tests/testthat/test-ccdr_ivn.R

In ccdrAlgorithm: CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks

context("ccdr.run with ivn")

suppressMessages({
    X.test <- generate_fixed_data_frame()
    pp <- ncol(X.test)
    nn <- nrow(X.test)
    ivnvector <- as.integer(c(1, 3, 2, 3, 5, 4))
    dat.test <- sparsebnUtils::sparsebnData(X.test, type = "c", ivn = as.list(ivnvector))
    betas.test <- matrix(runif(pp*pp), ncol = pp)
    lambdas.test <- c(sqrt(97), 50, 6, pi, exp(1), 1, 0.05)
    lambdas.length.test <- 10
})

# ccdr.run <- function(data,
#                      betas,
#                      lambdas,
#                      lambdas.length = NULL,
#                      gamma = 2.0,
#                      error.tol = 1e-4,
#                      max.iters = NULL,
#                      alpha = 10,
#                      verbose = FALSE
# )

test_that("ccdr.run runs as expected", {
    ### No error / Also tests default values for other parameters
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test), NA)
})

test_that("Check special case ivn = list(NULL, NULL, ...)", {
    ### No error if ivn = list(NULL, NULL, ...)
    data.null <- sparsebnUtils::sparsebnData(X.test, type = "c", ivn = vector("list", nn))
    expect_error(ccdr.run(data = data.null, lambdas.length = lambdas.length.test), NA)
})

test_that("Check input: ivn", {
    ### ivn must be a list
    dat.test.notlist <- dat.test
    dat.test.notlist$ivn <- ivnvector
    expect_error(ccdr.run(data = dat.test.notlist, lambdas.length = lambdas.length.test), "ivn must be a list of NULLs or vectors!")
    rm("dat.test.notlist")

    ### each component of ivn must be either NULL or vectors
    dat.test.ivncomp <- dat.test
    dat.test.ivncomp$ivn[[1]] <- matrix(1:pp, 1, pp)
    expect_error(ccdr.run(data = dat.test.ivncomp, lambdas.length = lambdas.length.test), "ivn must be a list of NULLs or vectors!")
    rm("dat.test.ivncomp")

    ### ivn must have the length same as the number of sample rows
    dat.test.length <- dat.test
    dat.test.length$ivn <- as.list(1:(nn+1))
    expect_error(ccdr.run(data = dat.test.length, lambdas.length = lambdas.length.test), sprintf("Length of ivn is %d, expected to match the number of rows in data: %d.", length(dat.test.length$ivn), nn))
    rm("dat.test.length")

    ### labels in each must be appropriate
    dat.test.notint <- dat.test
    dat.test.notint$ivn[[1]] <- c(1L, "2")
    expect_error(ccdr.run(data = dat.test.notint, lambdas.length = lambdas.length.test), "Non-integer label(s) found in one or more components in ivn.", fixed = TRUE)

    ### This is OK -- for now (in order to allow 1,2,... instead of 1L,2L,...)
    # dat.test.notint$ivn[[1]] <- c(1L, 1.5)
    # expect_error(ccdr.run(data = dat.test.notint, lambdas.length = lambdas.length.test), "Non-integer label(s) found in one or more components in ivn.", fixed = TRUE)

    dat.test.notint$ivn[[1]] <- c(3L, 1L)
    expect_error(ccdr.run(data = dat.test.notint, lambdas.length = lambdas.length.test), NA)
    ## labels do not have to be sorted

    dat.test.notint$ivn[[1]] <- c(1L, NA, 3L)
    expect_error(ccdr.run(data = dat.test.notint, lambdas.length = lambdas.length.test), "Non-integer label(s) found in one or more components in ivn.", fixed = TRUE)

    dat.test.notint$ivn[[1]] <- c(0L, 1L)
    expect_error(ccdr.run(data = dat.test.notint, lambdas.length = lambdas.length.test), sprintf("Labels should all be between 1 and %d to refer to the columns of data.", pp))

    dat.test.notint$ivn[[1]] <- c(100L, 1L)
    expect_error(ccdr.run(data = dat.test.notint, lambdas.length = lambdas.length.test), sprintf("Labels should all be between 1 and %d to refer to the columns of data.", pp))

    dat.test.notint$ivn[[1]] <- c(1L, 2L, 1L)
    expect_error(ccdr.run(data = dat.test.notint, lambdas.length = lambdas.length.test), "Duplicated label(s) found in one component in ivn.", fixed = TRUE)

    rm("dat.test.notint")
})

test_that("Check input: lambdas", {
    ### No error
    expect_error(ccdr.run(data = dat.test, lambdas = lambdas.test), NA)

    ### Negative values not allowed
    lambdas.test.neg <- lambdas.test
    lambdas.test.neg[3] <- -1 * lambdas.test.neg[3]
    expect_error(ccdr.run(data = dat.test, lambdas = lambdas.test.neg), "only nonnegative values!")

    #   ### Integers not allowed
    #     lambdas.test.int <- as.integer(lambdas.test)
    #     expect_error(ccdr.run(data = dat.test, lambdas = lambdas.test.int), "lambdas must be a numeric vector!")
})

test_that("Check input: lambdas.length", {
    ### Negative values not allowed
    expect_error(ccdr.run(data = dat.test, lambdas.length = -5), "must be positive!")

    ### Zero not allowed
    expect_error(ccdr.run(data = dat.test, lambdas.length = 0), "must be positive!")

    ### Cannot leave both lambdas and lambdas.length empty
    expect_error(ccdr.run(data = dat.test), "Both lambdas and lambdas.length unspecified")
})

test_that("Check input: max.iters", {
    ### maxIters is not an integer
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, maxx.ters = pi))

    ### maxIters is negative
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, maxx.ters = -5))
})

test_that("Check input: error.tol", {
    ### error.tol cannot be negative
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, error.tol = -1), "must be >= 0!")

    ### warning if error.tol is zero
    expect_warning(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, error.tol = 0), "eps is set to zero")
})

test_that("Check input: gamma", {
    ### gamma = -1 is OK
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, gamma = -1), NA)

    ### gamma cannot be arbitrary negative number
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, gamma = -5), "gamma must be >= 0")
})

test_that("Check input: alpha", {
    ### alpha is negative
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, alpha = -5))
})

test_that("Check input: verbose", {
    ### Works when verbose = TRUE
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, verbose = TRUE), NA)

    ### Works when verbose = FALSE
    expect_error(ccdr.run(data = dat.test, lambdas.length = lambdas.length.test, verbose = FALSE), NA)
})