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devel stuff: notes for test update (bladen)

Max Bladen edited this page May 2, 2022 · 33 revisions

Test types:

  • basic
    • just tests the simplest use case works for ALL possible input objects
  • data
    • similar to basic, but uses different input datasets
  • parameter
    • tests the functionality of a specific parameter (or set of parameters)
  • edge.case
    • tests for warnings or odd scenarios
  • error
    • tests that a specific error is raised in the appropriate scenario

What has been completed:

  • auroc
    • mint.block.(s)plsda needs test cases once auroc() is implemented for these object types
  • background_predict
  • cim
  • circosPlot
  • diablo
  • network
  • pca
  • perf.diablo
  • perf.mint.splsda
  • plotIndiv
  • plotLoadings
    • due to the nature of PR #180, these test cases have barely been worked on. Once that PR is merged, come back and complete the upgrade of this document

What do we already have that needs to be updated:

  • internals-.get-pch

    • doesn't use any mixOmics datasets
    • explore different parameters and error states
  • internals

    • tests .get.ind.colors,.are.colors, .get.colors, .get.character.vector, .check_test.keepX and .check_ncomp
    • see if there are more internals to test, explore different datasets with these tests
  • plotVar

    • needs tons of work, only one test
  • predict

    • 4 datasets, mint.splsda, block.splsda, pls, plsda
    • add any remaining methods (eg splsda) and test for more parameters
  • tune.block.splsda

    • only one test (one dataset), no parameter tests
  • tune.mint.splsda

    • two tests, one dataset. test more parameters (not just signif.threshold)
  • tune.spls

    • one test, one dataset, with/without parallel
    • needs work
  • tune.splsda

    • one test, one dataset

What do we need new test files for:

Front end functions:

  • biplot
  • block.(s)pls
  • block.(s)plsda
  • cimDiablo
  • ipca
  • mint.block.(s)pls
  • mint.block.(s)plsda
  • mint.pca
  • mint.(s)pls
  • mint.(s)plsda
  • network
  • nipals
  • all perf variants
  • all plot variants
  • all plot.tune variants
  • plotMarkers
  • (s)pls
  • (s)plsda
  • rcc
  • selectVar
  • sipca
  • spca
  • all tune variants (pca, rcc, spca, splslevel)
  • wrapper.rgcca
  • wrapper.sgcca

Back end functions:

  • explained_variance
  • get.confusion_matrix
  • impute.nipals
  • logratio-transformations
  • map
  • nearZeroVar
  • study_split
  • unmap
  • vip
  • withinVariation
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