diff options
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | docs/articles/FOCUS_L.html | 40 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 10 | ||||
| -rw-r--r-- | docs/news/index.html | 10 | ||||
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 12 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 46 | ||||
| -rw-r--r-- | docs/reference/mkinmod.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 6 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 6 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 24 | ||||
| -rw-r--r-- | test.log | 13 | ||||
| -rw-r--r-- | tests/testthat/test_FOCUS_D_UBA_expertise.R | 70 | ||||
| -rw-r--r-- | tests/testthat/test_mkinpredict_SFO_SFO.R | 4 | ||||
| -rw-r--r-- | tests/testthat/test_parent_only.R | 3 | ||||
| -rw-r--r-- | tests/testthat/test_synthetic_data_for_UBA_2014.R | 1 | ||||
| -rw-r--r-- | tests/testthat/test_twa.R | 8 |
18 files changed, 128 insertions, 145 deletions
@@ -4,8 +4,6 @@ - Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times) -# mkin 0.9.47.4 - - Exclude more example code from testing on CRAN to avoid NOTES from long execution times # mkin 0.9.47.3 diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index f1a91c04..2a99a609 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -110,15 +110,15 @@ <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 18:22:23 2018 -## Date of summary: Fri Sep 14 18:22:23 2018 +## Date of fit: Fri Sep 14 21:00:22 2018 +## Date of summary: Fri Sep 14 21:00:22 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.092 s +## Fitted with method Port using 37 model solutions performed in 0.087 s ## ## Weighting: none ## @@ -201,15 +201,15 @@ <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 18:22:25 2018 -## Date of summary: Fri Sep 14 18:22:25 2018 +## Date of fit: Fri Sep 14 21:00:23 2018 +## Date of summary: Fri Sep 14 21:00:23 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.355 s +## Fitted with method Port using 611 model solutions performed in 1.352 s ## ## Weighting: none ## @@ -296,8 +296,8 @@ <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 18:22:25 2018 -## Date of summary: Fri Sep 14 18:22:25 2018 +## Date of fit: Fri Sep 14 21:00:24 2018 +## Date of summary: Fri Sep 14 21:00:24 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -367,8 +367,8 @@ <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 18:22:26 2018 -## Date of summary: Fri Sep 14 18:22:26 2018 +## Date of fit: Fri Sep 14 21:00:25 2018 +## Date of summary: Fri Sep 14 21:00:25 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -377,7 +377,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.756 s +## Fitted with method Port using 336 model solutions performed in 0.758 s ## ## Weighting: none ## @@ -459,8 +459,8 @@ <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 18:22:27 2018 -## Date of summary: Fri Sep 14 18:22:28 2018 +## Date of fit: Fri Sep 14 21:00:26 2018 +## Date of summary: Fri Sep 14 21:00:26 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -469,7 +469,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.322 s +## Fitted with method Port using 137 model solutions performed in 0.31 s ## ## Weighting: none ## @@ -560,15 +560,15 @@ <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 18:22:28 2018 -## Date of summary: Fri Sep 14 18:22:28 2018 +## Date of fit: Fri Sep 14 21:00:26 2018 +## Date of summary: Fri Sep 14 21:00:27 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.101 s +## Fitted with method Port using 46 model solutions performed in 0.102 s ## ## Weighting: none ## @@ -620,15 +620,15 @@ <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 18:22:28 2018 -## Date of summary: Fri Sep 14 18:22:28 2018 +## Date of fit: Fri Sep 14 21:00:26 2018 +## Date of summary: Fri Sep 14 21:00:27 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.16 s +## Fitted with method Port using 66 model solutions performed in 0.151 s ## ## Weighting: none ## diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 12c192f0..9aac1ab2 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -125,9 +125,9 @@ <a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.115 1.000 2.114 0 -## 1 deSolve, not compiled 3 16.235 7.676 16.228 0 -## 2 Eigenvalue based 3 2.589 1.224 2.587 0 +## 3 deSolve, compiled 3 2.134 1.000 2.132 0 +## 1 deSolve, not compiled 3 16.165 7.575 16.157 0 +## 2 Eigenvalue based 3 2.597 1.217 2.595 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -156,8 +156,8 @@ <a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 3.887 1.000 3.885 0 -## 1 deSolve, not compiled 