tests/testthat/test-DAISIE_SR_loglik.R

In xieshu95/DAISIE_new: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

context("DAISIE_SR_loglik")

test_that("The SR simulation and inference code works", {
  Biwa_datalist <- NULL
  rm(Biwa_datalist)
  utils::data(Biwa_datalist, package = "DAISIE")
  pars1 <- c(
    0.077,
    0.956,
    Inf,
    0.138,
    0.442,
    0.077,
    0.956,
    Inf,
    0.655,
    0.442,
    0.1951
  )
  pars2 <- c(100, 11, 0, 0)
  loglik <- DAISIE_SR_loglik_CS(pars1 = pars1,
                                pars2 = pars2,
                                datalist = Biwa_datalist)
  testthat::expect_equal(loglik, -232.0618, tol = 1E-3)

  Macaronesia_datalist <- NULL
  rm(Macaronesia_datalist)
  utils::data(Macaronesia_datalist, package = "DAISIE")
  pars1 <- c(
    0.1,
    1.1,
    10,
    0.6,
    0.05,
    0.1,
    1.1,
    10,
    0.6,
    0.05,
    7
  )
  pars1mat <- matrix(pars1, nrow = 8, ncol = 11, byrow = T)
  expected_loglik <- c(
    -Inf,
    -266.9125,
    -Inf,
    -262.7665,
    -Inf,
    -291.6965,
    -Inf,
    -261.9222
  )
  # No shift in cladogenesis rate older before
  # colonization of diversifying lineages
  pars1mat[1, 1] <- 0.01; pars1mat[1, 6] <- 0.3
  pars1mat[2, 1] <- 0.01; pars1mat[2, 6] <- 0.3; pars1mat[2, 11] <- 2.1
  # No shift in extinction rate older than known ages
  pars1mat[3, 2] <- 0.1; pars1mat[3, 11] <- 12
  pars1mat[4, 2] <- 0.1;
  # No shift in colonization rate older than known ages
  pars1mat[5, 4] <- 0.1; pars1mat[5, 9] <- 1.5; pars1mat[5, 11] <- 10
  pars1mat[6, 4] <- 0.1; pars1mat[6, 9] <- 0.8; pars1mat[6, 11] <- 7
  # No shift in anagenetic rate older than any known non-endemic
  pars1mat[7, 5] <- 0.01; pars1mat[7, 10] <- 0.1;
  pars1mat[8, 5] <- 0.01; pars1mat[8, 10] <- 0.1; pars1mat[8, 11] <- 2.9
  for (i in 1:8) {
    loglik <- DAISIE_SR_loglik_CS(
      pars1 = pars1mat[i, -12],
      pars2 = pars2,
      datalist = Macaronesia_datalist[[2]]
    )
    testthat::expect_equal(loglik, expected_loglik[i], tol = 1E-3)
  }
})