassifyRDario Strbenac authored on 02/08/2022 04:00:15 |
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Viewedf8416b
Fix for function not found if SnowParam parallelisation used.Dario Strbenac authored on 02/08/2022 04:00:10 |