test_tronco.R
In TRONCO: TRONCO, an R package for TRanslational ONCOlogy

data(test_dataset)
data(test_dataset_no_hypos)

capri = tronco.capri(test_dataset, nboot = 1, silent = TRUE)
caprese = tronco.caprese(test_dataset_no_hypos, silent = TRUE)
chowliu = tronco.chowliu(test_dataset_no_hypos, nboot = 1, silent = TRUE)
edmonds = tronco.edmonds(test_dataset_no_hypos, nboot = 1, silent = TRUE)
gabow = tronco.gabow(test_dataset_no_hypos, nboot = 1, silent = TRUE)
prim = tronco.prim(test_dataset_no_hypos, nboot = 1, silent = TRUE)
npb = tronco.bootstrap(capri, nboot = 1, silent = TRUE, cores.ratio = 0)
sb = tronco.bootstrap(capri, nboot = 1, type = 'statistical', silent = TRUE, cores.ratio = 0)


context("CAPRESE")

test_that("tronco caprese is working", {
    expect_output(tronco.caprese(test_dataset_no_hypos), "CAPRESE")
    expect_warning(tronco.caprese(test_dataset))
    expect_error(tronco.caprese(NULL))
    expect_error(tronco.caprese(test_dataset_no_hypos, lambda = -1))
    expect_error(tronco.caprese(test_dataset_no_hypos, lambda = 2))
})

context("CAPRI")

test_that("tronco capri is working", {
    expect_output(tronco.capri(test_dataset,
        nboot = 1,
        regularization = c('bic', 'aic', 'loglik')),
    "CAPRI")
    expect_output(tronco.capri(test_dataset,
        nboot = 1,
        regularization = c('bic'),
        command = 'tabu',
        do.boot = FALSE),
    "CAPRI")
    expect_output(tronco.capri(test_dataset,
        nboot = 1,
        boot.seed = 1),
    "CAPRI")
    expect_error(tronco.capri(NULL))
    expect_error(tronco.capri(test_dataset,
        command = 'banana'))
    expect_error(tronco.capri(test_dataset,
        pvalue = -1))
    expect_error(tronco.capri(test_dataset,
        pvalue = 2))
    expect_error(tronco.capri(test_dataset,
        regularization = 'banana'))
})

context("EDMONDS")

test_that("tronco edmonds is working", {
    expect_output(tronco.edmonds(test_dataset_no_hypos,
        nboot = 1,
        regularization = c('no_reg', 'loglik', 'bic', 'aic')),
    "Edmonds")
    expect_output(tronco.edmonds(test_dataset_no_hypos,
        nboot = 1,
        boot.seed = 1),
    "Edmonds")
    expect_warning(tronco.edmonds(test_dataset,
        nboot = 1))
    expect_error(tronco.edmonds(NULL))
    expect_error(tronco.edmonds(test_dataset_no_hypos,
        command = 'banana'))
    expect_error(tronco.edmonds(test_dataset_no_hypos,
        pvalue = -1))
    expect_error(tronco.edmonds(test_dataset_no_hypos,
        pvalue = 2))
    expect_error(tronco.edmonds(test_dataset_no_hypos,
        regularization = 'banana'))
})

context("GABOW")

test_that("tronco gabow is working", {
    expect_output(tronco.gabow(test_dataset_no_hypos,
        nboot = 1,
        regularization = c('no_reg', 'loglik', 'bic', 'aic')),
    "Gabow")
    expect_output(tronco.gabow(test_dataset_no_hypos,
        nboot = 1,
        boot.seed = 1),
    "Gabow")
    expect_warning(tronco.gabow(test_dataset,
        nboot = 1))
    expect_error(tronco.gabow(NULL))
    expect_error(tronco.gabow(test_dataset_no_hypos,
        command = 'banana'))
    expect_error(tronco.gabow(test_dataset_no_hypos,
        pvalue = -1))
    expect_error(tronco.gabow(test_dataset_no_hypos,
        pvalue = 2))
    expect_error(tronco.gabow(test_dataset_no_hypos,
        regularization = 'banana'))
})

context("CHOW LIU")

test_that("tronco chow liu is working", {
    expect_output(tronco.chowliu(test_dataset_no_hypos,
        nboot = 1,
        regularization = c('loglik', 'bic', 'aic')),
    "Chow")
    expect_output(tronco.chowliu(test_dataset_no_hypos,
        nboot = 1,
        boot.seed = 1),
    "Chow")
    expect_warning(tronco.chowliu(test_dataset,
        nboot = 1))
    expect_error(tronco.chowliu(NULL))
    expect_error(tronco.chowliu(test_dataset_no_hypos,
        command = 'banana'))
    expect_error(tronco.chowliu(test_dataset_no_hypos,
        pvalue = -1))
    expect_error(tronco.chowliu(test_dataset_no_hypos,
        pvalue = 2))
    expect_error(tronco.chowliu(test_dataset_no_hypos,
        regularization = 'banana'))
})

