From aeb6ff55560fa1c704312576be82e3e7ab4ab364 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Feb 2019 16:24:50 +0100 Subject: Test printing the summary of an mkinfit object --- tests/testthat/test_plots_summary_twa.R | 76 +++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 tests/testthat/test_plots_summary_twa.R (limited to 'tests/testthat/test_plots_summary_twa.R') diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R new file mode 100644 index 00000000..83a6a040 --- /dev/null +++ b/tests/testthat/test_plots_summary_twa.R @@ -0,0 +1,76 @@ +# 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 + +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) +}) + -- cgit v1.2.1