tests/testthat/test-focei-preprocess.R

In nlmixr2est: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

nmTest({
  model <- function() {
    ini({
      foo <- 1
    })
    model({
      bar <- foo
      bar ~ add(foo)
    })
  }

  ui <- .nlmixr(model)

  test_that(".foceiPreProcessData errors with missing info", {

    env_orig <- new.env()
    df_noid <- data.frame(DV=1:2, time=1:2)
    df_nodv <- data.frame(ID=1, time=1:2)
    df_notime <- data.frame(ID=1, DV=1:2)

    expect_error(
      .foceiPreProcessData(data = df_nodv, env = env_orig, ui = ui),
      regexp = "missing elements {'DV'}",
      fixed = TRUE
    )

    expect_error(
      .foceiPreProcessData(data = df_notime, env = env_orig, ui = ui),
      regexp = "missing elements {'TIME'}",
      fixed = TRUE
    )

  })

  test_that(".foceiPreProcessData works with data.frame and tibble data", {
    env_orig <- new.env()
    df <- data.frame(ID=1, DV=1:2, time=1:2)
    .foceiPreProcessData(data = df, env = env_orig, ui = ui)
    expect_equal(env_orig$dataSav$nlmixrRowNums, c(NA, 1, 2))
    tib <- tibble::tibble(ID=1, DV=1:2, time=1:2)
    .foceiPreProcessData(data = tib, env = env_orig, ui = ui)
    expect_equal(env_orig$dataSav$nlmixrRowNums, c(NA, 1, 2))
  })

  test_that(".foceiPreProcessData preserves rxEt extra columns", {
    env_orig <- new.env()
    et <- rxode2::et(amt=0)
    et <- rxode2::et(et, 1)
    et$DV <- 100

    expect_equal(nrow(et), 2L)
    .foceiPreProcessData(data = et, env = env_orig, ui = ui)

    expect_equal(env_orig$origData$DV, c(100, 100))
    expect_true("DV" %in% names(env_orig$dataSav))
  })

  test_that(".foceiPreProcessData works with ID as character or factor", {
    env_orig <- new.env()
    df <- data.frame(ID=c("A", "B"), DV=1:2, time=1:2)
    .foceiPreProcessData(data = df, env = env_orig, ui = ui)
    expect_equal(env_orig$dataSav$ID, rep(1L:2L, each = 2))
    # Confirm row order
    expect_equal(env_orig$dataSav$DV, c(NA, 1, NA, 2))

    df <- data.frame(ID=factor(c("A", "B")), DV=3:4, time=1:2)
    .foceiPreProcessData(data = df, env = env_orig, ui = ui)
    expect_equal(env_orig$dataSav$ID, rep(1L:2L, each = 2))
    # Confirm row order
    expect_equal(env_orig$dataSav$DV, c(NA, 3, NA, 4))

    df <- data.frame(ID=factor(c("B", "A")), DV=5:6, time=1:2)
    .foceiPreProcessData(data = df, env = env_orig, ui = ui)
    # IDs are assigned in the order that they are found not in factor order
    expect_equal(env_orig$dataSav$ID, rep(1L:2L, each = 2))
    # Confirm row order
    expect_equal(env_orig$dataSav$DV, c(NA, 5, NA, 6))
  })
})