tests/testthat/test-cov-focei.R

In nlmixr2est: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

nmTest({

  test_that("cov-focei", {

    dat <-
      warfarin %>%
      dplyr::filter(dvid == "cp")

      #### doesn't work with FOCEI ### doesn't work with SAEM with CRWES=True but does iwth CWRES=FALSE
      One.SD.ODE <- function() {
        ini({
          # Where initial conditions/variables are specified
          lcl <- log(0.135) # log Cl (L/h)
          lv <- log(8) # log V (L)
          lmtt <- log(1.1) # log MTx

          prop.err <- 0.15 # proportional error (SD/mean)
          add.err <- 0.6 # additive error (mg/L)
          eta.cl + eta.v + eta.mtt ~ c(
            0.1,
            0.001, 0.1,
            0.001, 0.001, 0.1
          )
        })
        model({
          # Where the model is specified
          cl <- exp(lcl + eta.cl)
          v <- exp(lv + eta.v)
          mtt <- exp(lmtt + eta.mtt)
          ktr <- 6 / mtt

          ## ODE example
          d / dt(depot) <- -ktr * depot
          d / dt(central) <- ktr * trans5 - (cl / v) * central
          d / dt(trans1) <- ktr * depot - ktr * trans1
          d / dt(trans2) <- ktr * trans1 - ktr * trans2
          d / dt(trans3) <- ktr * trans2 - ktr * trans3
          d / dt(trans4) <- ktr * trans3 - ktr * trans4
          d / dt(trans5) <- ktr * trans4 - ktr * trans5

          ## Concentration is calculated
          cp <- central / v
          ## And is assumed to follow proportional and additive error
          cp ~ prop(prop.err) + add(add.err)
        })
      }

      f <- suppressMessages(suppressWarnings(nlmixr(One.SD.ODE, dat, "posthoc")))

      expect_s3_class(f, "nlmixr2.posthoc")

  })

})