19 files changed, 3 insertions, 329 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R
index cfd40504..62f16e73 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -52,8 +52,8 @@
 #'     The coefficient matrix, if the system of differential equations can be
 #'     represented by one.
 #'   }
-#'   \item{ll}{
-#'     The likelihood function, taking the parameter vector as the first argument.
+#'   \item{cf}{
+#'     If generated, the compiled function as returned by cfunction.
 #'   }
 #' @note The IORE submodel is not well tested for metabolites. When using this
 #'   model for metabolites, you may want to read the second note in the help
@@ -365,7 +365,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
     model$coefmat <- m
   }#}}}
 
-  # Try to create a function compiled from C code there is more than one observed variable {{{
+  # Try to create a function compiled from C code if there is more than one observed variable {{{
   # and a compiler is available
   if (length(obs_vars) > 1 & has_compiler()) {
 
diff --git a/tests/testthat/slow/test_parent_only.R b/tests/testthat/slow/test_parent_only.R
index 7521e145..d9a56931 100644
--- a/tests/testthat/slow/test_parent_only.R
+++ b/tests/testthat/slow/test_parent_only.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2015,2018 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/>
-
 context("Fitting of parent only models")
 
 calc_dev.percent <- function(fitlist, reference, endpoints = TRUE, round_results = NULL) {
diff --git a/tests/testthat/slow/test_roundtrip_error_parameters.R b/tests/testthat/slow/test_roundtrip_error_parameters.R
index 7fa6c4e1..1a68d8db 100644
--- a/tests/testthat/slow/test_roundtrip_error_parameters.R
+++ b/tests/testthat/slow/test_roundtrip_error_parameters.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2018,2019 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/>
-
 context("Roundtripping error model parameters")
 
 # Per default (on my box where I set NOT_CRAN) use all cores minus one
diff --git a/tests/testthat/test_CAKE_export.R b/tests/testthat/test_CAKE_export.R
index a95a27ee..8445b69a 100644
--- a/tests/testthat/test_CAKE_export.R
+++ b/tests/testthat/test_CAKE_export.R
@@ -1,21 +1,3 @@
-# Copyright (C) 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/>
-
 context("Export dataset for reading into CAKE")
 
 test_that("Exporting is reproducible", {
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index 614305b1..f3b12bd9 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2015,2019 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/>
-
 context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
 
 # Results are from p. 40
diff --git a/tests/testthat/test_FOCUS_chi2_error_level.R b/tests/testthat/test_FOCUS_chi2_error_level.R
index d091cb95..d8d48bd3 100644
--- a/tests/testthat/test_FOCUS_chi2_error_level.R
+++ b/tests/testthat/test_FOCUS_chi2_error_level.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2014,2015,2018,2019 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/>
-
 context("Calculation of FOCUS chi2 error levels")
 
 errmin.FOCUS_2006_D_rounded = data.frame(
diff --git a/tests/testthat/test_SFORB.R b/tests/testthat/test_SFORB.R
index bc9ab646..b168a4ee 100644
--- a/tests/testthat/test_SFORB.R
+++ b/tests/testthat/test_SFORB.R
@@ -1,21 +1,3 @@
-# Copyright (C) 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/>
-
 context("Fitting the SFORB model")
 
 test_that("Fitting the SFORB model is equivalent to fitting DFOP", {
diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R
index 4b3667ed..2dfb2e37 100644
--- a/tests/testthat/test_error_models.R
+++ b/tests/testthat/test_error_models.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2018,2019 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/>
-
 context("Error model fitting")
 
 test_that("Error model 'obs' works", {
diff --git a/tests/testthat/test_from_max_mean.R b/tests/testthat/test_from_max_mean.R
index 3edf5969..002b39e2 100644
--- a/tests/testthat/test_from_max_mean.R
+++ b/tests/testthat/test_from_max_mean.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2018,2019 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/>
-
 context("Test fitting the decline of metabolites from their maximum")
 
 test_that("Fitting from maximum mean value works", {
diff --git a/tests/testthat/test_logistic.R b/tests/testthat/test_logistic.R
index 5a89fbf5..df8a7d5e 100644
--- a/tests/testthat/test_logistic.R
+++ b/tests/testthat/test_logistic.R
@@ -1,21 +1,3 @@
-# Copyright (C) 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/>
-
 context("Fitting the logistic model")
 
