tests/testthat/test-transPk.R

In nlmixr2lib: A Model Library for 'nlmixr2'

test_that("transPk -- k", {

  p3k <- readModelDb("PK_3cmt_des") |>
    pkTrans("k")
  expect_true(all(c("lkel", "lk12", "lk21", "lk13", "lk31") %in% names(p3k$theta)))

  # Issue #87 -- Make sure depot is not dropped
  expect_equal(rxode2::modelExtract(p3k, "d/dt(depot)"),
               "d/dt(depot) <- -ka * depot")

  p2k <- readModelDb("PK_2cmt_des") |>
    pkTrans("k")
  expect_true(all(c("lkel", "lk12", "lk21") %in% names(p2k$theta)))
  expect_true(!any(c("lk13", "lk31") %in% names(p2k$theta)))

  p1k <- readModelDb("PK_1cmt_des") |>
    pkTrans("k")
  expect_true(all("lkel" %in% names(p1k$theta)))
  expect_true(!any(c("lk12", "lk21", "lk13", "lk31") %in% names(p1k$theta)))

})

test_that("transPk -- vss", {

  expect_error(readModelDb("PK_3cmt_des") |>
                 pkTrans("vss"),
               "vss transformation only works for 2 compartment models")

  expect_error(readModelDb("PK_1cmt_des") |>
                 pkTrans("vss"),
               "vss transformation only works for 2 compartment models")

  pk2 <- readModelDb("PK_2cmt_des") |>
    pkTrans("vss")

  expect_true(all(c("lcl", "lq", "lvc", "lvss") %in% names(pk2$theta)))

})



test_that("transPk -- aob", {

  expect_error(readModelDb("PK_3cmt_des") |>
                 pkTrans("aob"),
               "aob transformation only works for 2 compartment models")

  expect_error(readModelDb("PK_1cmt_des") |>
                 pkTrans("aob"),
               "aob transformation only works for 2 compartment models")

  pk2 <- readModelDb("PK_2cmt_des") |>
    pkTrans("aob")

  expect_true(all(c("laob", "lalpha", "lbeta", "lvc") %in% names(pk2$theta)))
})

test_that("transPk --k21", {

  pk3 <-readModelDb("PK_3cmt_des") |>
    pkTrans("k21")

  expect_true(all(c("lalpha", "lbeta", "lgam",
                    "lk21", "lk31") %in% names(pk3$theta)))
  expect_true(!any(c("lk12", "lk13") %in% names(pk3$theta)))

  pk2 <- readModelDb("PK_2cmt_des") |>
    pkTrans("k21")

  expect_true(all(c("lalpha", "lbeta",
                    "lk21") %in% names(pk2$theta)))
  expect_true(!any("lk12" %in% names(pk2$theta)))


  expect_error(readModelDb("PK_1cmt_des") |>
                 pkTrans("k21"),
               "k21 transformation only works for 2 and 3 compartment models")
})

test_that("transPk -- alpha", {
  pk3 <- readModelDb("PK_3cmt_des") |>
    pkTrans("alpha")

  expect_true(all(c("lalpha", "lbeta", "lgam",
                    "lA", "lB", "lC") %in% names(pk3$theta)))

  pk2 <- readModelDb("PK_2cmt_des") |>
    pkTrans("alpha")

  expect_true(all(c("lalpha", "lbeta",
                    "lA", "lB") %in% names(pk2$theta)))
  expect_true(!any(c("lgam", "lC") %in% names(pk2$theta)) )

  pk1 <- readModelDb("PK_1cmt_des") |>
    pkTrans("alpha")

  expect_true(all(c("lalpha", "lA") %in% names(pk1$theta)))
  expect_true(!any(c("lbeta","lgam", "lB", "lC") %in% names(pk1$theta)) )
})