From b2b5c0f2294e19178e95c9adc5351a1b73218a34 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 27 Feb 2019 12:57:10 +0100 Subject: Further increase test coverage --- test.log | 13 +++---- tests/testthat/SFO_SFO_printed.txt | 12 +++++++ tests/testthat/test_from_max_mean.R | 18 ++++++++++ tests/testthat/test_mkinds.R | 18 ++++++++++ tests/testthat/test_mkinfit_errors.R | 19 ++++++++-- tests/testthat/test_mkinmod.R | 52 +++++++++++++++++++++++++++ tests/testthat/test_schaefer07_complex_case.R | 4 +-- 7 files changed, 125 insertions(+), 11 deletions(-) create mode 100644 tests/testthat/SFO_SFO_printed.txt create mode 100644 tests/testthat/test_mkinmod.R diff --git a/test.log b/test.log index aee7acf6..a7e44fd8 100644 --- a/test.log +++ b/test.log @@ -3,7 +3,7 @@ Testing mkin ✔ | OK F W S | Context ⠏ | 0 | Export dataset for reading into CAKE ⠋ | 1 | Export dataset for reading into CAKE ✔ | 1 | Export dataset for reading into CAKE ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ✔ | 2 | Calculation of FOCUS chi2 error levels [2.3 s] - ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [7.9 s] + ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [8.0 s] ⠏ | 0 | Test fitting the decline of metabolites from their maximum ⠋ | 1 | Test fitting the decline of metabolites from their maximum ⠙ | 2 | Test fitting the decline of metabolites from their maximum ⠹ | 3 | Test fitting the decline of metabolites from their maximum ✔ | 3 | Test fitting the decline of metabolites from their maximum [0.6 s] ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting ⠹ | 2 1 | Iteratively reweighted least squares (IRLS) fitting ✔ | 2 1 | Iteratively reweighted least squares (IRLS) fitting [15.9 s] ──────────────────────────────────────────────────────────────────────────────── @@ -16,11 +16,12 @@ test_logistic.R:41: skip: The logistic fit can be done via differential equation Skip slow fit of logistic model using deSolve without compilation ──────────────────────────────────────────────────────────────────────────────── ⠏ | 0 | Test dataset class mkinds used in gmkin ⠋ | 1 | Test dataset class mkinds used in gmkin ✔ | 1 | Test dataset class mkinds used in gmkin - ⠏ | 0 | Special cases of mkinfit calls ⠋ | 1 | Special cases of mkinfit calls ⠙ | 2 | Special cases of mkinfit calls ⠹ | 3 | Special cases of mkinfit calls ⠸ | 4 | Special cases of mkinfit calls ⠼ | 5 | Special cases of mkinfit calls ⠴ | 6 | Special cases of mkinfit calls ⠦ | 7 | Special cases of mkinfit calls ⠧ | 8 | Special cases of mkinfit calls ⠇ | 9 | Special cases of mkinfit calls ⠏ | 10 | Special cases of mkinfit calls ⠋ | 11 | Special cases of mkinfit calls ⠙ | 12 | Special cases of mkinfit calls ⠹ | 12 1 | Special cases of mkinfit calls ⠸ | 13 1 | Special cases of mkinfit calls ⠼ | 14 1 | Special cases of mkinfit calls ⠴ | 15 1 | Special cases of mkinfit calls ⠦ | 16 1 | Special cases of mkinfit calls ✔ | 16 1 | Special cases of mkinfit calls [3.0 s] + ⠏ | 0 | Special cases of mkinfit calls ⠋ | 1 | Special cases of mkinfit calls ⠙ | 2 | Special cases of mkinfit calls ⠹ | 3 | Special cases of mkinfit calls ⠸ | 4 | Special cases of mkinfit calls ⠼ | 5 | Special cases of mkinfit calls ⠴ | 6 | Special cases of mkinfit calls ⠦ | 7 | Special cases of mkinfit calls ⠧ | 8 | Special cases of mkinfit calls ⠇ | 9 | Special cases of mkinfit calls ⠏ | 