tests/testthat/test-ignore-state.R

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

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

  ## 6.1
  mod <- rxode2({
    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))
  })

  mod <- rxode2({
    a <- 6
    b <- 0.6
    d / dt(intestine) ~ -a * intestine
    d / dt(blood) <- a * intestine - b * blood
  })

  mod.f <- rxode2({
    a <- 6
    b <- 0.6
    f(intestine) <- 1
    d / dt(intestine) ~ -a * intestine
    d / dt(blood) <- a * intestine - b * blood
  })

  mod.alag <- rxode2({
    a <- 6
    b <- 0.6
    alag(intestine) <- 0
    d / dt(intestine) ~ -a * intestine
    d / dt(blood) <- a * intestine - b * blood
  })

  mod.rate <- rxode2({
    a <- 6
    b <- 0.6
    rate(intestine) <- 2
    d / dt(intestine) ~ -a * intestine
    d / dt(blood) <- a * intestine - b * blood
  })

  mod.dur <- rxode2({
    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 <- rxode2({
    a <- 6
    b <- 0.6
    d / dt(intestine) <- -a * intestine
    d / dt(blood) ~ a * intestine - b * blood
  })

  mod.f <- rxode2({
    a <- 6
    b <- 0.6
    f(blood) <- 1
    d / dt(intestine) <- -a * intestine
    d / dt(blood) ~ a * intestine - b * blood
  })

  mod.alag <- rxode2({
    a <- 6
    b <- 0.6
    alag(blood) <- 0
    d / dt(intestine) <- -a * intestine
    d / dt(blood) ~ a * intestine - b * blood
  })

  mod.rate <- rxode2({
    a <- 6
    b <- 0.6
    rate(blood) <- 2
    d / dt(intestine) <- -a * intestine
    d / dt(blood) ~ a * intestine - b * blood
  })

  mod.dur <- rxode2({
    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)$state.ignore, c(0L, 1L))
    expect_equal(rxModelVars(mod.f)$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"))
  })

  mod.f <- rxode2({
    a <- 6
    b <- 0.6
    d / dt(intestine) <- -a * intestine
    f(blood) <- 1
    d / dt(blood) ~ a * intestine - b * blood
  })

  mod.alag <- rxode2({
    a <- 6
    b <- 0.6
    d / dt(intestine) <- -a * intestine
    alag(blood) <- 0
    d / dt(blood) ~ a * intestine - b * blood
  })

  mod.rate <- rxode2({
    a <- 6
    b <- 0.6
    d / dt(intestine) <- -a * intestine
    rate(blood) <- 2
    d / dt(blood) ~ a * intestine - b * blood
  })

  mod.dur <- rxode2({
    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"))
  })

})