context("test_secsse_sim")

test_that("test secsse_sim", {
  testthat::skip_on_cran()

  parenthesis <- "(((6:0.2547423371,(1:0.0496153503,4:0.0496153503):0.2051269868):0.1306304758,(9:0.2124135406,5:0.2124135406):0.1729592723):1.151205247,(((7:0.009347664296,3:0.009347664296):0.2101416075,10:0.2194892718):0.1035186448,(2:0.2575886319,8:0.2575886319):0.06541928469):1.213570144);" # nolint
  phylotree <- ape::read.tree(file = "", parenthesis)
  traits <- c(2, 0, 1, 0, 2, 0, 1, 2, 2, 0)
  num_concealed_states <- 3
  idparslist <- cla_id_paramPos(traits, num_concealed_states)
  idparslist$lambdas[2, ] <- rep(1, 9)
  idparslist[[2]][] <- 4
  masterBlock <- matrix(5, ncol = 3, nrow = 3, byrow = TRUE)
  diag(masterBlock) <- NA
  diff.conceal <- FALSE
  idparslist[[3]] <- q_doubletrans(traits, masterBlock, diff.conceal)
  testthat::expect_output(
    startingpoint <- DDD::bd_ML(brts = ape::branching.times(phylotree))
  )
  intGuessLamba <- startingpoint$lambda0
  intGuessMu <- startingpoint$mu0
  idparsopt <- c(1)
  initparsopt <- c(rep(intGuessLamba, 1))
  idparsfix <- c(0, 4, 5)
  parsfix <- c(0, 0, 0.01)
  tol <- c(1e-04, 1e-05, 1e-07)
  maxiter <- 1000 * round((1.25)^length(idparsopt))
  optimmethod <- "subplex"
  cond <- "proper_cond"
  root_state_weight <- "proper_weights"
  sampling_fraction <- c(1, 1, 1)

  testthat::expect_warning(
  model_R <- secsse::cla_secsse_ml(
    phylotree,
    traits,
    num_concealed_states,
    idparslist,
    idparsopt,
    initparsopt,
    idparsfix,
    parsfix,
    cond,
    root_state_weight,
    sampling_fraction,
    tol,
    maxiter,
    optimmethod,
    num_cycles = 1,
    verbose = FALSE)
  )

  qs <- model_R$MLpars[[3]]
  diag(qs) <- 0

  lambdas <- model_R$MLpars[[1]]
  mus <- model_R$MLpars[[2]]
  maxSpec <- 10000
  num_repl <- 100

  max_time <- 1

  tree1 <- secsse::secsse_sim(lambdas = lambdas,
                             mus = mus,
                             qs = qs,
                             num_concealed_states = num_concealed_states,
                             crown_age = max_time,
                             maxSpec = maxSpec,
                             conditioning = "obs_states")

  all_obs_present <- c(0, 1, 2) %in% tree1$obs_traits
  testthat::expect_equal(sum(all_obs_present), 3)

  tree2 <- secsse::secsse_sim(lambdas = lambdas,
                             mus = mus,
                             qs = qs,
                             num_concealed_states = num_concealed_states,
                             crown_age = max_time,
                             maxSpec = maxSpec,
                             conditioning = "true_states")

  all_obs_present <- names(mus) %in% tree2$true_traits
  testthat::expect_equal(sum(all_obs_present), 9)

  if (requireNamespace("ape")) {
    testthat::expect_equal(max(ape::branching.times(tree1$phy)), 1)
  }
})