From f6b6ecd0f925799aaced3fb5ceb9e5817a99d884 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 22 Apr 2020 14:37:27 +0200 Subject: Remove GPL header from test files --- R/mkinmod.R | 6 +++--- tests/testthat/slow/test_parent_only.R | 18 ------------------ .../testthat/slow/test_roundtrip_error_parameters.R | 18 ------------------ tests/testthat/test_CAKE_export.R | 18 ------------------ tests/testthat/test_FOCUS_D_UBA_expertise.R | 18 ------------------ tests/testthat/test_FOCUS_chi2_error_level.R | 18 ------------------ tests/testthat/test_SFORB.R | 18 ------------------ tests/testthat/test_error_models.R | 18 ------------------ tests/testthat/test_from_max_mean.R | 18 ------------------ tests/testthat/test_logistic.R | 18 ------------------ tests/testthat/test_mkinds.R | 18 ------------------ tests/testthat/test_mkinfit_errors.R | 18 ------------------ tests/testthat/test_mkinmod.R | 18 ------------------ tests/testthat/test_mkinpredict_SFO_SFO.R | 20 -------------------- tests/testthat/test_nafta.R | 18 ------------------ tests/testthat/test_plots_summary_twa.R | 18 ------------------ tests/testthat/test_schaefer07_complex_case.R | 18 ------------------ tests/testthat/test_summary_old_objects.R | 18 ------------------ tests/testthat/test_synthetic_data_for_UBA_2014.R | 18 ------------------ 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - -# 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 - 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 - 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 - 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 - 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 - context("Results for synthetic data established in expertise for UBA (Ranke 2014)") -- cgit v1.2.1