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- Data sets and feature names are converted into safe names such as Dataset1 and Feature1 for use inside of feature selection and classification functions. ClasifyResult class gains a featuresInfo slot which stores original identifiers as well as sanitised ones. - elasticNetPreval defunct parameter set removed.Dario Strbenac authored on 12/07/2022 14:35:03 |
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Double colons used for DataFrame function so classification works when parallelised on Windows. - Missing usage section restored by adding @rdname to all of the non-class S4 methods.Dario Strbenac authored on 11/03/2022 07:08:44 |
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Repair of Roxygen documentation completed. No warnings or errors (from functions I wrote).Dario Strbenac authored on 10/03/2022 11:45:30 |
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-Improvements to sparsediscrim's DLDA code to better handle leave-one-out cross-validation. - Major progress repairing Roxygen documentation and its flawed creation by Rd2roxygen. - Some renaming of ClassifyResult accessors to make it clearer what they do from the function name.Dario Strbenac authored on 10/03/2022 05:40:56 |
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Added man folderEllis Patrick authored on 17/01/2022 01:55:15 |
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Transitioned manuals to roxygen.Ellis Patrick authored on 14/01/2022 10:15:31 |
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- Can specify colData column of MultiAssayExperiment containing outcome. - More fine-grained cross-validation control for quickClassify. - No functions set seed internally. - quickClassify accepts list of data sets as input. Can do all pairs of data sets for training and prediction. - Unused imports removed from NAMESPACE.Dario Strbenac authored on 19/12/2021 10:45:03 |
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Outdated examples in function documentation changed to new syntax.Dario Strbenac authored on 02/12/2021 09:54:46 |
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- Major changes to function definitions. None of them require fixed annotations like datasetName and classificationName any longer but ClassifyResult stores a table of characteristics which can be any pairs of characteristic and value. Plotting functions can group by any characteristic now. - performances no longer require the user to specify higher or lower is better. That detail is stored internally in a lookup table.Dario Strbenac authored on 05/11/2021 19:34:35 |
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- ClassifyResult object now store the trained classifiers. They may be reused in a future classification task using the function named previousTrained.Dario Strbenac authored on 24/09/2018 07:30:05 |
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- plotFeatureClasses plot width sizing now utilises cowplot's align_plots function. - Modified distribution, rankingPlot, selectionPlot to work with selected features that are Pairs objects.Dario Strbenac authored on 03/08/2018 07:10:06 |
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- Restructured vignette to summarise included functions early. - Vignette code simplfied. - sets of params commonly used together added to vignette. - tTestSelection added and made the default selection method for cross-validation. - ROCplot example fixed. - subtractFromLocation for DataFrame and MultiAssayExperiment fixed. - naiveBayesKernel and mixtures of normals now only using one weighting scheme by default. - Mixtures of normals uninitialised variable for some weighting scheme mistake fixed. - Change tuning optimisation metric specification to be independent of resubstitution classification.Dario Strbenac authored on 03/07/2018 03:00:04 |
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- Removed mention of previously used data set from vingette. - Removed sum-of-differences weighting for mixtures of normals and naive Bayes kernel classifiers.Dario Strbenac authored on 18/06/2018 01:30:13 |
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- Functions for gene-set and network-based metafeature creation and feature selection added. - Data set changed to asthma diagnosis RNA-seq. - Classes vector no longer needs to be named. Sample names as column names of measurements matrix or row names of DataFrame is enforced. - All predictions tables now ensure that the sample ID is a character, not a factor. - Some documentation cross-links fixed.Dario Strbenac authored on 14/06/2018 07:56:38 |
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- Added section to vignette summarising the feature selection and classification functions provided by ClassifyR. - Spell checking of documentation files. - Shortening of function names for nearest shrunken centroid methods.Dario Strbenac authored on 05/03/2018 06:00:04 |