tests/testthat/test-plots-multiple-endpoints.R

In nlmixr2plot: Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions

test_that("multiple endpoint plots", {
  skip_on_cran()

  pk.turnover.emax3 <- function() {
    ini({
      tktr <- log(1)
      tka <- log(1)
      tcl <- log(0.1)
      tv <- log(10)

      eta.ktr ~ 1
      eta.ka ~ 1
      eta.cl ~ 2
      eta.v ~ 1
      prop.err <- 0.1
      pkadd.err <- 0.1

      temax <- logit(0.8)
      tec50 <- log(0.5)
      tkout <- log(0.05)
      te0 <- log(100)

      eta.emax ~ .5
      eta.ec50  ~ .5
      eta.kout ~ .5
      eta.e0 ~ .5

      pdadd.err <- 10
    })
    model({
      ktr <- exp(tktr + eta.ktr)
      ka <- exp(tka + eta.ka)
      cl <- exp(tcl + eta.cl)
      v <- exp(tv + eta.v)
      emax = expit(temax+eta.emax)
      ec50 =  exp(tec50 + eta.ec50)
      kout = exp(tkout + eta.kout)
      e0 = exp(te0 + eta.e0)

      DCP = center/v
      PD=1-emax*DCP/(ec50+DCP)

      effect(0) = e0
      kin = e0*kout

      d/dt(depot) = -ktr * depot
      d/dt(gut) =  ktr * depot -ka * gut
      d/dt(center) =  ka * gut - cl / v * center
      d/dt(effect) = kin*PD -kout*effect

      cp = center / v
      cp ~ prop(prop.err) + add(pkadd.err)
      effect ~ add(pdadd.err) | pca
    })
  }

  suppressMessages(
    fit <-
      nlmixr2est::nlmixr(
        pk.turnover.emax3,
        nlmixr2data::warfarin,
        est = "saem",
        control=nlmixr2est::saemControl(print=0, nBurn = 10, nEm = 20),
        table=list(cwres=TRUE, npde=TRUE)
      )
  )

  apo <- nlmixr2est::augPred(fit)
  expect_error(plot(apo), NA)
  expect_error(vpcPlot(fit, n = 10), NA)
  expect_error(vpcPlot(fit, pred_corr=TRUE, n = 10), NA)

  suppressWarnings(
    expect_error(plot(fit), NA)
  )
  suppressWarnings(
    expect_named(plot(fit))
  )
  expect_error(traceplot(fit), NA)

  #vdiffr::expect_doppelganger("vpc plot", vp)
  #vdiffr::expect_doppelganger("vpc pred_corr plot", vp2)
  #vdiffr::expect_doppelganger("traceplot", tp)

  #for (i in seq_along(ap)) {
  #    vdiffr::expect_doppelganger(sprintf("augPred %03d", i), ap[[i]])
  #}

  #for (i in seq_along(gof)) {
  #    vdiffr::expect_doppelganger(sprintf("gof %03d", i), gof[[i]])
  #}

})