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authorJohannes Ranke <jranke@uni-bremen.de>2019-02-25 14:50:13 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-02-25 14:57:28 +0100
commitbe809ea23b256f627216958fcd90489ee0844ab8 (patch)
treeaac8e1ce221d79cd58e4fa62c5e5149a3b0c659f /tests/testthat/test_plots_twa.R
parentdd6c4a8f895fd470345e7ae773299daaa4de7aef (diff)
Add plotting tests, add nafta to pkgdown
Diffstat (limited to 'tests/testthat/test_plots_twa.R')
-rw-r--r--tests/testthat/test_plots_twa.R61
1 files changed, 61 insertions, 0 deletions
diff --git a/tests/testthat/test_plots_twa.R b/tests/testthat/test_plots_twa.R
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+++ b/tests/testthat/test_plots_twa.R
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+# 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)
+})
+

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