devel stuff: notes for test update (bladen)

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
• background_predict
• cim
• circosPlot
• diablo
• network
• pca
• perf.diablo
• perf.mint.splsda

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

• plotIndiv

  • one of the better ones - though only one or two values tested for each case, maybe just a few few parameter tests and any remaining methods (ie pca) and expand on how many components each test checks
  • test for rcc x2, (s)pls x2, (s)plsda, mint.(s)plsda, sgcca x2 and sgccada x3
  • 4 datasets

• plotLoadings

  • tests spls, splsda, block.splsda, mint.splsda. 3 datasets
  • add some more parameter tests + more numerical values

• 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