tests/testthat/test-ignore-state.R

In nlmixrdevelopment/RxODE: Facilities for Simulating from ODE-Based Models

rxodeTest(
  {
    context("Make sure the right state is ignored.")
    ## https://cran.r-project.org/web/packages/diffEq/vignettes/ODEinR.pdf p11

    ## 6.1
    mod <- RxODE({
      a <- 6
      b <- 0.6
      d / dt(intestine) <- -a * intestine
      d / dt(blood) <- a * intestine - b * blood
    })

    test_that("Nothing ignored", {
      expect_equal(rxModelVars(mod)$state.ignore, c(0L, 0L))
    })


    .rxWithOptions(list(RxODE.syntax.require.ode.first = FALSE), {
      mod <- RxODE({
        a <- 6
        b <- 0.6
        d / dt(intestine) ~ -a * intestine
        d / dt(blood) <- a * intestine - b * blood
      })

      mod.f <- RxODE({
        a <- 6
        b <- 0.6
        f(intestine) <- 1
        d / dt(intestine) ~ -a * intestine
        d / dt(blood) <- a * intestine - b * blood
      })

      mod.alag <- RxODE({
        a <- 6
        b <- 0.6
        alag(intestine) <- 0
        d / dt(intestine) ~ -a * intestine
        d / dt(blood) <- a * intestine - b * blood
      })

      mod.rate <- RxODE({
        a <- 6
        b <- 0.6
        rate(intestine) <- 2
        d / dt(intestine) ~ -a * intestine
        d / dt(blood) <- a * intestine - b * blood
      })


      mod.dur <- RxODE({
        a <- 6
        b <- 0.6
        dur(intestine) <- 2
        d / dt(intestine) ~ -a * intestine
        d / dt(blood) <- a * intestine - b * blood
      })

      test_that("Ignore first comparment", {
        expect_equal(rxModelVars(mod)$state.ignore, c(1L, 0L))
        expect_equal(rxModelVars(mod.f)$state.ignore, c(1L, 0L))
        expect_equal(rxModelVars(mod.alag)$state.ignore, c(1L, 0L))
        expect_equal(rxModelVars(mod.rate)$state.ignore, c(1L, 0L))
        expect_equal(rxModelVars(mod.dur)$state.ignore, c(1L, 0L))
      })

      mod <- RxODE({
        a <- 6
        b <- 0.6
        d / dt(intestine) <- -a * intestine
        d / dt(blood) ~ a * intestine - b * blood
      })

      mod.f <- RxODE({
        a <- 6
        b <- 0.6
        f(blood) <- 1
        d / dt(intestine) <- -a * intestine
        d / dt(blood) ~ a * intestine - b * blood
      })

      mod.alag <- RxODE({
        a <- 6
        b <- 0.6
        alag(blood) <- 0
        d / dt(intestine) <- -a * intestine
        d / dt(blood) ~ a * intestine - b * blood
      })

      mod.rate <- RxODE({
        a <- 6
        b <- 0.6
        rate(blood) <- 2
        d / dt(intestine) <- -a * intestine
        d / dt(blood) ~ a * intestine - b * blood
      })

      mod.dur <- RxODE({
        a <- 6
        b <- 0.6
        dur(blood) <- 2
        d / dt(intestine) <- -a * intestine
        d / dt(blood) ~ a * intestine - b * blood
      })

      test_that("Nothing ignored", {
        expect_equal(rxModelVars(mod)$state.ignore, c(0L, 1L))
        expect_equal(rxModelVars(mod)$state, c("intestine", "blood"))
        expect_equal(rxModelVars(mod.f)$state.ignore, c(1L, 0L))
        expect_equal(rxModelVars(mod.f)$state, c("blood", "intestine"))
        expect_equal(rxModelVars(mod.alag)$state.ignore, c(1L, 0L))
        expect_equal(rxModelVars(mod.alag)$state, c("blood", "intestine"))
        expect_equal(rxModelVars(mod.rate)$state.ignore, c(1L, 0L))
        expect_equal(rxModelVars(mod.rate)$state, c("blood", "intestine"))
        expect_equal(rxModelVars(mod.dur)$state.ignore, c(1L, 0L))
        expect_equal(rxModelVars(mod.dur)$state, c("blood", "intestine"))
      })

