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test: added test cases for `tune.spls()`. These are just placeholders as more robust testing criteria needs to be established as well as this document will be fully updated as part of PR #206
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,59 +1,30 @@ | ||
| context("tune.spls") | ||
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| test_that("tune.spls works with and without parallel", code = { | ||
| test_that("tune.spls works ", code = { | ||
| data("nutrimouse") | ||
| X <- nutrimouse$gene | ||
| Y <- nutrimouse$lipid | ||
| test.keepX <- c(5,10) | ||
| ncomp <- 2 | ||
| nrepeat <- 3 | ||
| folds <- 3 | ||
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| RNGversion(.mixo_rng()) ## in case RNG changes! | ||
| set.seed(42) | ||
| tune.spls.res = tune.spls(X, Y, ncomp = 3, | ||
| test.keepX = seq(5, 10, 5), | ||
| test.keepY = seq(3, 6, 3), measure = "cor", | ||
| folds = 5, nrepeat = 3, progressBar = F) | ||
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| ## ----------- tune.spls works fine ----------- | ||
| set.seed(12) | ||
| tune.spls11 <- | ||
| tune.spls( | ||
| X = X, | ||
| Y = Y, | ||
| ncomp = ncomp, | ||
| measure = 'cor', | ||
| test.keepX = test.keepX, | ||
| test.keepY = test.keepX, | ||
| folds = folds, | ||
| nrepeat = nrepeat | ||
| ) | ||
| expect_is(tune.spls11, "tune.spls") | ||
| expect_equal(c(comp1 = 10, comp2 = 5), tune.spls11$choice.keepX) | ||
| expect_equal(c(comp1 = 5, comp2 = 5), tune.spls11$choice.keepY) | ||
| expect_equal(class(tune.spls.res), c("tune.pls", "tune.spls")) | ||
| }) | ||
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| test_that("tune.spls works in parallel", code = { | ||
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| ## ----------- tune(method="spls") same as tune.spls ----------- | ||
| set.seed(12) | ||
| tune.spls12 <- | ||
| tune( | ||
| method = "spls", | ||
| X = X, | ||
| Y = Y, | ||
| ncomp = ncomp, | ||
| measure = 'cor', | ||
| test.keepX = test.keepX, | ||
| test.keepY = test.keepX, | ||
| folds = folds, | ||
| nrepeat = nrepeat | ||
| ) | ||
| library(BiocParallel) | ||
| data("nutrimouse") | ||
| X <- nutrimouse$gene | ||
| Y <- nutrimouse$lipid | ||
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| .almost_identical(tune.spls11, tune.spls12) | ||
| set.seed(42) | ||
| tune.spls.res = suppressWarnings(tune.spls(X, Y, ncomp = 3, | ||
| test.keepX = seq(1, 10, 1), | ||
| test.keepY = seq(3, 6, 3), measure = "cor", | ||
| folds = 5, nrepeat = 3, progressBar = F, | ||
| BPPARAM = SnowParam(workers = 4))) | ||
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| ## ----------- tune.spls parallel works fine ----------- | ||
| # set.seed(12) | ||
| # tune.spls31 <- tune.spls(X, Y, ncomp = ncomp, test.keepX = test.keepX, folds = folds, | ||
| # nrepeat = nrepeat, BPPARAM = SnowParam(workers = 2, RNGseed = 12)) | ||
| # TODO tune.spls runs full model nrepeat times for each keepX and keepY! | ||
| # TODO tune.spls fails with SnowParam | ||
| # expect_is(tune.spls31, "tune.spls") | ||
| # set.seed(12) | ||
| # tune.spls13 <- tune(method = "spls", X = X, Y = Y, ncomp = ncomp, test.keepX = test.keepX, folds = folds, | ||
| # nrepeat = nrepeat, cpus = 2) | ||
| # .almost_identical(tune.spls13, tune.spls31) | ||
| }) | ||
| expect_equal(class(tune.spls.res), c("tune.pls", "tune.spls")) | ||
| }) |