### Test for validate_occumbData() ---------------------------------------------
## Tests for sequence read counts

test_that("Mode check for y works", {
    expect_error(new("occumbData", y = array(list(), dim = rep(2, 3))),
                 "Elements of 'y' are lists but should be integers")
})

test_that("Dimension check for y works", {
    expect_error(new("occumbData", y = array(1:4, dim = rep(2, 1))),
                 "'y' is not a 3D-array")
    expect_error(new("occumbData", y = array(1:4, dim = rep(2, 2))),
                 "'y' is not a 3D-array")
    expect_error(new("occumbData", y = array(1:16, dim = rep(2, 4))),
                 "'y' is not a 3D-array")
    expect_error(new("occumbData", y = array(numeric(), dim = c(2, 2, 0))),
                 "'y' is an empty array")
})

test_that("Check for missing values for y works", {
    expect_error(new("occumbData", y = array(c(NA, 1:7), dim = rep(2, 3))),
                 "'y' contains missing value.")
})

test_that("Integer check for y works", {
    expect_error(new("occumbData", y = array(1:8 + 0.1, dim = rep(2, 3))),
                 "'y' contains non-integer value")
    expect_error(new("occumbData", y = array(c(Inf, 1:7), dim = rep(2, 3))),
                 "'y' contains non-integer value")
})

test_that("Check for non-negative values for y works", {
    expect_error(new("occumbData", y = array(c(-1, 1:7), dim = rep(2, 3))),
                 "'y' contains negative value")
})

test_that("Check for non-zero values for y works", {
    expect_error(new("occumbData", y = array(0, dim = rep(2, 3))),
                 "'y' contains only zero values")
})

## Tests for covariates
test_that("Check for covariate names works", {
    unnamed_list1 <- unnamed_list2 <- list(rep(1, 2), rep(1, 2))
    names(unnamed_list2) <- c("a", "")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = unnamed_list1),
                 "'spec_cov' contains unnamed element")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = unnamed_list2),
                 "'spec_cov' contains unnamed element")
    unnamed_list1 <- unnamed_list2 <- list(rep(1, 3), rep(1, 3))
    names(unnamed_list2) <- c("a", "")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   site_cov = unnamed_list1),
                 "'site_cov' contains unnamed element")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   site_cov = unnamed_list2),
                 "'site_cov' contains unnamed element")
    unnamed_list1 <- unnamed_list2 <-
        list(matrix(1:2, 1, 2), matrix(1:2, 1, 2))
    names(unnamed_list2) <- c("a", "")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   repl_cov = unnamed_list1),
                 "'repl_cov' contains unnamed element")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   repl_cov = unnamed_list2),
                 "'repl_cov' contains unnamed element")
})

test_that("Check for covariate name overlap works", {
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = list(a = NULL, b = NULL),
                                   site_cov = list(a = NULL)),
                 "Duplicated covariate names are not allowed: 'a'")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = list(a = NULL, b = NULL),
                                   site_cov = list(a = NULL, b = NULL)),
                 "Duplicated covariate names are not allowed: 'a', 'b'")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = list(a = NULL, b = NULL),
                                   repl_cov = list(a = NULL)),
                 "Duplicated covariate names are not allowed: 'a'")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = list(a = NULL, b = NULL),
                                   repl_cov = list(a = NULL, b = NULL)),
                 "Duplicated covariate names are not allowed: 'a', 'b'")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   site_cov = list(a = NULL, b = NULL),
                                   repl_cov = list(a = NULL)),
                 "Duplicated covariate names are not allowed: 'a'")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   site_cov = list(a = NULL, b = NULL),
                                   repl_cov = list(a = NULL, b = NULL)),
                 "Duplicated covariate names are not allowed: 'a', 'b'")
})

test_that("Dimension check for covariates works", {
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = list(a = rep(1, 1))),
        "'a' must have a length equal to the number of species")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = list(a = rep(1, 1),
                                                   b = rep(1, 3))),
        "'a' and 'b' must have a length equal to the number of species")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   site_cov = list(a = rep(1, 1))),
        "'a' must have a length equal to the number of sites")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   site_cov = list(a = rep(1, 1),
                                                   b = rep(1, 3))),
        "'a' and 'b' must have a length equal to the number of sites")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   repl_cov = list(a = rep(1, 1))),
        "'a' must have a number of rows equal to the number of species and a number of columns equal to the number of sites")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   repl_cov = list(a = rep(1, 1),
                                                   b = rep(1, 3))),
        "'a' and 'b' must have a number of rows equal to the number of species and a number of columns equal to the number of sites")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   repl_cov = list(a = matrix(1:2, 1, 2))),
                 "'a' must have a number of rows equal to the number of species and a number of columns equal to the number of sites")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   repl_cov = list(a = matrix(1:2, 1, 2),
                                                   b = matrix(1:2, 2, 1))),
        "'a' and 'b' must have a number of rows equal to the number of species and a number of columns equal to the number of sites")
})

test_that("Check for covariate classes works", {
    # complex
    spec_cov <- list(a = rnorm(2), b = rep(0 + 1i, 2))
    site_cov <- list(c = rnorm(2), d = rep(0 + 1i, 2))
    repl_cov <- list(e = matrix(1:4, 2, 2), f = matrix(rep(0 + 1i, 4), 2, 2))
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = spec_cov,
                                   site_cov = site_cov,
                                   repl_cov = repl_cov),
                 "'b', 'd', and 'f' must be logical, numeric, integer, factor, or character")
})

test_that("Check for missing covariate values works", {
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = list(a = c(1, NA))),
                 "'spec_cov' contains missing value")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   site_cov = list(b = c(1, NA))),
                 "'site_cov' contains missing value")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   repl_cov = list(c = matrix(c(1:3, NA), 2, 2))),
                 "'repl_cov' contains missing value")
})

test_that("Check for infinite covariate values works", {
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   spec_cov = list(a = c(1, Inf))),
                 "'spec_cov' contains infinite value")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   site_cov = list(b = c(1, Inf))),
                 "'site_cov' contains infinite value")
    expect_error(new("occumbData", y = array(1:8, dim = rep(2, 3)),
                                   repl_cov = list(c = matrix(c(1:3, Inf), 2, 2))),
                 "'repl_cov' contains infinite value")
})