context("PRIM")

test_that("tronco prim is working", {
    expect_output(tronco.prim(test_dataset_no_hypos,
        nboot = 1,
        regularization = c('no_reg', 'loglik', 'bic', 'aic')),
    "Prim")
    expect_output(tronco.prim(test_dataset_no_hypos,
        nboot = 1,
        boot.seed = 1),
    "Prim")
    expect_warning(tronco.prim(test_dataset,
        nboot = 1))
    expect_error(tronco.prim(NULL))
    expect_error(tronco.prim(test_dataset_no_hypos,
        command = 'banana'))
    expect_error(tronco.prim(test_dataset_no_hypos,
        pvalue = -1))
    expect_error(tronco.prim(test_dataset_no_hypos,
        pvalue = 2))
    expect_error(tronco.prim(test_dataset_no_hypos,
        regularization = 'banana'))
})

context("bootstrap")

test_that("tronco bootstrap is working", {
    expect_output(tronco.bootstrap(capri, nboot = 1, cores.ratio = 0), 'non-parametric')
    expect_output(tronco.bootstrap(capri, nboot = 1, type = 'statistical', cores.ratio = 0), 'statistical')
    expect_output(tronco.bootstrap(caprese, nboot = 1, cores.ratio = 0), 'non-parametric')
    expect_output(tronco.bootstrap(prim, nboot = 1, cores.ratio = 0), 'non-parametric')
    expect_output(tronco.bootstrap(prim, nboot = 1, type = 'statistical', cores.ratio = 0), 'statistical')
    expect_output(tronco.bootstrap(edmonds, nboot = 1, cores.ratio = 0), 'non-parametric')
    expect_output(tronco.bootstrap(edmonds, nboot = 1, type = 'statistical', cores.ratio = 0), 'statistical')
    expect_output(tronco.bootstrap(chowliu, nboot = 1, cores.ratio = 0), 'non-parametric')
    expect_output(tronco.bootstrap(chowliu, nboot = 1, type = 'statistical', cores.ratio = 0), 'statistical')
    expect_error(tronco.bootstrap(test_dataset, nboot = 1, cores.ratio = 0))
    expect_error(tronco.bootstrap(capri, type = 'supergiovane', cores.ratio = 0))
    expect_error(tronco.bootstrap(caprese, type = 'statistical', cores.ratio = 0))
})

context("confidences")

test_that('as.confidence work with reconstruction and bootstrap', {
    expect_equal(length(as.confidence(caprese, conf=c('pr', 'tp', 'hg'))), 3)
    expect_equal(length(as.confidence(npb, conf = 'npb')), 1)
    expect_error(as.confidence(capri, conf = 'npb'))
    expect_equal(length(as.confidence(sb, conf = 'sb')), 1)
    expect_error(as.confidence(capri, conf = 'sb'))
})

context("probabilities")

test_that('as.prob work with reconstruction', {
    expect_equal(length(as.joint.probs(capri)), 2)
    expect_error(as.joint.probs(capri, events = c('a')))
    expect_error(as.joint.probs(capri, type = 'banana'))
    expect_error(as.joint.probs(capri, models = 'banana'))
    expect_equal(length(as.conditional.probs(capri)), 2)
    expect_error(as.conditional.probs(capri, events = c('a')))
    expect_error(as.conditional.probs(capri, type = 'banana'))
    expect_error(as.conditional.probs(capri, models = 'banana'))
    expect_equal(length(as.marginal.probs(capri)), 2)
    expect_error(as.marginal.probs(capri, events = c('a')))
    expect_error(as.marginal.probs(capri, type = 'banana'))
    expect_error(as.marginal.probs(capri, models = 'banana'))
    expect_equal(length(as.error.rates(capri)), 2)
    expect_error(as.error.rates(capri, models = 'banana'))
})

context("as.bootstrap.scores")

test_that('as.bootstrap.scores return results', {
    expect_equal(length(as.bootstrap.scores(npb)), 2)
    expect_equal(length(as.bootstrap.scores(sb)), 2)
    expect_error(as.bootstrap.scores(npb, events = 'asd'))
    expect_error(as.bootstrap.scores(npb, models = 'banana'))
})