tests/testthat/test-dollar-names.R

In nlmixr2/rxode2: Facilities for Simulating from ODE-Based Models

rxTest({
  test_that(".DollarNames", {

    mod2 <- rxode2({
      ## the order of variables do not matter, the type of compartmental
      ## model is determined by the parameters specified.
      CL ~ TCL * exp(eta.Cl)
      C2 ~ linCmt(KA, CL, V2, Q, V3)
      eff(0) <- 1 ## This specifies that the effect compartment starts at 1.
      d / dt(eff) ~ Kin - Kout * (1 - C2 / (EC50 + C2)) * eff
      ##
      resp <- eff + err1
      pk <- C2 * exp(err2)
    })

    ev <- eventTable(amount.units = "mg", time.units = "hours") %>%
      add.dosing(dose = 10000, nbr.doses = 10, dosing.interval = 12, dosing.to = 2) %>%
      add.dosing(dose = 20000, nbr.doses = 5, start.time = 120, dosing.interval = 24, dosing.to = 2) %>%
      add.sampling(0:240)

    expect_equal(
      .DollarNames(ev, ""),
      c(
        "canResize", "IDs", "show", "ndose", "nobs", "expand", "getSampling",
        "get.sampling", "getDosing", "get.dosing", "get.nobs", "get.obs.rec",
        "getEventTable", "get.EventTable", "copy", "importEventTable",
        "import.EventTable", "simulate", "clearDosing", "clear_dosing",
        "clear.dosing", "clearSampling", "clear_sampling", "clear.sampling",
        "addSampling", "add_sampling", "add.sampling", "addDosing", "add_dosing",
        "add.dosing", "get_units", "getUnits", "get.units", "units",
        "dur", "ss", "evid", "addl", "ii", "rate", "amt", "cmt", "high",
        "time", "low", "id", "env"
      )
    )

    p <- data.frame(a = 6, b = seq(0.4, 0.9, length.out = 4))

    ## "Study" Differences
    thetaMat <- diag(3) * 0.01
    dimnames(thetaMat) <- list(NULL, c("KA", "TCL", "V2"))

    sigma <- diag(2) * 0.05
    dimnames(sigma) <- list(c("err1", "err2"), c("err1", "err2"))


    pk4 <-
      suppressWarnings(rxSolve(
        mod2,
        c(
          KA = 2.94E-01, TCL = 1.86E+01, V2 = 4.02E+01, Q = 1.05E+01, V3 = 2.97E+02,
          Kin = 1, Kout = 1, EC50 = 200
        ),
        omega = matrix(0.2, dimnames = list("eta.Cl", "eta.Cl")), dfSub = 100, dfObs = 100,
        nSub = 4, nStud = 8, thetaMat = thetaMat, sigma = sigma, ev, cores = 1
      ))
    expect_equal(sort(.DollarNames(pk4, "")), sort(c(
      "pk", "resp", "time", "sim.id", "EC50", "Kout", "Kin", "KA",
      "V3", "Q", "V2", "eta.Cl", "TCL", "sim.id", "eff0", "units",
      "nobs", "import.EventTable", "get.units", "get.sampling", "get.obs.rec",
      "get.nobs", "get.dosing", "get.EventTable", "dll", "counts",
      "clear.sampling", "clear.dosing", "add.sampling", "add.dosing",
      "env", "model", "params", "inits", "t", "rxode2", "thetaMat",
      "sigmaList", "omegaList"
    )))


    pk4 <-
      suppressWarnings(rxSolve(
        mod2,
        c(
          KA = 2.94E-01, TCL = 1.86E+01, V2 = 4.02E+01, Q = 1.05E+01, V3 = 2.97E+02,
          Kin = 1, Kout = 1, EC50 = 200
        ),
        omega = matrix(0.2, dimnames = list("eta.Cl", "eta.Cl")), dfSub = 100,
        nSub = 4, nStud = 8, thetaMat = thetaMat, sigma = sigma, ev, cores = 1
      ))

    expect_equal(sort(.DollarNames(pk4, "")), sort(c(
      "pk", "resp", "time", "sim.id", "EC50", "Kout", "Kin", "KA",
      "V3", "Q", "V2", "eta.Cl", "TCL", "sim.id", "eff0", "units",
      "nobs", "import.EventTable", "get.units", "get.sampling", "get.obs.rec",
      "get.nobs", "get.dosing", "get.EventTable", "dll", "counts",
      "clear.sampling", "clear.dosing", "add.sampling", "add.dosing",
      "env", "model", "params", "inits", "t", "rxode2", "thetaMat",
      "omegaList")
    ))

    pk4 <-
      suppressWarnings(rxSolve(
        mod2,
        c(
          KA = 2.94E-01, TCL = 1.86E+01, V2 = 4.02E+01, Q = 1.05E+01, V3 = 2.97E+02,
          Kin = 1, Kout = 1, EC50 = 200
        ),
        omega = matrix(0.2, dimnames = list("eta.Cl", "eta.Cl")),
        nSub = 4, nStud = 8, thetaMat = thetaMat, sigma = sigma, ev, cores = 1
      ))

    expect_equal(sort(.DollarNames(pk4, "")), sort(c(
      "pk", "resp", "time", "sim.id", "EC50", "Kout", "Kin", "KA",
      "V3", "Q", "V2", "eta.Cl", "TCL", "sim.id", "eff0", "units",
      "nobs", "import.EventTable", "get.units", "get.sampling", "get.obs.rec",
      "get.nobs", "get.dosing", "get.EventTable", "dll", "counts",
      "clear.sampling", "clear.dosing", "add.sampling", "add.dosing",
      "env", "model", "params", "inits", "t", "rxode2", "thetaMat"
    )))

    pk4 <-
      suppressWarnings(rxSolve(
        mod2,
        c(
          KA = 2.94E-01, TCL = 1.86E+01, V2 = 4.02E+01, Q = 1.05E+01, V3 = 2.97E+02,
          Kin = 1, Kout = 1, EC50 = 200
        ),
        omega = matrix(0.2, dimnames = list("eta.Cl", "eta.Cl")),
        nSub = 4, nStud = 8, sigma = sigma, ev, cores = 1
      ))

    expect_equal(sort(.DollarNames(pk4, "")), sort(c(
      "pk", "resp", "time", "sim.id", "EC50", "Kout", "Kin", "KA",
      "V3", "Q", "V2", "eta.Cl", "TCL", "sim.id", "eff0", "units",
      "nobs", "import.EventTable", "get.units", "get.sampling", "get.obs.rec",
      "get.nobs", "get.dosing", "get.EventTable", "dll", "counts",
      "clear.sampling", "clear.dosing", "add.sampling", "add.dosing",
      "env", "model", "params", "inits", "t", "rxode2"
    )))
  })
})