Add plotting tests, add nafta to pkgdown

1 files changed, 61 insertions, 0 deletions

diff --git a/tests/testthat/test_plots_twa.R b/tests/testthat/test_plots_twa.R
new file mode 100644
index 00000000..fe0ba325
--- /dev/null
+++ b/tests/testthat/test_plots_twa.R
@@ -0,0 +1,61 @@
+# 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("Plotting")
+
+test_that("Plotting mmkin objects is reproducible", {
+  skip_on_cran()
+  mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"])
+  mmkin_SFO <- function() plot(fits["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)
+})
+