10 | Special cases of mkinfit calls ⠋ | 11 | Special cases of mkinfit calls ⠙ | 12 | Special cases of mkinfit calls ⠹ | 12 1 | Special cases of mkinfit calls ⠸ | 13 1 | Special cases of mkinfit calls ⠼ | 14 1 | Special cases of mkinfit calls ⠴ | 15 1 | Special cases of mkinfit calls ⠦ | 16 1 | Special cases of mkinfit calls ✔ | 16 1 | Special cases of mkinfit calls [2.9 s] ──────────────────────────────────────────────────────────────────────────────── -test_mkinfit_errors.R:52: skip: mkinfit warns if the user chooses the SANN method +test_mkinfit_errors.R:67: skip: mkinfit warns if the user chooses the SANN method The SANN algorithm takes very long with the default maximum number of iterations of 10000 ──────────────────────────────────────────────────────────────────────────────── + ⠏ | 0 | mkinmod model generation and printing ⠋ | 1 | mkinmod model generation and printing ⠙ | 2 | mkinmod model generation and printing ⠹ | 3 | mkinmod model generation and printing ⠸ | 4 | mkinmod model generation and printing ⠼ | 5 | mkinmod model generation and printing ⠴ | 6 | mkinmod model generation and printing ⠦ | 7 | mkinmod model generation and printing ⠧ | 8 | mkinmod model generation and printing ⠇ | 9 | mkinmod model generation and printing ✔ | 9 | mkinmod model generation and printing [0.2 s] ⠏ | 0 | Model predictions with mkinpredict ⠋ | 1 | Model predictions with mkinpredict ⠙ | 2 | Model predictions with mkinpredict ⠹ | 3 | Model predictions with mkinpredict ✔ | 3 | Model predictions with mkinpredict [0.3 s] ⠏ | 0 | Evaluations according to 2015 NAFTA guidance ⠋ | 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 2 | Evaluations according to 2015 NAFTA guidance ⠹ | 3 | Evaluations according to 2015 NAFTA guidance ⠸ | 4 | Evaluations according to 2015 NAFTA guidance ⠼ | 5 | Evaluations according to 2015 NAFTA guidance ⠴ | 6 | Evaluations according to 2015 NAFTA guidance ⠦ | 7 | Evaluations according to 2015 NAFTA guidance ⠧ | 8 | Evaluations according to 2015 NAFTA guidance ⠇ | 9 | Evaluations according to 2015 NAFTA guidance ⠏ | 9 1 | Evaluations according to 2015 NAFTA guidance ⠏ | 10 | Evaluations according to 2015 NAFTA guidance ⠋ | 11 | Evaluations according to 2015 NAFTA guidance ⠙ | 12 | Evaluations according to 2015 NAFTA guidance ⠹ | 13 | Evaluations according to 2015 NAFTA guidance ⠸ | 14 | Evaluations according to 2015 NAFTA guidance ⠼ | 15 | Evaluations according to 2015 NAFTA guidance ⠴ | 16 | Evaluations according to 2015 NAFTA guidance ⠦ | 17 | Evaluations according to 2015 NAFTA guidance ✔ | 17 | Evaluations according to 2015 NAFTA guidance [1.5 s] ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [23.8 s] @@ -28,13 +29,13 @@ The SANN algorithm takes very long with the default maximum number of iterations ⠏ | 0 | Summary ⠋ | 1 | Summary ✔ | 1 | Summary ⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 2 | Plotting ⠹ | 3 | Plotting ⠸ | 4 | Plotting ✔ | 4 | Plotting [0.3 s] ⠏ | 0 | AIC calculation ⠋ | 1 | AIC calculation ⠙ | 2 | AIC calculation ✔ | 2 | AIC calculation - ⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.8 s] + ⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.9 s] ⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.4 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 74.2 s +Duration: 74.5 s -OK: 97 +OK: 106 Failed: 0 Warnings: 0 Skipped: 