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Diffstat (limited to 'docs/articles')
| -rw-r--r-- | docs/articles/FOCUS_D.html | 10 | ||||
| -rw-r--r-- | docs/articles/FOCUS_L.html | 58 | ||||
| -rw-r--r-- | docs/articles/mkin.html | 2 | ||||
| -rw-r--r-- | docs/articles/twa.html | 2 | ||||
| -rw-r--r-- | docs/articles/web_only/FOCUS_Z.html | 2 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 14 |
6 files changed, 44 insertions, 44 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 9acab53a..6a8500a0 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -85,7 +85,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-01-31</h4> + <h4 class="date">2019-02-21</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -161,10 +161,10 @@ <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.5 +<pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Jan 31 16:52:37 2019 -## Date of summary: Thu Jan 31 16:52:38 2019 +## Date of fit: Thu Feb 21 14:32:03 2019 +## Date of summary: Thu Feb 21 14:32:04 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -172,7 +172,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.695 s +## Fitted with method Port using 153 model solutions performed in 0.735 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index e3ca9aff..265dd96c 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -85,7 +85,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-01-31</h4> + <h4 class="date">2019-02-21</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -109,17 +109,17 @@ <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.5 +<pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Jan 31 16:52:39 2019 -## Date of summary: Thu Jan 31 16:52:39 2019 +## Date of fit: Thu Feb 21 14:32:06 2019 +## Date of summary: Thu Feb 21 14:32:06 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.094 s +## Fitted with method Port using 37 model solutions performed in 0.097 s ## ## Weighting: none ## @@ -200,17 +200,17 @@ <a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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 +<pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Jan 31 16:52:41 2019 -## Date of summary: Thu Jan 31 16:52:41 2019 +## Date of fit: Thu Feb 21 14:32:08 2019 +## Date of summary: Thu Feb 21 14:32:08 2019 ## ## 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 1.49 s +## Fitted with method Port using 611 model solutions performed in 1.547 s ## ## Weighting: none ## @@ -295,17 +295,17 @@ <a class="sourceLine" id="cb11-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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 +<pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Jan 31 16:52:42 2019 -## Date of summary: Thu Jan 31 16:52:42 2019 +## Date of fit: Thu Feb 21 14:32:08 2019 +## Date of summary: Thu Feb 21 14:32:08 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.198 s +## Fitted with method Port using 81 model solutions performed in 0.201 s ## ## Weighting: none ## @@ -366,10 +366,10 @@ <a class="sourceLine" id="cb14-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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 +<pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Jan 31 16:52:43 2019 -## Date of summary: Thu Jan 31 16:52:43 2019 +## Date of fit: Thu Feb 21 14:32:09 2019 +## Date of summary: Thu Feb 21 14:32:09 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -378,7 +378,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.839 s +## Fitted with method Port using 336 model solutions performed in 0.86 s ## ## Weighting: none ## @@ -458,10 +458,10 @@ <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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 +<pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Jan 31 16:52:44 2019 -## Date of summary: Thu Jan 31 16:52:44 2019 +## Date of fit: Thu Feb 21 14:32:10 2019 +## Date of summary: Thu Feb 21 14:32:11 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -470,7 +470,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.341 s +## Fitted with method Port using 137 model solutions performed in 0.351 s ## ## Weighting: none ## @@ -559,17 +559,17 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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 +<pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Jan 31 16:52:44 2019 -## Date of summary: Thu Jan 31 16:52:45 2019 +## Date of fit: Thu Feb 21 14:32:11 2019 +## Date of summary: Thu Feb 21 14:32:11 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.11 s +## Fitted with method Port using 46 model solutions performed in 0.113 s ## ## Weighting: none ## @@ -619,17 +619,17 @@ ## DT50 DT90 ## parent 106 352</code></pre> <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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 +<pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Jan 31 16:52:45 2019 -## Date of summary: Thu Jan 31 16:52:45 2019 +## Date of fit: Thu Feb 21 14:32:11 2019 +## Date of summary: Thu Feb 21 14:32:11 2019 ## ## 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 0.162 s +## Fitted with method Port using 66 model solutions performed in 0.168 s ## ## Weighting: none ## diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 488ca302..c5b0d9c1 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -85,7 +85,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-01-31</h4> + <h4 class="date">2019-02-21</h4> <div class="hidden name"><code>mkin.Rmd</code></div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index d50b23ba..8a1f82a8 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -85,7 +85,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-01-31</h4> + <h4 class="date">2019-02-21</h4> <div class="hidden name"><code>twa.Rmd</code></div> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 84bd971f..c55abdbc 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -85,7 +85,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-01-31</h4> + <h4 class="date">2019-02-21</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 08bb9b44..3a37d114 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -85,7 +85,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-01-31</h4> + <h4 class="date">2019-02-21</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -126,9 +126,9 @@ <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 2.353 1.000 2.352 0 -## 1 deSolve, not compiled 3 17.619 7.488 17.609 0 -## 2 Eigenvalue based 3 2.899 1.232 2.898 0 +## 3 deSolve, compiled 3 2.429 1.000 2.427 0 +## 1 deSolve, not compiled 3 17.826 7.339 17.815 0 +## 2 Eigenvalue based 3 2.968 1.222 2.967 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -157,13 +157,13 @@ <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 4.180 1.000 4.177 0 -## 1 deSolve, not compiled 3 37.331 8.931 37.312 0 +## 2 deSolve, compiled 3 4.234 1.000 4.232 0 +## 1 deSolve, not compiled 3 37.807 8.929 37.785 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> <p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.47.5 on</p> +<p>This vignette was built with mkin 0.9.47.6 on</p> <pre><code>## R version 3.5.2 (2018-12-20) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 9 (stretch)</code></pre> |