 logistic <- mkinmod(parent = mkinsub("logistic"))
diff --git a/tests/testthat/test_mkinds.R b/tests/testthat/test_mkinds.R
index 6e932ee8..cb0d2686 100644
--- a/tests/testthat/test_mkinds.R
+++ b/tests/testthat/test_mkinds.R
@@ -1,21 +1,3 @@
-# Copyright (C) 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/>
-
 context("Test dataset class mkinds used in gmkin")
 
 test_that("An mkinds object can be created and printed", {
diff --git a/tests/testthat/test_mkinfit_errors.R b/tests/testthat/test_mkinfit_errors.R
index 3a04e9c6..7987d291 100644
--- a/tests/testthat/test_mkinfit_errors.R
+++ b/tests/testthat/test_mkinfit_errors.R
@@ -1,21 +1,3 @@
-# Copyright (C) 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/>
-
 context("Special cases of mkinfit calls")
 
 test_that("mkinfit stops to prevent and/or explain user errors", {
diff --git a/tests/testthat/test_mkinmod.R b/tests/testthat/test_mkinmod.R
index 1f8ec166..1bdf094b 100644
--- a/tests/testthat/test_mkinmod.R
+++ b/tests/testthat/test_mkinmod.R
@@ -1,21 +1,3 @@
-# Copyright (C) 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/>
-
 context("mkinmod model generation and printing")
 
 test_that("mkinmod stops to prevent and/or explain user errors", {
diff --git a/tests/testthat/test_mkinpredict_SFO_SFO.R b/tests/testthat/test_mkinpredict_SFO_SFO.R
index d0d856fa..347aa50b 100644
--- a/tests/testthat/test_mkinpredict_SFO_SFO.R
+++ b/tests/testthat/test_mkinpredict_SFO_SFO.R
@@ -1,23 +1,3 @@
-# Copyright (C) 2012-2015,2018 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/>
-
-# This was migrated from an RUnit test in inst/unitTests/runit.mkinpredict.R
-
 context("Model predictions with mkinpredict")
 test_that("Variants of model predictions for SFO_SFO model give equivalent results", {
   # Check model specification and solution types for SFO_SFO
diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R
index 8cb1895b..a0acd152 100644
--- a/tests/testthat/test_nafta.R
+++ b/tests/testthat/test_nafta.R
@@ -1,21 +1,3 @@
-# Copyright (C) 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/>
-
 context("Evaluations according to 2015 NAFTA guidance")
 
 test_that("Data for more than one compound are rejected",
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index 3981bde7..19ae8770 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2016-2020 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/>
-
 context("Calculation of maximum time weighted average concentrations (TWAs)")
 
 test_that("Time weighted average concentrations are correct", {
diff --git a/tests/testthat/test_schaefer07_complex_case.R b/tests/testthat/test_schaefer07_complex_case.R
index 66ebc03b..703298d5 100644
--- a/tests/testthat/test_schaefer07_complex_case.R
+++ b/tests/testthat/test_schaefer07_complex_case.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2014-2015,2018,2019 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/>
-
 context("Complex test case from Schaefer et al. (2007) Piacenza paper")
 
 test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", {
diff --git a/tests/testthat/test_summary_old_objects.R b/tests/testthat/test_summary_old_objects.R
index 11e63553..9766ffd6 100644
--- a/tests/testthat/test_summary_old_objects.R
+++ b/tests/testthat/test_summary_old_objects.R
@@ -1,21 +1,3 @@
-# Copyright (C) 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/>
-
 context("Summaries of old mkinfit objects")
 
 test_that("A fit generated with mkin 0.9.48.1 can be summarised", {
diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R
index 6856a9a3..4bff1b5a 100644
--- a/tests/testthat/test_synthetic_data_for_UBA_2014.R
+++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R
@@ -1,21 +1,3 @@
-# Copyright (C) 2015, 2018 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/>
-
 context("Results for synthetic data established in expertise for UBA (Ranke 2014)")