3 diff --git a/tests/testthat/SFO_SFO_printed.txt b/tests/testthat/SFO_SFO_printed.txt new file mode 100644 index 00000000..8a188152 --- /dev/null +++ b/tests/testthat/SFO_SFO_printed.txt @@ -0,0 +1,12 @@ + model generated with +Use of formation fractions $use_of_ff: min +Specification $spec: +$parent +$type: SFO; $to: m1; $sink: TRUE +$m1 +$type: SFO; $sink: TRUE +Coefficient matrix $coefmat available +Compiled model $cf available +Differential equations: +d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 diff --git a/tests/testthat/test_from_max_mean.R b/tests/testthat/test_from_max_mean.R index 8e5953b9..7529c5f2 100644 --- a/tests/testthat/test_from_max_mean.R +++ b/tests/testthat/test_from_max_mean.R @@ -1,3 +1,21 @@ +# Copyright (C) 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("Test fitting the decline of metabolites from their maximum") test_that("Fitting from maximum mean value works", { diff --git a/tests/testthat/test_mkinds.R b/tests/testthat/test_mkinds.R index e017301c..1046449b 100644 --- a/tests/testthat/test_mkinds.R +++ b/tests/testthat/test_mkinds.R @@ -1,3 +1,21 @@ +# 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 50032628..50d528e0 100644 --- a/tests/testthat/test_mkinfit_errors.R +++ b/tests/testthat/test_mkinfit_errors.R @@ -1,5 +1,20 @@ -library(mkin) -library(testthat) +# 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") diff --git a/tests/testthat/test_mkinmod.R b/tests/testthat/test_mkinmod.R new file mode 100644 index 00000000..430fad61 --- /dev/null +++ b/tests/testthat/test_mkinmod.R @@ -0,0 +1,52 @@ +# 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", { + expect_error(mkinmod(compound_x = mkinsub("SFO", to = "compound_x_y"), + compound_x_y = mkinsub("SFO")), + "variable names can not contain each other") + expect_error(mkinmod(compound_to_x = mkinsub("SFO")), + "can not contain _to_") + expect_error(mkinmod(sink = mkinsub("SFO")), + "Naming") + + expect_error(mkinmod(parent = mkinsub("SFO"), use_of_ff = "foo")) + + expect_error(mkinmod(parent = mkinsub("foo"))) + + expect_error(mkinmod(parent = mkinsub("SFO", "m1"), + m1 = mkinsub("FOMC")), + "only implemented for the first compartment") + + expect_error(mkinmod(parent = mkinsub("IORE", "m1"), + m1 = mkinsub("SFO"), use_of_ff = "min"), + "only supported with formation fractions") + + expect_error(mkinmod(parent = mkinsub("SFORB", "m1"), + m1 = mkinsub("SFO"), use_of_ff = "max"), + "not supported") +}) + +test_that("Printing mkinmod models is reproducible", { + expect_known_output(print(mkinmod(parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO"), + quiet = TRUE)), + file = "SFO_SFO_printed.txt") +}) diff --git a/tests/testthat/test_schaefer07_complex_case.R b/tests/testthat/test_schaefer07_complex_case.R index 80306bbe..844dd88f 100644 --- a/tests/testthat/test_schaefer07_complex_case.R +++ b/tests/testthat/test_schaefer07_complex_case.R @@ -1,4 +1,4 @@ -# Copyright (C) 2014-2015,2018 Johannes Ranke +# Copyright (C) 2014-2015,2018,2019 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -16,8 +16,6 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see -# This test was migrated from a RUnit test inst/unitTests/runit.mkinfit.R - context("Complex test case from Schaefer et al. (2007) Piacenza paper") test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", { -- cgit v1.2.1