Nothing
library(testthat)
context("Test all methods that may be applied on compartments")
test_that("add method can't be used to add a compartment (add an ODE instead)", {
model <- model_suite$testing$nonmem$advan4_trans4
expect_error(model %>% add(Compartment(index=model@compartments %>% length() + 1, name="OUTPUT2")),
regexp="No default function is provided")
})
test_that("contains method works with compartments", {
model <- model_suite$testing$nonmem$advan4_trans4
expect_true(model %>% contains(Compartment(1)))
expect_false(model %>% contains(Compartment(5)))
})
test_that("delete method can't be used to delete a compartment (at least for now)", {
model <- model_suite$testing$nonmem$advan4_trans4
expect_error(model %>% delete(Compartment(index=1)), regexp="No default function is provided")
})
test_that("find method may return a compartment", {
# Example 1
model <- model_suite$testing$nonmem$advan4_trans4
compartment <- model %>% find(Compartment(index=2))
expect_equal(compartment@index, 2)
expect_equal(compartment@name, "CENTRAL")
# Example 2
model <- model_suite$testing$nonmem$advan1_trans1
compartments <- model@compartments
compartment1 <- compartments %>% find(Compartment(index=1))
compartment2 <- compartments %>% find(Compartment(index=2))
expect_equal(compartments %>% length(), 2)
expect_equal(compartment1@name, "CENTRAL")
expect_equal(compartment2@name, "OUTPUT")
})
test_that("getCompartmentIndex method works as expected", {
model <- model_suite$testing$nonmem$advan4_trans4
index_depot <- model %>% getCompartmentIndex("DEPOT")
index_central <- model %>% getCompartmentIndex("CENTRAL")
expect_equal(index_depot, 1)
expect_equal(index_central, 2)
expect_error(model %>% getCompartmentIndex("XX"), regexp="Compartment XX not found")
})
test_that("replace method may be used to adapt the name of a compartment", {
model <- model_suite$testing$nonmem$advan4_trans4 %>% add(Bioavailability(1, "0.75"))
# Replace compartment and ODE
model <- model %>% replace(Compartment(1, "ABS")) %>%
delete(Ode("A_DEPOT")) %>%
add(Ode("A_ABS", "-KA*ABS"), Position(Ode("A_CENTRAL"), after=FALSE))
# Replace occurrence in CENTRAL compartment
central <- model %>% find(Ode("A_CENTRAL"))
central@rhs <- gsub(pattern="A_DEPOT", replacement="A_ABS", x=central@rhs)
model <- model %>% replace(central)
# Check compartment has been correctly replaced
compartment <- model %>% find(Compartment(1))
expect_equal(compartment@name, "ABS")
# Check 2 first ODE's
abs <- model %>% find(Ode("A_ABS"))
central <- model %>% find(Ode("A_CENTRAL"))
expect_equal(abs@rhs, "-KA*ABS")
expect_equal(central@rhs, "KA*A_ABS + Q*A_PERIPHERAL/V3 + (-CL/V2 - Q/V2)*A_CENTRAL")
# Check bioavailability equation will be adapted too
expect_equal(model %>% find(Bioavailability(1)) %>% toString(model=model, dest="campsis"), "A_ABS=0.75")
})
test_that("toString method works as expected on compartment", {
cmt <- Compartment(index=1)
expect_equal(cmt %>% toString(), "A_1")
cmt <- Compartment(index=1, name="CENTRAL")
expect_equal(cmt %>% toString(), "A_CENTRAL")
})
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