August 31, 2022
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- 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
August 25, 2022
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Merge branch 'master' of

Dario Strbenac authored on 25/08/2022 07:03:14
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- 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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- ROCplot's comparison value chosen automatically be default. - All tune parameter combinations now stored in result alongside the index of the best combination.

Dario Strbenac authored on 25/08/2022 05:15:03
August 24, 2022
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Merge branch 'master' of

Dario Strbenac authored on 24/08/2022 11:07:28
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- All mcols prefixed with S4Vectors for Windows.

Dario Strbenac authored on 24/08/2022 11:06:23
August 23, 2022
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Update rankingDifferentMeans.R

Ellis Patrick authored on 23/08/2022 21:22:56 • GitHub committed on 23/08/2022 21:22:56
August 22, 2022
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- Fixed remainder of old-format parameter construction in examples and a couple of typos.

Dario Strbenac authored on 22/08/2022 05:30:05
August 21, 2022
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- 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
August 18, 2022
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Ellis Patrick authored on 18/08/2022 05:10:00 • GitHub committed on 18/08/2022 05:10:00
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Update crossValidate.R

Ellis Patrick authored on 18/08/2022 05:07:13 • GitHub committed on 18/08/2022 05:07:13
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Ellis Patrick authored on 18/08/2022 04:40:55 • GitHub committed on 18/08/2022 04:40:55
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Update rankingDifferentMeans.R

Ellis Patrick authored on 18/08/2022 04:35:55 • GitHub committed on 18/08/2022 04:35:55
August 17, 2022
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- 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
August 14, 2022
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- 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