# Author: Quentin Grimonprez

context("Bootstrap functions")

test_that("getSignReference works", {
  alpha <- list(matrix(1:9, nrow = 3), matrix(-1 * (9:1), nrow = 3), matrix(c(1:5, 4:1), nrow = 3))
  expectedOut <- list(
    position = c(9, 1, 5), isNegative = c(FALSE, TRUE, FALSE),
    allNegative = list(
      matrix(1:9, nrow = 3) < 0,
      matrix(-1 * (9:1), nrow = 3) < 0,
      matrix(c(1:5, 4:1), nrow = 3) < 0
    )
  )

  out <- getSignReference(alpha)

  expect_equal(out, expectedOut)
})


test_that("unifySign works when all are present", {
  ref <- list(position = c(9, 1, 5), isNegative = c(FALSE, TRUE, FALSE))

  encod <- list(
    list(
      alpha = list(matrix(1:9, nrow = 3), matrix(1:9, nrow = 3), matrix(1:9, nrow = 3)),
      pc = matrix(1:9, nrow = 3)
    ),
    list(
      alpha = list(matrix(-1 * (9:1), nrow = 3), matrix(-1 * (9:1), nrow = 3), matrix(-1 * (9:1), nrow = 3)),
      pc = matrix(-1 * (9:1), nrow = 3)
    )
  )

  expectedOut <- list(
    list(
      alpha = list(matrix(1:9, nrow = 3), matrix(-1 * (1:9), nrow = 3), matrix(1:9, nrow = 3)),
      pc = matrix(c(1:3, -4, -5, -6, 7:9), nrow = 3)
    ),
    list(
      alpha = list(matrix((9:1), nrow = 3), matrix(-1 * (9:1), nrow = 3), matrix((9:1), nrow = 3)),
      pc = matrix(c(9:7, -6, -5, -4, 3:1), nrow = 3)
    )
  )

  out <- unifySign(encod, ref)

  expect_equal(out, expectedOut)
})


test_that("unifySign works when there are some NULL elements", {
  ref <- list(position = c(9, 1, 5), isNegative = c(FALSE, TRUE, FALSE))

  encod <- list(
    list(
      alpha = list(matrix(1:9, nrow = 3), matrix(1:9, nrow = 3), matrix(1:9, nrow = 3)),
      pc = matrix(1:9, nrow = 3)
    ),
    NULL,
    list(
      alpha = list(matrix(-1 * (9:1), nrow = 3), matrix(-1 * (9:1), nrow = 3), matrix(-1 * (9:1), nrow = 3)),
      pc = matrix(-1 * (9:1), nrow = 3)
    )
  )

  expectedOut <- list(
    list(
      alpha = list(matrix(1:9, nrow = 3), matrix(-1 * (1:9), nrow = 3), matrix(1:9, nrow = 3)),
      pc = matrix(c(1:3, -4, -5, -6, 7:9), nrow = 3)
    ),
    NULL,
    list(
      alpha = list(matrix((9:1), nrow = 3), matrix(-1 * (9:1), nrow = 3), matrix((9:1), nrow = 3)),
      pc = matrix(c(9:7, -6, -5, -4, 3:1), nrow = 3)
    )
  )

  out <- unifySign(encod, ref)

  expect_equal(out, expectedOut)
})



test_that("compute_optimal_encoding throws error", {
  set.seed(42)
  K <- 2
  d_JK <- generate_2State(n = 10)
  d_JK2 <- cut_data(d_JK, 1)

  # create basis object
  m <- 10
  b <- create.bspline.basis(c(0, 1), nbasis = m, norder = 4)

  expect_error(
    compute_optimal_encoding(d_JK2, b, nCores = 1, computeCI = 2),
    regexp = "computeCI must be either TRUE or FALSE."
  )

  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = 0, propBootstrap = 0.5),
    regexp = "nBootstrap must be an integer > 0."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = 10.5, propBootstrap = 0.5),
    regexp = "nBootstrap must be an integer > 0."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = NA, propBootstrap = 0.5),
    regexp = "nBootstrap must be an integer > 0."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = c(), propBootstrap = 0.5),
    regexp = "nBootstrap must be an integer > 0."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = c(20, 50), propBootstrap = 0.5),
    regexp = "nBootstrap must be an integer > 0."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = NaN, propBootstrap = 0.5),
    regexp = "nBootstrap must be an integer > 0."
  )

