tests/testthat/test-multi.R

In RxODE: Facilities for Simulating from ODE-Based Models

## (Regression) test 3 multiple instances of RxODE objects to ensure
## C symbols and operations don't conflict.
rxodeTest(
  {
    library(RxODE)
    context("Make sure C operations and symbols don't conflict")

    test.dir <- tempfile("Rxmult-")

    ## RxODE instance 1
    m1 <-
      RxODE(
        model = "
         C2 = centr/V2;
         C3 = peri/V3;
         d/dt(depot) =-KA*depot;
         d/dt(centr) = KA*depot - CL*C2 - Q*C2 + Q*C3;
         d/dt(peri)  =                    Q*C2 - Q*C3;
         d/dt(eff)  = Kin - Kout*(1-C2/(EC50+C2))*eff;",
        modName = "inst1",
        wd = test.dir
      )

    test_that("RxODE instance 1 is created", {
      expect_equal(class(m1), "RxODE")
    })

    et1 <- eventTable(amount.units = "ug", time.units = "hours")
    et1$add.dosing(dose = 10000, nbr.doses = 5, dosing.interval = 24)
    et1$add.sampling(0:24)
    et1$add.sampling(seq(from = 24 + 8, to = 5 * 24, by = 8))


    test_that("RxODE event table 1 was created", {
      expect_true(inherits(et1, "rxEt"))
      expect_equal(et1$get.nobs(), 37)
      expect_equal(length(et1$get.dosing()[, 1]), 1)
    })

    o1.first <- NULL
    test_that("warning", {
      expect_warning({
        o1.first <<- m1$solve(
          params = c(
            KA = .291, CL = 18.6, V2 = 40.2, Q = 10.5, V3 = 297.0,
            Kin = 1.0, Kout = 1.0, EC50 = 200.0
          ),
          events = et1,
          inits = c(0, 0, 0, 1)
        )
      })
    })


    test_that("RxODE event 1 solved.", {
      expect_equal(length(o1.first[, 1]), et1$get.nobs())
    })

    ## RxODE instance 2 (complete example)
    m2 <-
      RxODE(
        model = "d/dt(y) = r * y * (1.0 - y/K);",
        modName = "inst2",
        wd = test.dir
      )

    test_that("RxODE instance 2 was created", {
      expect_equal(class(m1), "RxODE")
    })

    et2 <- eventTable(time.units = NA)
    et2$add.sampling(seq(from = 0, to = 20, by = 0.2))

    test_that("RxODE event table 2 was created", {
      expect_true(inherits(et1, "rxEt"))
      expect_equal(et2$get.nobs(), 101)
      expect_equal(length(et2$get.dosing()[, 1]), 0)
    })

    o2.s <-
      m2$solve(params = c(r = 1, K = 10), events = et2, inits = c(y = 2), method = "lsoda")

    test_that("RxODE instance 2 was solved", {
      expect_equal(length(o2.s[, 1]), et2$get.nobs())
    })

    ## RxODE instance 3 (complete example)
    m3 <-
      RxODE(
        model = "
         d/dt(X) = a*X + Y*Z;
         d/dt(Y) = b*(Y - Z);
         d/dt(Z) = -X*Y + c*Y - Z;",
        modName = "inst3",
        wd = tempdir() # don't pollute "./tests"
      )

    test_that("RxODE instance 3 is created", {
      expect_equal(class(m3), "RxODE")
    })

    et3 <- eventTable() # default time units
    et3$add.sampling(seq(from = 0, to = 100, by = 0.01))

    test_that("RxODE instance 3 event table is created", {
      expect_true(inherits(et3, "rxEt"))
      expect_equal(et3$get.nobs(), 10001)
    })

    o3 <-
      m3$solve(
        params = c(a = -8 / 3, b = -10, c = 28),
        events = et3,
        inits = c(X = 1, Y = 1, Z = 1)
      )

    test_that("RxODE instance 3 was solved", {
      expect_equal(et3$get.nobs(), length(o3[, 1]))
    })

    ## Now go back to model 1 for (same) integration
    o1.second <- NULL
    test_that("Warning when inits is unnamed", {
      expect_warning({
        o1.second <<- m1$solve(
          params = c(
            KA = .291, CL = 18.6, V2 = 40.2, Q = 10.5, V3 = 297.0,
            Kin = 1.0, Kout = 1.0, EC50 = 200.0
          ),
          events = et1,
          inits = c(0, 0, 0, 1)
        )
      })
    })

    test_that("Second solve of model 1 gives the same results", {
      expect_equal(o1.first, o1.second)
    })

    ## and go back to model 2 for different ode solver
    o2.ns <-
      m2$solve(params = c(r = 1, K = 10), events = et2, inits = c(y = 12), method = "dop853")

    test_that("Differnt solve of Model 1 still works", {
      expect_equal(length(o2.ns[, 1]), length(o2.s[, 1]))
    })


    ## Inspect the internal compilation manager in each of the RxODE objects
    prt <-
      function(obj, expect) {
        ## cat(
        ##     sprintf('Model name: %s\nDyn lib: %s\node_solver symbol: %s\n',
        ##             obj$modName, obj$cmpMgr$dllfile, obj$cmpMgr$ode_solver
        ##             ))
        expect_equal(obj$modName, expect)
        expect_match(obj$cmpMgr$dllfile, expect)
      }

    test_that("Compilation manager elements make sense.", {
      prt(m1, "inst1")
      prt(m2, "inst2")
      prt(m3, "inst3")
    })



    ## Unload object code (this is platform-dependent, as documented in the
    ## "Note" section of help("dyn.load"). Remove test.dir.
    test_that("Unloading will allow removal of directory", {
      m1$dynUnload()
      m2$dynUnload()
      m3$dynUnload()
      .ret <- unlink(test.dir, recursive = TRUE)
      skip_on_os("windows")
      expect_equal(.ret, 0) # 0==success, 1==failed
    })
  },
  silent = TRUE,
  test = "lvl2"
)