      mod.f <- RxODE({
        a <- 6
        b <- 0.6
        d / dt(intestine) <- -a * intestine
        f(blood) <- 1
        d / dt(blood) ~ a * intestine - b * blood
      })

      mod.alag <- RxODE({
        a <- 6
        b <- 0.6
        d / dt(intestine) <- -a * intestine
        alag(blood) <- 0
        d / dt(blood) ~ a * intestine - b * blood
      })

      mod.rate <- RxODE({
        a <- 6
        b <- 0.6
        d / dt(intestine) <- -a * intestine
        rate(blood) <- 2
        d / dt(blood) ~ a * intestine - b * blood
      })

      mod.dur <- RxODE({
        a <- 6
        b <- 0.6
        d / dt(intestine) <- -a * intestine
        dur(blood) <- 2
        d / dt(blood) ~ a * intestine - b * blood
      })


      test_that("Ignore Compartment #2", {
        expect_equal(rxModelVars(mod)$state.ignore, c(0L, 1L))
        expect_equal(rxModelVars(mod)$state, c("intestine", "blood"))
        expect_equal(rxModelVars(mod.f)$state.ignore, c(0L, 1L))
        expect_equal(rxModelVars(mod.f)$state, c("intestine", "blood"))
        expect_equal(rxModelVars(mod.alag)$state.ignore, c(0L, 1L))
        expect_equal(rxModelVars(mod.alag)$state, c("intestine", "blood"))
        expect_equal(rxModelVars(mod.rate)$state.ignore, c(0L, 1L))
        expect_equal(rxModelVars(mod.rate)$state, c("intestine", "blood"))
        expect_equal(rxModelVars(mod.dur)$state.ignore, c(0L, 1L))
        expect_equal(rxModelVars(mod.dur)$state, c("intestine", "blood"))
      })
    })



    .rxWithOptions(list(RxODE.syntax.require.ode.first = TRUE), {
      test_that("errors usually occur", {
        expect_error(RxODE({
          a <- 6
          b <- 0.6
          d / dt(intestine) <- -a * intestine
          alag(blood) <- 0
          d / dt(blood) ~ a * intestine - b * blood
        }))

        expect_error(RxODE({
          a <- 6
          b <- 0.6
          d / dt(intestine) <- -a * intestine
          rate(blood) <- 2
          d / dt(blood) ~ a * intestine - b * blood
        }))

        expect_error(RxODE({
          a <- 6
          b <- 0.6
          d / dt(intestine) <- -a * intestine
          dur(blood) <- 2
          d / dt(blood) ~ a * intestine - b * blood
        }))

        expect_error(RxODE({
          a <- 6
          b <- 0.6
          f(blood) <- 1
          d / dt(intestine) <- -a * intestine
          d / dt(blood) ~ a * intestine - b * blood
        }))

        expect_error(RxODE({
          a <- 6
          b <- 0.6
          alag(blood) <- 0
          d / dt(intestine) <- -a * intestine
          d / dt(blood) ~ a * intestine - b * blood
        }))

        expect_error(RxODE({
          a <- 6
          b <- 0.6
          rate(blood) <- 2
          d / dt(intestine) <- -a * intestine
          d / dt(blood) ~ a * intestine - b * blood
        }))

        expect_error(RxODE({
          a <- 6
          b <- 0.6
          dur(blood) <- 2
          d / dt(intestine) <- -a * intestine
          d / dt(blood) ~ a * intestine - b * blood
        }))
      })
    })
  },
  test = "lvl2"
)