tests/testthat/test-focei-cens.R

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

nlmixrTest(
  {
    context("M2 -- all observations")

    .nlmixr <- function(...) {
      try(suppressWarnings(nlmixr(...)))
    }

    dat <- Wang2007
    dat$DV <- dat$Y # Add the required DV data item

    f <- function() {
      ini({
        tvK <- 0.5 # Typical Value of K
        bsvK ~ 0.04 # Between Subject Variance of K
        prop.sd <- sqrt(0.1)
      })
      model({
        ke <- tvK * exp(bsvK)
        v <- 1
        ipre <- 10 * exp(-ke * t)
        ipre ~ prop(prop.sd)
      })
    }

    dat2 <- dat
    dat2$limit <- 0

    dat3 <- dat
    dat3$limit <- 3

    dat4 <- dat
    dat4$limit <- 12

    f.focei <- .nlmixr(f, dat, "posthoc")

    f.focei2 <- .nlmixr(f, dat2, "posthoc")

    expect_false(isTRUE(all.equal(f.focei$objf, f.focei2$objf)))

    ## Limit affects values

    f.focei3 <- .nlmixr(f, dat3, "posthoc")

    expect_false(isTRUE(all.equal(f.focei2$objf, f.focei3$objf)))

    f.focei4 <- .nlmixr(f, dat4, "posthoc")

    f.foce <- .nlmixr(f, dat, "posthoc", control = list(interaction = FALSE))

    f.foce2 <- .nlmixr(f, dat2, "posthoc", control = list(interaction = FALSE))

    expect_false(isTRUE(all.equal(f.foce$objf, f.foce2$objf)))

    f.foce3 <- .nlmixr(f, dat3, "posthoc", control = list(interaction = FALSE))

    expect_false(isTRUE(all.equal(f.foce2$objf, f.foce3$objf)))

    test_that("M3/M4 -- Missing, assume LLOQ=3 at t=1.5", {
      context("M3/M4 -- Missing, assume LLOQ=3 at t=1.5")
      skip_if(Sys.getenv("R_ARCH") == "/i386", "windows32")
      datL <- rbind(dat[, names(dat) != "Y"], data.frame(ID = 1:10, Time = 1.5, DV = 3))
      datL$cens <- ifelse(datL$Time == 1.5, 1, 0)
      datL <- datL[order(datL$ID, datL$Time), ]

      datL4 <- datL
      datL4$limit <- 0

      f.foceiL <- .nlmixr(f, datL, "posthoc")
      expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL$objf)))

      f.foceiL4 <- .nlmixr(f, datL4, "posthoc")
      expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL4$objf)))
      expect_false(isTRUE(all.equal(f.foceiL$objf, f.foceiL4$objf)))

      datL <- rbind(dat[, names(dat) != "Y"], data.frame(ID = 1:10, Time = 1.5, DV = 3))
      datL$cens <- ifelse(datL$Time == 1.5, 1, 0)
      datL <- datL[order(datL$ID, datL$Time), ]

      datL4 <- datL
      datL4$limit <- 0

      f.foceiL <- .nlmixr(f, datL, "posthoc")
      expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL$objf)))

      f.foceiL4 <- .nlmixr(f, datL4, "posthoc")
      expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL4$objf)))
      expect_false(isTRUE(all.equal(f.foceiL$objf, f.foceiL4$objf)))

      ## foce

      datL <- rbind(dat[, names(dat) != "Y"], data.frame(ID = 1:10, Time = 1.5, DV = 3))
      datL$cens <- ifelse(datL$Time == 1.5, 1, 0)
      datL <- datL[order(datL$ID, datL$Time), ]

      datL4 <- datL
      datL4$limit <- 0

      f.foceL <- .nlmixr(f, datL, "posthoc", control = list(interaction = FALSE))
      expect_false(isTRUE(all.equal(f.foce$objf, f.foceL$objf)))

      f.foceL4 <- .nlmixr(f, datL4, "posthoc", control = list(interaction = FALSE))
      expect_false(isTRUE(all.equal(f.foce$objf, f.foceL4$objf)))
      expect_false(isTRUE(all.equal(f.foceL$objf, f.foceL4$objf)))

    })


  },
  test = "focei"
)