tests/testthat/test-back-transform.R

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

nlmixrTest(
  {
    context("Back Transformation tests")

    test_that("PK106 mixed mu-referenced and non mu-referenced covariates", {
      PK106 <- function() {
        ini({
          ## Where initial conditions/variables are specified
          lktr <- log(1.15) # log k transit (/h)
          lcl <- log(0.135) # log Cl (L/hr)
          lv <- log(8) # log V (L)
          ALLC <- fix(0.75) # allometric exponent cl
          ALLV <- fix(1.00) # allometric exponent v
          Sex_V <- 0.1 # log Sex on v
          prop.err <- 0.15
          add.err <- 0.6
          eta.ktr ~ 0.5 # IIV ktr
          eta.cl ~ 0.1 # IIV Cl
          eta.v ~ 0.1 # IIV V
        })
        model({
          ## Allometric scaling on weight
          cl <- exp(lcl + eta.cl + ALLC * (log(WT / 70)))
          v <- exp(lv + eta.v + Sex_V * SEX + ALLV * (log(WT / 70)))
          ktr <- exp(lktr + eta.ktr)
          ## RxODE-style differential equations are supported
          d / dt(depot) <- -ktr * depot
          d / dt(gut) <- ktr * depot - ktr * gut
          d / dt(center) <- ktr * gut - (cl / v) * center
          ## Concentration is calculated
          cp <- center / v
          ## And is assumed to follow proportional and additive error
          cp ~ prop(prop.err) + add(add.err)
        })
      }
      nm <- nlmixr(PK106)
      expect_equal(nm$logThetasList, list(1:6, c(1, 2, 3)))
    })

    test_that("PK106 with non mu-referenced exp(lktr)", {
      PK106 <- function() {
        ini({
          ## Where initial conditions/variables are specified
          lktr <- log(1.15) # log k transit (/h)
          lcl <- log(0.135) # log Cl (L/hr)
          lv <- log(8) # log V (L)
          ALLC <- fix(0.75) # allometric exponent cl
          ALLV <- fix(1.00) # allometric exponent v
          Sex_V <- 0.1 # log Sex on v
          prop.err <- 0.15
          add.err <- 0.6
          eta.cl ~ 0.1 # IIV Cl
          eta.v ~ 0.1 # IIV V
        })
        model({
          ## Allometric scaling on weight
          cl <- exp(lcl + eta.cl + ALLC * (log(WT / 70)))
          v <- exp(lv + eta.v + Sex_V * SEX + ALLV * (log(WT / 70)))
          ktr <- exp(lktr)
          ## RxODE-style differential equations are supported
          d / dt(depot) <- -ktr * depot
          d / dt(gut) <- ktr * depot - ktr * gut
          d / dt(center) <- ktr * gut - (cl / v) * center
          ## Concentration is calculated
          cp <- center / v
          ## And is assumed to follow proportional and additive error
          cp ~ prop(prop.err) + add(add.err)
        })
      }
      nm <- nlmixr(PK106)
      expect_equal(nm$logThetasList, list(1:6, 1:3))
    })


    test_that("PK106 with non mu-referenced lktr", {
      PK106 <- function() {
        ini({
          # Where initial conditions/variables are specified
          lktr <- log(1.15) # log k transit (/h)
          lcl <- log(0.135) # log Cl (L/hr)
          lv <- log(8) # log V (L)
          ALLC <- fix(0.75) # allometric exponent cl
          ALLV <- fix(1.00) # allometric exponent v
          Sex_V <- 0.1 # log Sex on v
          prop.err <- 0.15
          add.err <- 0.6
          eta.cl ~ 0.1 # IIV Cl
          eta.v ~ 0.1 # IIV V
        })
        model({
          # Allometric scaling on weight
          cl <- exp(lcl + eta.cl + ALLC * (log(WT / 70)))
          v <- exp(lv + eta.v + Sex_V * SEX + ALLV * (log(WT / 70)))
          ktr <- lktr
          # RxODE-style differential equations are supported
          d / dt(depot) <- -ktr * depot
          d / dt(gut) <- ktr * depot - ktr * gut
          d / dt(center) <- ktr * gut - (cl / v) * center
          ## Concentration is calculated
          cp <- center / v
          # And is assumed to follow proportional and additive error
          cp ~ prop(prop.err) + add(add.err)
        })
      }
      nm <- nlmixr(PK106)
      expect_equal(nm$logThetasList, list(2:6, 2:3))
    })
  },
  test = "cran"
)