tests/testthat/test-pipeline.R

In RxODE: Facilities for Simulating from ODE-Based Models

rxodeTest(
  {
    library(RxODE)
    context("Test pipeline style of interacting with RxODE")

    mod <- RxODE({
      eff(0) <- 1
      C2 <- centr / V2
      C3 <- peri / V3
      CL <- TCl * exp(eta.Cl) ## This is coded as a variable in the model
      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
    })

    fun <- function(type) {
      set.seed(12)
      p1 <- mod %>%
        rxParams(
          params = c(
            KA = 2.94E-01, TCl = 1.86E+01, V2 = 4.02E+01, # central
            Q = 1.05E+01, V3 = 2.97E+02, # peripheral
            Kin = 1, Kout = 1, EC50 = 200
          ),
          inits = c(eff = 1),
          omega = lotri(eta.Cl ~ 0.4^2)
        ) %>%
        et(amountUnits = "mg", timeUnits = "hours") %>%
        et(amt = 10000, cmt = 2, ii = 12, until = 48) %>%
        et(seq(0, 48, length.out = 100))
      if (type == "rxSolve") {
        p1 <- p1 %>%
          rxSolve(nSub = 30)
      } else if (type == "solve") {
        p1 <- p1 %>%
          solve(nSub = 30)
      } else if (type == "simulate") {
        p1 <- p1 %>%
          simulate(nSub = 30)
      } else if (type == "predict") {
        p1 <- p1 %>%
          predict(nSub = 30)
      }
      ##
      set.seed(12)
      p2 <- mod %>%
        et(amountUnits = "mg", timeUnits = "hours") %>%
        et(amt = 10000, cmt = 2, ii = 12, until = 48) %>%
        et(seq(0, 48, length.out = 100)) %>%
        rxParams(
          params = c(
            KA = 2.94E-01, TCl = 1.86E+01, V2 = 4.02E+01, # central
            Q = 1.05E+01, V3 = 2.97E+02, # peripheral
            Kin = 1, Kout = 1, EC50 = 200
          ),
          inits = c(eff = 1),
          omega = lotri(eta.Cl ~ 0.4^2)
        )
      if (type == "rxSolve") {
        p2 <- p2 %>%
          rxSolve(nSub = 30)
      } else if (type == "solve") {
        p2 <- p2 %>%
          solve(nSub = 30)
      } else if (type == "simulate") {
        p2 <- p2 %>%
          simulate(nSub = 30)
      } else if (type == "predict") {
        p2 <- p2 %>%
          predict(nSub = 30)
      }
      test_that(sprintf(
        "mod > et > rxParams > %s == mod > rxParams > et > %s",
        type, type
      ), {
        expect_equal(as.data.frame(p1), as.data.frame(p2))
      })
    }

    fun("rxSolve")
    fun("solve")
    fun("simulate")
    fun("predict")


    p1 <- mod %>%
      rxParams(
        params = c(
          KA = 2.94E-01, TCl = 1.86E+01, V2 = 4.02E+01, # central
          Q = 1.05E+01, V3 = 2.97E+02, # peripheral
          Kin = 1, Kout = 1, EC50 = 200
        ),
        inits = c(eff = 1),
        omega = lotri(eta.Cl ~ 0.4^2)
      ) %>%
      et(amountUnits = "mg", timeUnits = "hours") %>%
      et(amt = 10000, cmt = 2, ii = 12, until = 48) %>%
      et(seq(0, 48, length.out = 100)) %>%
      rxSolve(nSub = 4)

    ps1 <- p1 %>%
      rxParams(inits = c(eff = 2), dfSub = 4) %>%
      rxSolve(nSub = 6, nStud = 3)

    test_that("can update parameters from solve", {
      expect_true(is(ps1, "rxSolve"))
      expect_false(is.null(ps1$omegaList))
    })

    ps2 <- p1 %>%
      et(amt = 10000, cmt = 2, ii = 24, until = 48) %>%
      et(seq(0, 48, length.out = 100)) %>%
      rxSolve(nSub = 4)

    test_that("Can update event table in pipline solve", {
      expect_true(is(ps1, "rxSolve"))
    })
  },
  test = "lvl2"
)