tests/testthat/test-cov-focei.R

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

nlmixrTest(
  {
    context("full cov FOCEi (posthoc surrogate)")

    library(dplyr)

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

    #### 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 <- suppressWarnings(nlmixr(One.SD.ODE, dat, "posthoc"))
    expect_true(inherits(f, "nlmixrPosthoc"))
  },
  test = "focei"
)