Nothing
test_that("The SR loglik 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,
0.138,
0.442,
0.1951
)
pars2 <- c(100, 11, 0, 0)
loglik_shift <- DAISIE_SR_loglik_CS(pars1 = pars1,
pars2 = pars2,
datalist = Biwa_datalist,
methode = 'odeint::runge_kutta_fehlberg78')
loglik_no_shift <- DAISIE_loglik_CS(pars1 = pars1[1:5],
pars2 = pars2,
datalist = Biwa_datalist)
testthat::expect_equal(loglik_shift, loglik_no_shift, tol = 1E-3)
testthat::expect_equal(loglik_no_shift, -245.6298, 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,
-252.7293,
-Inf,
-246.9084,
-Inf,
-272.9101,
-Inf,
-247.1446
)
# 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
loglik <- rep(0,8)
for (i in 1:8) {
loglik[i] <- DAISIE_SR_loglik_CS(
pars1 = pars1mat[i, -12],
pars2 = pars2,
datalist = Macaronesia_datalist[[2]],
methode = 'odeint::runge_kutta_fehlberg78'
)
}
testthat::expect_equal(loglik, expected_loglik, tol = 1E-3)
})
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