Test printing the summary of an mkinfit object

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)
+})
+