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
  • mint.block.(s)plsda needs test cases once auroc() can be used these object types. A node has been made in the project to address this.
• background_predict
  • mint.(s)plsda needs test cases once background.predict() can be used these object types. A node has been made in the project to address this.
• cim
  • need to clean this guy up. cant test for ddr and ddc components as part of the new GT generation system
• circosPlot
• diablo
• network
• pca
• perf.diablo
• perf.mint.splsda
• plotIndiv
• plotLoadings
  • once PR #212 is merged, then come back here and add test cases for the mint.(s)pls functions, block parameter and the errors for study parameter
• plotVar
  • uncomment all basic block test cases, unknown source of error
• predict
  • uncomment basic mint.spls and parameter multilevel test cases, unknown source of error
• tune.block.splsda
  • validation = "loo" raising weird error. Noted on the project workflow. Uncomment associated test when bug is resolved
  • dist = c("centroids.dist", "mahalanobis.dist") raising weird error. Noted on the project workflow. Update the dist test to include both distances once resolved
  • in BPPARAM test, warnings are not suppressed for some reason - something to do with bplapply()
• tune.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
• tune.spls - NOTE CHANGES IN PR FOR ISSUE #214, LEAVE THIS FOR NOW
  • 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
  • just realised that I havent included this as a basic type for most plotting functions (eg. plotLoadings(), plotVar()) - go back and add these
• 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