tests/testthat/test-ui-bounds-err.R

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

rxTest({
  # Make sure there are lower bounds for appropriate errors

  test_that("add/prop have appropriate errors", {

    run7.mod <- function() {
      ini({
        tcl <- log(0.008) ; label("typical value of clearance")
        tv <- log(0.6) ; label("typical value of volume")
        all.cl <- 1 ; label("allometric exponent on CL")
        eta.cl + eta.v ~ c(
          1,
          0.01, 1
        ) ; label("interindividual variability on clearance and volume")
        add.err <- 0.1 ; label("residual variability")
        prop.err <- 0.1
      })
      model({
        cl <- exp(tcl + all.cl * log_allo_wt + eta.cl) # individual value of clearance
        v <- exp(tv + eta.v) # individual value of volume
        ke <- cl / v # elimination rate constant
        d / dt(A1) <- -ke * A1 # model differential equation
        cp <- A1 / v # concentration in plasma
        cp ~ add(add.err) + prop(prop.err) # define error model
      })
    }

    f <- rxode2(run7.mod)
    expect_equal(f$iniDf$lower, c(-Inf, -Inf, -Inf, 0, 0, -Inf, -Inf, -Inf))

    run7.mod <- function() {
      ini({
        tcl <- log(0.008) ; label("typical value of clearance")
        tv <- log(0.6) ; label("typical value of volume")
        all.cl <- 1 ; label("allometric exponent on CL")
        eta.cl + eta.v ~ c(
          1,
          0.01, 1
        ) ; label("interindividual variability on clearance and volume")
        add.err <- c(0.001, 0.1) ; label("residual variability")
        prop.err <- c(0.001, 0.1)
      })
      model({
        cl <- exp(tcl + all.cl * log_allo_wt + eta.cl) # individual value of clearance
        v <- exp(tv + eta.v) # individual value of volume
        ke <- cl / v # elimination rate constant
        d / dt(A1) <- -ke * A1 # model differential equation
        cp <- A1 / v # concentration in plasma
        cp ~ add(add.err) + prop(prop.err) # define error model
      })
    }
    f <- rxode2(run7.mod)
    expect_equal(f$iniDf$lower, c(-Inf, -Inf, -Inf, 0.001, 0.001, -Inf, -Inf, -Inf))

    run7.mod <- function() {
      ini({
        tcl <- log(0.008) ; label("typical value of clearance")
        tv <- log(0.6) ; label("typical value of volume")
        all.cl <- 1 ; label("allometric exponent on CL")
        eta.cl + eta.v ~ c(
          1,
          0.01, 1
        ) ; label("interindividual variability on clearance and volume")
        add.err <- -1 ; label("residual variability")
        prop.err <- c(0.001, 0.1)
      })
      model({
        cl <- exp(tcl + all.cl * log_allo_wt + eta.cl) # individual value of clearance
        v <- exp(tv + eta.v) # individual value of volume
        ke <- cl / v # elimination rate constant
        d / dt(A1) <- -ke * A1 # model differential equation
        cp <- A1 / v # concentration in plasma
        cp ~ add(add.err) + prop(prop.err) # define error model
      })
    }

    expect_error(rxode2(run7.mod))


    run7.mod <- function() {
      ini({
        tcl <- log(0.008) ; label("typical value of clearance")
        tv <- log(0.6) ; label("typical value of volume")
        all.cl <- 1 ; label("allometric exponent on CL")
        eta.cl + eta.v ~ c(
          1,
          0.01, 1
        ) ; label("interindividual variability on clearance and volume")
        add.err <- 2 ; label("residual variability")
      })
      model({
        cl <- exp(tcl + all.cl * log_allo_wt + eta.cl) # individual value of clearance
        v <- exp(tv + eta.v) # individual value of volume
        ke <- cl / v # elimination rate constant
        d / dt(A1) <- -ke * A1 # model differential equation
        cp <- A1 / v # concentration in plasma
        cp ~ bern(add.err)  # define error model
      })
    }
    expect_error(rxode2(run7.mod))

    run7.mod <- function() {
      ini({
        tcl <- log(0.008) ; label("typical value of clearance")
        tv <- log(0.6) ; label("typical value of volume")
        all.cl <- 1 ; label("allometric exponent on CL")
        eta.cl + eta.v ~ c(
          1,
          0.01, 1
        ) ; label("interindividual variability on clearance and volume")
        add.err <- c(-1, 0.5, 1) ; label("residual variability")
      })
      model({
        cl <- exp(tcl + all.cl * log_allo_wt + eta.cl) # individual value of clearance
        v <- exp(tv + eta.v) # individual value of volume
        ke <- cl / v # elimination rate constant
        d / dt(A1) <- -ke * A1 # model differential equation
        cp <- A1 / v # concentration in plasma
        cp ~ bern(add.err)  # define error model
      })
    }

    expect_warning(rxode2(run7.mod), NA)

    run7.mod <- function() {
      ini({
        tcl <- log(0.008) ; label("typical value of clearance")
        tv <- log(0.6) ; label("typical value of volume")
        all.cl <- 1 ; label("allometric exponent on CL")
        eta.cl + eta.v ~ c(
          1,
          0.01, 1
        ) ; label("interindividual variability on clearance and volume")
        add.err <- c(0, 0.5, 1) ; label("residual variability")
      })
      model({
        cl <- exp(tcl + all.cl * log_allo_wt + eta.cl) # individual value of clearance
        v <- exp(tv + eta.v) # individual value of volume
        ke <- cl / v # elimination rate constant
        d / dt(A1) <- -ke * A1 # model differential equation
        cp <- A1 / v # concentration in plasma
        cp ~ bern(add.err)  # define error model
      })
    }

    expect_warning(rxode2(run7.mod), NA)

  })
})