Nothing
test_that("log-likelihood gives expected error", {
# error for too many params
expect_error(suppressMessages(lik_profile(x = Lemna_Schmitt(),
par = Lemna_Schmitt()@param,
data = data.frame(t = c(0, 3, 5, 7, 7.01, 10, 12, 14),
obs = c(12, 38, 92, 176, 176, 627, 1283, 2640)),
output = "BM")))
# error for model
# # error because of misspecified model (not calibration set nor scenario)
# expect_error(lik_profile(x = "model",
# par = c(k_phot_max = 5.6,
# k_resp = 1.9),
# output = "BM"))
# error because data missing for EffectScenario
expect_error(suppressMessages(lik_profile(x = Lemna_Schmitt(),
output = "BM",
par = c(k_phot_max = 5.6,
k_resp = 1.9))))
# errors for pars_profile
# error because parameter vector is not a vector
expect_error(suppressMessages(lik_profile(x = Lemna_Schmitt(),
output = "BM",
data = data.frame(t = c(0, 3, 5, 7, 7.01, 10, 12, 14),
obs = c(12, 38, 92, 176, 176, 627, 1283, 2640)),
par = Lemna_Schmitt()@param[c(1,2)])))
# # error because parameter vector is not named
# expect_error(lik_profile(x = Lemna_Schmitt(),
# output = "BM",
# data = data.frame(t = c(0, 3, 5, 7, 7.01, 10, 12, 14),
# obs = c(12, 38, 92, 176, 176, 627, 1283, 2640)),
# par = as.numeric(Lemna_Schmitt()@param[c(1,2)])))
# errors for output
expect_error(suppressMessages(lik_profile(x = Lemna_Schmitt(),
output = list("BM"),
data = data.frame(t = c(0, 3, 5, 7, 7.01, 10, 12, 14),
obs = c(12, 38, 92, 176, 176, 627, 1283, 2640)),
par = c(k_phot_max = 5.6,
k_resp = 1.9))))
# errors for profile type
expect_error(suppressMessages(lik_profile(x = Lemna_Schmitt(),
output = "BM",
data = data.frame(t = c(0, 3, 5, 7, 7.01, 10, 12, 14),
obs = c(12, 38, 92, 176, 176, 627, 1283, 2640)),
par = c(k_phot_max = 5.6,
k_resp = 1.9),
type = "slow")))
})
test_that("likelihood profiling works", {
# Inputs for likelihood profiling
obs <- Schmitt2013 %>%
dplyr::filter(ID == "T0") %>%
dplyr::select(t, obs)
colnames(obs) = c("t", "BM")
params <- c(k_phot_max = 3.979200,
k_resp = 7.700779e-08)
sc <- metsulfuron %>%
set_param(params)
# Likelihood profiling
suppressMessages(
res <- lik_profile(
x = sc,
data = obs,
output = "BM",
par = params[1],
type = "fine"
)
)
# tests
expect_equal(length(res$k_phot_max$confidence_interval), 2)
expect_equal(dim(res$k_phot_max$likelihood_profile)[2], 4)
expect_equal(res$k_phot_max$orig_par_value, 3.9792)
})
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