aboutsummaryrefslogtreecommitdiff
path: root/tests/testthat/test_plots_summary_twa.R
blob: 83a6a04056783b69425a4dd81cfd7840d9c88e29 (plain) (blame)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
# Copyright (C) 2016-2019 Johannes Ranke
# Contact: jranke@uni-bremen.de

# This file is part of the R package mkin

# mkin is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.

# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
# details.

# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>

models <- c("SFO", "FOMC", "DFOP", "HS")
fits <- mmkin(models,
  list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
  quiet = TRUE, cores = if (Sys.getenv("TRAVIS") == "") 15 else 1)

context("Calculation of maximum time weighted average concentrations (TWAs)")

test_that("Time weighted average concentrations are correct", {
  skip_on_cran()

  outtimes_10 <- seq(0, 10, length.out = 10000)

  for (ds in c("FOCUS_C", "FOCUS_D")) {
    for (model in models) {
      fit <- fits[[model, ds]]
      bpar <- summary(fit)$bpar[, "Estimate"]
      pred_10 <- mkinpredict(fit$mkinmod,
                  odeparms = bpar[2:length(bpar)],
                  odeini = c(parent = bpar[[1]]),
                  outtimes = outtimes_10)
      twa_num <- mean(pred_10$parent)
      names(twa_num) <- 10
      twa_ana <- max_twa_parent(fit, 10)

      # Test for absolute difference (scale = 1)
      # The tolerance can be reduced if the length of outtimes is increased,
      # but this needs more computing time so we stay with lenght.out = 10k
      expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1)
    }
  }
})

context("Summary")

test_that("The summary is reproducible", {
  skip_on_cran()
  fit <- fits[["DFOP", "FOCUS_C"]]
  undebug(summary.mkinfit)
  test_summary$fit_version <- "Dummy 0.0 for testing"
  test_summary$fit_Rversion <- "Dummy R version for testing"
  test_summary$date.fit <- "Dummy date for testing"
  test_summary$date.summary <- "Dummy date for testing"
  expect_known_output(print(test_summary), "summary_DFOP_FOCUS_C.txt")
})

context("Plotting")

test_that("Plotting mmkin objects is reproducible", {
  skip_on_cran()
  plot_sep_FOCUS_C_SFO <- function() plot_sep(fits[["SFO", "FOCUS_C"]])
  mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"])
  mmkin_SFO <- function() plot(fits["SFO",])

  vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with sep = TRUE", plot_sep_FOCUS_C_SFO)
  vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C)
  vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
})

Contact - Imprint