3 35.492 9.131 35.474 0 +## 2 deSolve, compiled 3 3.717 1.000 3.715 0 +## 1 deSolve, not compiled 3 34.646 9.321 34.630 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> diff --git a/docs/news/index.html b/docs/news/index.html index cbfcdde0..73eb7aa2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -124,14 +124,7 @@ <ul> <li><p>Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows</p></li> <li><p>Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)</p></li> -</ul> -</div> - <div id="mkin-0-9-47-4" class="section level1"> -<h1 class="page-header"> -<a href="#mkin-0-9-47-4" class="anchor"></a>mkin 0.9.47.4<small> Unreleased </small> -</h1> -<ul> -<li>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</li> +<li><p>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</p></li> </ul> </div> <div id="mkin-0-9-47-3" class="section level1"> @@ -666,7 +659,6 @@ <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li> - <li><a href="#mkin-0-9-47-4">0.9.47.4</a></li> <li><a href="#mkin-0-9-47-3">0.9.47.3</a></li> <li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li> <li><a href="#mkin-0-9-47-1-2018-02-06">0.9.47.1</a></li> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 91226e69..97562d44 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.166 0.000 0.166 +#> 0.177 0.000 0.176 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd812a0> -#> <environment: 0x55555bc871e8> +#> <bytecode: 0x55555bd7f230> +#> <environment: 0x55555bc85178> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555caa1d18> -#> <environment: 0x55555bc871e8> +#> <bytecode: 0x55555ca9fca8> +#> <environment: 0x55555bc85178> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Sep 14 18:20:46 2018" +#> [1] "Fri Sep 14 20:58:46 2018" #> #> $version #> [1] "0.9.47.5" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index d91431f3..52c09969 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -158,8 +158,8 @@ <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:20:57 2018 -#> Date of summary: Fri Sep 14 18:20:57 2018 +#> Date of fit: Fri Sep 14 20:58:58 2018 +#> Date of summary: Fri Sep 14 20:58:58 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -169,7 +169,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.418 s +#> Fitted with method Port using 574 model solutions performed in 3.393 s #> #> Weighting: none #> @@ -247,8 +247,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:20:59 2018 -#> Date of summary: Fri Sep 14 18:20:59 2018 +#> Date of fit: Fri Sep 14 20:58:59 2018 +#> Date of summary: Fri Sep 14 20:59:00 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.458 s +#> Fitted with method Port using 246 model solutions performed in 1.451 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 261d48fb..f3c6d595 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -434,15 +434,15 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:02 2018 -#> Date of summary: Fri Sep 14 18:21:02 2018 +#> Date of fit: Fri Sep 14 20:59:02 2018 +#> Date of summary: Fri Sep 14 20:59:02 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.143 s +#> Fitted with method Port using 64 model solutions performed in 0.141 s #> #> Weighting: none #> @@ -511,7 +511,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> User System verstrichen -#> 0.918 0.000 0.919 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.895 0.000 0.897 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -586,7 +586,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.757 0.000 0.757 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.726 0.000 0.726 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -624,8 +624,8 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:13 2018 -#> Date of summary: Fri Sep 14 18:21:13 2018 +#> Date of fit: Fri Sep 14 20:59:13 2018 +#> Date of summary: Fri Sep 14 20:59:13 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -633,7 +633,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.775 s +#> Fitted with method Port using 186 model solutions performed in 0.757 s #> #> Weighting: none #> @@ -741,8 +741,8 @@ #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:15 2018 -#> Date of summary: Fri Sep 14 18:21:15 2018 +#> Date of fit: Fri Sep 14 20:59:15 2018 +#> Date of summary: Fri Sep 14 20:59:16 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -750,7 +750,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.282 s +#> Fitted with method Port using 551 model solutions performed in 2.329 s #> #> Weighting: none #> @@ -863,8 +863,8 @@ #> 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:16 2018 -#> Date of summary: Fri Sep 14 18:21:16 2018 +#> Date of fit: Fri Sep 14 20:59:16 2018 +#> Date of summary: Fri Sep 14 20:59:16 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -872,7 +872,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.653 s +#> Fitted with method Port using 155 model solutions performed in 0.628 s #> #> Weighting: mean #> @@ -981,8 +981,8 @@ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:17 2018 -#> Date of summary: Fri Sep 14 18:21:17 2018 +#> Date of fit: Fri Sep 14 20:59:17 2018 +#> Date of summary: Fri Sep 14 20:59:17 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -990,7 +990,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.721 s +#> Fitted with method Port using 174 model solutions performed in 0.713 s #> #> Weighting: manual #> @@ -1101,8 +1101,8 @@ <span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:18 2018 -#> Date of summary: Fri Sep 14 18:21:18 2018 +#> Date of fit: Fri Sep 14 20:59:18 2018 +#> Date of summary: Fri Sep 14 20:59:18 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1110,7 +1110,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.215 s +#> Fitted with method Port using 270 model solutions performed in 1.119 s #> #> Weighting: manual #> @@ -1219,8 +1219,8 @@ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) <span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:22 2018 -#> Date of summary: Fri Sep 14 18:21:22 2018 +#> Date of fit: Fri Sep 14 20:59:21 2018 +#> Date of summary: Fri Sep 14 20:59:21 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1228,7 +1228,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.114 s +#> Fitted with method Port using 692 model solutions performed in 2.955 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 9048c1b1..464178bc 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -229,7 +229,7 @@ For the definition of model types and their parameters, the equations given <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file49ec17c0788e.c 2> file49ec17c0788e.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file7aee6cc2a6d.c 2> file7aee6cc2a6d.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 6c30d7a8..dfcd08a8 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -321,17 +321,17 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.004 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.001 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.035 0.000 0.035 </div></pre> +#> 0.036 0.000 0.036 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index d630ef3e..383e5928 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -189,8 +189,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 0.059 0.027 6.918 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 21.127 0.000 21.141 </div><div class='input'> +#> 0.056 0.024 6.712 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 20.446 0.000 20.459 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index cb6beda2..317c7a87 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,15 +206,15 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:22:10 2018 -#> Date of summary: Fri Sep 14 18:22:10 2018 +#> Date of fit: Fri Sep 14 21:00:08 2018 +#> Date of summary: Fri Sep 14 21:00:08 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.076 s +#> Fitted with method Port using 35 model solutions performed in 0.081 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index db92667c..6f7ec4a4 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:22:17 2018 -#> Date of summary: Fri Sep 14 18:22:17 2018 +#> Date of fit: Fri Sep 14 21:00:16 2018 +#> Date of summary: Fri Sep 14 21:00:16 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.701 s +#> Fitted with method Port using 153 model solutions performed in 0.71 s #> #> Weighting: none #> @@ -276,8 +276,8 @@ The transformation of sets of formation fractions is fragile, as it supposes </div><div class='input'><span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:22:19 2018 -#> Date of summary: Fri Sep 14 18:22:19 2018 +#> Date of fit: Fri Sep 14 21:00:17 2018 +#> Date of summary: Fri Sep 14 21:00:17 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 350 model solutions performed in 1.431 s +#> Fitted with method Port using 350 model solutions performed in 1.417 s #> #> Weighting: none #> @@ -364,8 +364,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:22:20 2018 -#> Date of summary: Fri Sep 14 18:22:20 2018 +#> Date of fit: Fri Sep 14 21:00:18 2018 +#> Date of summary: Fri Sep 14 21:00:18 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.778 s +#> Fitted with method Port using 186 model solutions performed in 0.755 s #> #> Weighting: none #> @@ -448,8 +448,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:22:20 2018 -#> Date of summary: Fri Sep 14 18:22:20 2018 +#> Date of fit: Fri Sep 14 21:00:19 2018 +#> Date of summary: Fri Sep 14 21:00:19 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.417 s +#> Fitted with method Port using 104 model solutions performed in 0.416 s #> #> Weighting: none #> @@ -3,17 +3,16 @@ Loading required package: testthat Testing mkin ✔ | OK F W S | Context