  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = 50, propBootstrap = 0),
    regexp = "propBootstrap must be a real between 0 and 1."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = 50, propBootstrap = 1.5),
    regexp = "propBootstrap must be a real between 0 and 1."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = 50, propBootstrap = c(0.5, 0.8)),
    regexp = "propBootstrap must be a real between 0 and 1."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = 50, propBootstrap = NA),
    regexp = "propBootstrap must be a real between 0 and 1."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = 50, propBootstrap = NaN),
    regexp = "propBootstrap must be a real between 0 and 1."
  )
  expect_error(
    compute_optimal_encoding(d_JK2, b, computeCI = TRUE, nBootstrap = 50, propBootstrap = c()),
    regexp = "propBootstrap must be a real between 0 and 1."
  )
})




test_that("compute_optimal_encoding works with computeCI = TRUE", {
  skip_on_cran()
  set.seed(42)
  n <- 200
  Tmax <- 1
  K <- 2
  m <- 10
  d <- generate_2State(n)
  dT <- cut_data(d, Tmax)
  row.names(dT) <- NULL

  b <- create.bspline.basis(c(0, Tmax), nbasis = m, norder = 4)
  expect_silent(
    fmca <- compute_optimal_encoding(
      dT, b, computeCI = TRUE, nBootstrap = 50, propBootstrap = 0.5, nCores = 1, verbose = FALSE
    )
  )

  expect_type(fmca, "list")
  expect_named(
    fmca,
    c("eigenvalues", "alpha", "pc", "F", "G", "V", "basisobj", "label", "pt", "bootstrap", "varAlpha", "runTime")
  )

  ## bootstrap
  expect_length(fmca$bootstrap, 50)
  expect_named(fmca$bootstrap[[1]], c("eigenvalues", "alpha", "pc", "F", "G"))

  # eigenvalues
  expect_length(fmca$bootstrap[[1]]$eigenvalues, K * m)
  trueEigVal <- 1 / ((1:m) * (2:(m + 1)))
  expect_lte(max(abs(fmca$eigenvalues[1:m] - trueEigVal)), 0.01)

  # alpha
  expect_type(fmca$bootstrap[[1]]$alpha, "list")
  expect_length(fmca$bootstrap[[1]]$alpha, m * K)
  expect_equal(dim(fmca$bootstrap[[1]]$alpha[[1]]), c(m, K))

  # pc
  expect_equal(dim(fmca$bootstrap[[1]]$pc), c(100, m * K))

  # F
  expect_equal(dim(fmca$bootstrap[[1]]$F), c(2 * m, 2 * m))

  # G
  expect_equal(dim(fmca$bootstrap[[1]]$G), c(2 * m, 2 * m))

  # label
  expect_equal(fmca$label, data.frame(label = 0:1, code = 1:2))
})


test_that("plot.fmca works with addCI = TRUE", {
  skip_on_cran()
  set.seed(42)
  n <- 25
  Tmax <- 1
  K <- 2
  m <- 6
  d <- generate_2State(n)
  dT <- cut_data(d, Tmax)
  row.names(dT) <- NULL

  b <- create.bspline.basis(c(0, Tmax), nbasis = m, norder = 4)
  fmca <- compute_optimal_encoding(dT, b, computeCI = TRUE, nBootstrap = 25, propBootstrap = 1, nCores = 1, verbose = FALSE)

  expect_warning(plot(fmca, addCI = TRUE), regexp = NA)
  expect_warning(plot(fmca, addCI = TRUE, states = 1), regexp = NA)
  expect_warning(plot(fmca, addCI = TRUE, states = 1:3), regexp = NA) # only use correct states
  expect_warning(plot(fmca, addCI = TRUE, coeff = 5), regexp = NA)
  expect_warning(plot(fmca, addCI = TRUE, col = c("red", "blue")), regexp = NA)

  # bad parameters
  expect_error(plot(fmca, addCI = 6), regexp = "addCI must be either TRUE or FALSE.")
  expect_error(plot(fmca, addCI = TRUE, states = c("a", "b")), regexp = "No correct states given.")
  expect_error(plot(fmca, addCI = TRUE, coeff = -5), regexp = "coeff must be a positive real.")
})