tests/testthat/test-issue-164.R

In nlmixrdevelopment/nlmixr: Nonlinear Mixed Effects Models in Population PK/PD

nlmixrTest(
  {
    context("Make sure there are lower bounds for appropriate errors")
    test_that("add/prop have appropriate errors", {
      RxODE::rxClean()

      run7.mod <- function() {
        ini({
          tcl <- log(0.008) # typical value of clearance
          tv <- log(0.6) # typical value of volume
          all.cl <- 1 # allometric exponent on CL
          eta.cl + eta.v ~ c(
            1,
            0.01, 1
          )
          # interindividual variability on clearance and volume
          add.err <- 0.1 # 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 <- nlmixr(run7.mod)
      expect_equal(f$ini$lower, c(-Inf, -Inf, -Inf, -Inf, -Inf, -Inf, 0, 0))
      run7.mod <- function() {
        ini({
          tcl <- log(0.008) # typical value of clearance
          tv <- log(0.6) # typical value of volume
          all.cl <- 1 # allometric exponent on CL
          eta.cl + eta.v ~ c(
            1,
            0.01, 1
          )
          # interindividual variability on clearance and volume
          add.err <- c(0.001, 0.1) # 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 <- nlmixr(run7.mod)
      expect_equal(f$ini$lower, c(-Inf, -Inf, -Inf, -Inf, -Inf, -Inf, 0.001, 0.001))

      run7.mod <- function() {
        ini({
          tcl <- log(0.008) # typical value of clearance
          tv <- log(0.6) # typical value of volume
          all.cl <- 1 # allometric exponent on CL
          eta.cl + eta.v ~ c(
            1,
            0.01, 1
          )
          # interindividual variability on clearance and volume
          add.err <- -1 # 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(nlmixr(run7.mod))
    })
  },
  test = "cran"
)