⠏ | 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 [2.2 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)
✔ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [2.2 s] -
⠏ | 0 | The t-test for significant difference from zero
⠋ | 1 | The t-test for significant difference from zero
⠙ | 2 | The t-test for significant difference from zero
✔ | 2 | The t-test for significant difference from zero [4.3 s] -
⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting
⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting
⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting
⠹ | 3 | Iteratively reweighted least squares (IRLS) fitting
✔ | 3 | Iteratively reweighted least squares (IRLS) fitting [36.3 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)
✔ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [6.5 s] +
⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting
⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting
⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting
⠹ | 3 | Iteratively reweighted least squares (IRLS) fitting
✔ | 3 | Iteratively reweighted least squares (IRLS) fitting [36.6 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 | 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 [21.8 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 [5.4 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 [22.6 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 [5.5 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) [6.7 s] -
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs)
⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs)
⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs)
⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs)
✔ | 3 | Calculation of maximum time weighted average concentrations (TWAs) [4.6 s] +
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs)
⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs)
⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs)
⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs)
✔ | 3 | Calculation of maximum time weighted average concentrations (TWAs) [3.8 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 84.0 s +Duration: 84.2 s OK: 46 Failed: 0 diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R index 5d5a801a..3b241aa4 100644 --- a/tests/testthat/test_FOCUS_D_UBA_expertise.R +++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015 Johannes Ranke +# Copyright (C) 2015,2018 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -18,69 +18,59 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)") -SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), quiet = TRUE) -SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), - use_of_ff = "max", quiet = TRUE) +# Results are from p. 40 -fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) -fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) +test_that("Fits without formation fractions are correct for FOCUS D", { + SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), quiet = TRUE) + fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) -# Results are from p. 40 + expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), + c(7.02, 23.33)) + expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), + c(131.8, 437.7)) -test_that("Fitted parameters are correct for FOCUS D", { + expect_equal(signif(summary(fit.default)$bpar[, "t value"], 5), + c(parent_0 = 61.720, k_parent_sink = 12.777, k_parent_m1 = 24.248, k_m1_sink = 7.3486)) +}) + +test_that("Fits with formation fractions are correct for FOCUS D", { + skip_on_cran() + SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), + use_of_ff = "max", quiet = TRUE) + + fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)), c(99.60, 0.0987, 0.0053, 0.5145)) -}) -test_that("FOCUS chi2 error levels are correct for FOCUS D", { expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2), c(6.40, 6.46, 4.69)) -}) -test_that("DT50/90 are correct for FOCUS D when using formation fractions", { expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["parent", ]), 