diff options
| -rw-r--r-- | man/summary.mkinfit.Rd | 4 | ||||
| -rw-r--r-- | tests/testthat/summary_DFOP_FOCUS_C.txt | 79 | ||||
| -rw-r--r-- | tests/testthat/test_plots_summary_twa.R | 76 |
3 files changed, 157 insertions, 2 deletions
diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd index f8c8c9d6..3d71917e 100644 --- a/man/summary.mkinfit.Rd +++ b/man/summary.mkinfit.Rd @@ -23,7 +23,7 @@ an object of class \code{summary.mkinfit}.
}
\item{data}{
- logical, indicating whether the data should be included in the summary.
+ logical, indicating whether the data should be included in the summary.
}
\item{distimes}{
logical, indicating whether DT50 and DT90 values should be included.
@@ -64,7 +64,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration} Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+ \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
}
\author{
Johannes Ranke
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt new file mode 100644 index 00000000..d8a3e05a --- /dev/null +++ b/tests/testthat/summary_DFOP_FOCUS_C.txt @@ -0,0 +1,79 @@ +mkin version used for fitting: Dummy 0.0 for testing +R version used for fitting: Dummy R version for testing +Date of fit: Dummy date for testing +Date of summary: Dummy date for testing + +Equations: +d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * + time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) + * parent + +Model predictions using solution type analytical + +Fitted with method Port using 127 model solutions performed in 0.401 s + +Weighting: none + +Starting values for parameters to be optimised: + value type +parent_0 85.10 state +k1 0.10 deparm +k2 0.01 deparm +g 0.50 deparm + +Starting values for the transformed parameters actually optimised: + value lower upper +parent_0 85.100000 -Inf Inf +log_k1 -2.302585 -Inf Inf +log_k2 -4.605170 -Inf Inf +g_ilr 0.000000 -Inf Inf + +Fixed parameter values: +None + +Optimised, transformed parameters with symmetric confidence intervals: + Estimate Std. Error Lower Upper +parent_0 85.0000 0.89070 82.7100 87.2900 +log_k1 -0.7775 0.04430 -0.8914 -0.6636 +log_k2 -4.0260 0.17030 -4.4640 -3.5880 +g_ilr 1.2490 0.07619 1.0530 1.4450 + +Parameter correlation: + parent_0 log_k1 log_k2 g_ilr +parent_0 1.00000 0.4338 0.07924 -0.01897 +log_k1 0.43380 1.0000 0.46567 -0.66010 +log_k2 0.07924 0.4657 1.00000 -0.74183 +g_ilr -0.01897 -0.6601 -0.74183 1.00000 + +Residual standard error: 0.9341 on 5 degrees of freedom + +Backtransformed parameters: +Confidence intervals for internally transformed parameters are asymmetric. +t-test (unrealistically) based on the assumption of normal distribution +for estimators of untransformed parameters. + Estimate t value Pr(>t) Lower Upper +parent_0 85.00000 95.440 1.197e-09 82.71000 87.29000 +k1 0.45960 22.570 1.586e-06 0.41010 0.51500 +k2 0.01785 5.873 1.016e-03 0.01152 0.02765 +g 0.85390 63.540 9.135e-09 0.81590 0.88520 + +Chi2 error levels in percent: + err.min n.optim df +All data 2.661 4 5 +parent 2.661 4 5 + +Estimated disappearance times: + DT50 DT90 DT50_k1 DT50_k2 +parent 1.887 21.25 1.508 38.83 + +Data: + time variable observed predicted residual + 0 parent 85.1 85.003 0.09726 + 1 parent 57.9 58.039 -0.13912 + 3 parent 29.9 30.054 -0.15351 + 7 parent 14.6 13.866 0.73388 + 14 parent 9.7 9.787 -0.08657 + 28 parent 6.6 7.532 -0.93205 + 63 parent 4.0 4.033 -0.03269 + 91 parent 3.9 2.447 1.45348 + 119 parent 0.6 1.484 -0.88424 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 <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) +}) + |