Code

Issue 304 streamline tune#348

Code

Merged

evaham1 merged 75 commits intomastermixOmicsTeam/mixOmics:masterfrom issue-304-streamline-tunemixOmicsTeam/mixOmics:issue-304-streamline-tuneCopy head branch name to clipboardNov 28, 2024

+4,366-1,508

Commits

Commits on Nov 22, 2024

• update tune.splsda so runs perf if test.keepX=NULL, update docs and exampels

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• add unit testing for edited tune.splsda functionality

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• update tune.spca docs as these depended on tune.splsda docs

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• update tune.splsda docs

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• init tune.plsda which calls perf

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• add tune.plsda examples

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Commits on Nov 25, 2024

• update tune.spls to run perf if test.keepX and test.keepY are NULL, update docs to reflect

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• add unit test for new tune.spls functionality

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• add few more tests for different params to check tune.spls works

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• add tune.spls examples to docs

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• update tune.spls examples to include spls1 model

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• update tune.spls docs

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• init tune.pls

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• add tune.pls examples

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• update tune.block.splsda docs and exmples

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• typos in tune.block.splsda

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• unit testing for new tune.block.splsda functionality

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• init tune.block.plsda

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• add example for tune.block.plsda

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• update tune.mint.splsda docs and example

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• add examples to docs

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• add unit tests for tune.mint.splsda

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• no CV params in mint

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• init tune.mint.plsda

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• init tune.mint.plsda

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• update examples of tune.mint.plsda

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Commits on Nov 26, 2024

• update tune.rcc to remove plot arg to streamline

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• start streamlining tune wrapper function

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• streamline tune wrapper with exisiting functions

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• update unit test for removing plot from tune.rcc

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• hardcode limQ2 param in tune.pls and tune.spls to streamline functions

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• clean up input params docs

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• streamline tune.block.plsda, no measure arg

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• update tune.block.splsda docs to reflect how to use 'dist' and 'measure'

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• update dist default to 'all' for tune.block.plsda

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• streamline tune.plsda - no 'measure' arg

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• update docs for tune.splsda

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• make tune.spls example code lines less long

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• fix tune.pls docs

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• fix errors in tune.spls docs

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• allow tune.mint functions to take extra args

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• fixed docs warnings

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• fix tune.rcc example

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• fix warnings in tune.pls

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Commits on Nov 27, 2024

• fix note in perf.assess.pls

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• fix notes and warnings in tune docs

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• fix unit test errors

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• fix notes in docs

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• rmove dist checking so can plot multiple dist metrics using internal perf function

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• clean tune tune.plsda and tune.splsda input args

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• reorg tune.mint input args

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• how to use 'measure' arg in tune mint functions

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• fix unit test

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• add unit tests for tune.pca and match default args

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• add new functions to tune wrapper

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• update output docs for perf

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• update perf.assess docs

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• add examples to perf.assess

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• add unit tests for tune.plsda

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• unit tests for tune.pls

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• make sure tune.spls and tune wrapper match default args

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• add unit tests for tune.block.plsda

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• add unit test for tune.mint.plsda

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• shortern example lines

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• add testing to make sure tune outputs can plot without error

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Commits on Nov 28, 2024

• fix unit tests checking plotting properly

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• add example for tune.pca multilevel

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• add multilevel examples to tune.pls and tune.spls

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• doc

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• update tune.plsda to work on multilevel and add example

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• tune.splsda take multilevel and add exampel

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• install mixomics from github inside the vignette

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• fixed tune.splsda multilevel error

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• revert back vignette change

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• typo in example

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