2), c(7.02, 23.33)) expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1), c(131.8, 437.7)) }) -test_that("DT50/90 are correct for FOCUS D when not using formation fractions", { - expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), - c(7.02, 23.33)) - expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), - c(131.8, 437.7)) -}) - # References: # Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative # zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452 -context("The t-test for significant difference from zero") - -test_that("The t-value for fits using internal transformations corresponds with result from FME", { - - expect_equal(signif(summary(fit.default)$bpar[, "t value"], 5), - c(parent_0 = 61.720, k_parent_sink = 12.777, k_parent_m1 = 24.248, k_m1_sink = 7.3486)) - -}) - -m_synth_DFOP_par.minff <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), - M1 = mkinsub("SFO"), - M2 = mkinsub("SFO"), - use_of_ff = "min", quiet = TRUE) - -fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff, - synthetic_data_for_UBA_2014[[12]]$data, - quiet = TRUE) - test_that("The t-value for fits using internal transformations corresponds with results from FME, synthetic data", { + skip_on_cran() + m_synth_DFOP_par.minff <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), + M1 = mkinsub("SFO"), + M2 = mkinsub("SFO"), + use_of_ff = "min", quiet = TRUE) + + fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff, + synthetic_data_for_UBA_2014[[12]]$data, + quiet = TRUE) # Note that the k1 and k2 are exchanged in the untransformed fit evaluated with FME for this test expect_equal(signif(summary(fit_DFOP_par_c_2)$bpar[1:7, "t value"], 5), c(parent_0 = 80.054, k_M1_sink = 12.291, k_M2_sink = 10.588, f_parent_to_M1 = 21.4960, f_parent_to_M2 = 24.0890, k1 = 16.1450, k2 = 8.1747)) - }) diff --git a/tests/testthat/test_mkinpredict_SFO_SFO.R b/tests/testthat/test_mkinpredict_SFO_SFO.R index b7004f64..3fcdb3a2 100644 --- a/tests/testthat/test_mkinpredict_SFO_SFO.R +++ b/tests/testthat/test_mkinpredict_SFO_SFO.R @@ -1,6 +1,4 @@ -# $Id: jranke $
-
-# Copyright (C) 2012-2015 Johannes Ranke
+# Copyright (C) 2012-2015,2018 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
diff --git a/tests/testthat/test_parent_only.R b/tests/testthat/test_parent_only.R index ee0cc144..7521e145 100644 --- a/tests/testthat/test_parent_only.R +++ b/tests/testthat/test_parent_only.R @@ -165,6 +165,7 @@ test_that("Fits for FOCUS C deviate less than 0.1% from median of values from FO }) test_that("SFO fits give approximately (0.001%) equal results with different solution methods", { + skip_on_cran() fit.A.SFO.default <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE)$bparms.optim fits.A.SFO <- list() @@ -179,6 +180,7 @@ test_that("SFO fits give approximately (0.001%) equal results with different sol }) test_that("FOMC fits give approximately (0.001%) equal results with different solution methods", { + skip_on_cran() fit.C.FOMC.default <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)$bparms.optim fits.C.FOMC <- list() @@ -191,6 +193,7 @@ test_that("FOMC fits give approximately (0.001%) equal results with different so }) test_that("DFOP fits give approximately (0.001%) equal results with different solution methods", { + skip_on_cran() fit.C.DFOP.default <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)$bparms.optim fits.C.DFOP <- list() diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R index fd3e8bba..6856a9a3 100644 --- a/tests/testthat/test_synthetic_data_for_UBA_2014.R +++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R @@ -20,6 +20,7 @@ context("Results for synthetic data established in expertise for UBA (Ranke 2014 test_that("Results are correct for SFO_lin_a", { + skip_on_cran() m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO", "M2"), M2 = mkinsub("SFO"), diff --git a/tests/testthat/test_twa.R b/tests/testthat/test_twa.R index d5c0b98b..a84b2c4e 100644 --- a/tests/testthat/test_twa.R +++ b/tests/testthat/test_twa.R @@ -18,11 +18,13 @@ context("Calculation of maximum time weighted average concentrations (TWAs)") -twa_models <- c("SFO", "FOMC", "DFOP") -fits <- mmkin(twa_models, list(FOCUS_D = FOCUS_2006_D), - quiet = TRUE, cores = 1) test_that("Time weighted average concentrations are correct", { + skip_on_cran() + twa_models <- c("SFO", "FOMC", "DFOP") + fits <- mmkin(twa_models, list(FOCUS_D = FOCUS_2006_D), + quiet = TRUE, cores = 1) + outtimes_7 <- seq(0, 7, length.out = 10000) for (model in twa_models) { fit <- fits[[model, 1]] |