diff options
Diffstat (limited to 'docs')
34 files changed, 456 insertions, 154 deletions
diff --git a/docs/dev/404.html b/docs/dev/404.html index 9d14af1e..8ca69469 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -160,7 +160,7 @@ Content not found. Please use links in the navbar. </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index b8ba57d8..81d49aa3 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -173,7 +173,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html index 6865fe96..07627029 100644 --- a/docs/dev/articles/mkin.html +++ b/docs/dev/articles/mkin.html @@ -32,7 +32,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -80,7 +80,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -101,9 +101,9 @@ <h1 data-toc-skip>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-10-08</h4> + <h4 class="date">2020-10-15</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/mkin.rmd"><code>vignettes/mkin.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/mkin.rmd"><code>vignettes/mkin.rmd</code></a></small> <div class="hidden name"><code>mkin.rmd</code></div> </div> @@ -115,34 +115,35 @@ <h1 class="hasAnchor"> <a href="#abstract" class="anchor"></a>Abstract</h1> <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The <code>R</code> add-on package <code>mkin</code> implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p> -<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"mkin"</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +<div class="sourceCode" id="cb1"><pre class="downlit"> +<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># Define the kinetic model</span> -<span class="no">m_SFO_SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/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="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>), - <span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../reference/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>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +<span class="va">m_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>, + M1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>, + M2 <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, + use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># Produce model predictions using some arbitrary parameters</span> -<span class="no">sampling_times</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span>) -<span class="no">d_SFO_SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span>(<span class="no">m_SFO_SFO_SFO</span>, - <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">k_parent</span> <span class="kw">=</span> <span class="fl">0.03</span>, - <span class="kw">f_parent_to_M1</span> <span class="kw">=</span> <span class="fl">0.5</span>, <span class="kw">k_M1</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html">log</a></span>(<span class="fl">2</span>)/<span class="fl">100</span>, - <span class="kw">f_M1_to_M2</span> <span class="kw">=</span> <span class="fl">0.9</span>, <span class="kw">k_M2</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html">log</a></span>(<span class="fl">2</span>)/<span class="fl">50</span>), - <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></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="kw">M2</span> <span class="kw">=</span> <span class="fl">0</span>), - <span class="no">sampling_times</span>) +<span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span> +<span class="va">d_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, + <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.03</span>, + f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">100</span>, + f_M1_to_M2 <span class="op">=</span> <span class="fl">0.9</span>, k_M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">50</span><span class="op">)</span>, + <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, + <span class="va">sampling_times</span><span class="op">)</span> <span class="co"># Generate a dataset by adding normally distributed errors with</span> <span class="co"># standard deviation 3, for two replicates at each sampling time</span> -<span class="no">d_SFO_SFO_SFO_err</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span>(<span class="no">d_SFO_SFO_SFO</span>, <span class="kw">reps</span> <span class="kw">=</span> <span class="fl">2</span>, - <span class="kw">sdfunc</span> <span class="kw">=</span> <span class="kw">function</span>(<span class="no">x</span>) <span class="fl">3</span>, - <span class="kw">n</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">seed</span> <span class="kw">=</span> <span class="fl">123456789</span> ) +<span class="va">d_SFO_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_SFO_SFO</span>, reps <span class="op">=</span> <span class="fl">2</span>, + sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">3</span>, + n <span class="op">=</span> <span class="fl">1</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span> <span class="co"># Fit the model to the dataset</span> -<span class="no">f_SFO_SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">m_SFO_SFO_SFO</span>, <span class="no">d_SFO_SFO_SFO_err</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="va">f_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, <span class="va">d_SFO_SFO_SFO_err</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># Plot the results separately for parent and metabolites</span> -<span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">f_SFO_SFO_SFO</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></div> +<span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_SFO_SFO_SFO</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></pre></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> @@ -248,7 +249,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex bdc067c1..2f3d7a46 100644 --- a/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html index 09f40a7f..ebe4b84e 100644 --- a/docs/dev/articles/web_only/NAFTA_examples.html +++ b/docs/dev/articles/web_only/NAFTA_examples.html @@ -32,7 +32,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -80,7 +80,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -101,9 +101,9 @@ <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-10-08</h4> + <h4 class="date">2020-10-15</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> </div> @@ -123,12 +123,15 @@ <div id="example-on-page-5-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-upper-panel" class="anchor"></a>Example on page 5, upper panel</h2> -<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">p5a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p5a"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb1"><pre class="downlit"> +<span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p5a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb4"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p5a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb5"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -171,12 +174,15 @@ <div id="example-on-page-5-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2> -<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">p5b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p5b"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb7"><pre class="downlit"> +<span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p5b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb10"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p5b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb11"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -219,12 +225,15 @@ <div id="example-on-page-6" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2> -<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="no">p6</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p6"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb13"><pre class="downlit"> +<span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p6</span>)</pre></body></html></div> +<div class="sourceCode" id="cb16"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p6</span>)</pre></body></html></div> +<div class="sourceCode" id="cb17"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -267,12 +276,15 @@ <div id="example-on-page-7" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2> -<div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">p7</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p7"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb19"><pre class="downlit"> +<span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb22"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p7</span>)</pre></body></html></div> +<div class="sourceCode" id="cb22"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p7</span>)</pre></body></html></div> +<div class="sourceCode" id="cb23"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -320,12 +332,15 @@ <h2 class="hasAnchor"> <a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> -<div class="sourceCode" id="cb25"><html><body><pre class="r"><span class="no">p8</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p8"</span>]], <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">k__iore_parent</span> <span class="kw">=</span> <span class="fl">1e-3</span>))</pre></body></html></div> +<div class="sourceCode" id="cb25"><pre class="downlit"> +<span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p8</span>)</pre></body></html></div> +<div class="sourceCode" id="cb28"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p8</span>)</pre></body></html></div> +<div class="sourceCode" id="cb29"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -372,12 +387,15 @@ <div id="example-on-page-9-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2> -<div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="no">p9a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p9a"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb31"><pre class="downlit"> +<span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb34"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p9a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb34"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<div class="sourceCode" id="cb35"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p9a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb35"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -421,12 +439,15 @@ <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb37"><html><body><pre class="r"><span class="no">p9b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p9b"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb37"><pre class="downlit"> +<span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb40"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p9b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb40"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p9b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb41"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -470,12 +491,15 @@ <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb43"><html><body><pre class="r"><span class="no">p10</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p10"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb43"><pre class="downlit"> +<span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb46"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p10</span>)</pre></body></html></div> +<div class="sourceCode" id="cb46"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb47"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p10</span>)</pre></body></html></div> +<div class="sourceCode" id="cb47"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -523,12 +547,15 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb49"><html><body><pre class="r"><span class="no">p11</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p11"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb49"><pre class="downlit"> +<span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb52"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p11</span>)</pre></body></html></div> +<div class="sourceCode" id="cb52"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb53"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p11</span>)</pre></body></html></div> +<div class="sourceCode" id="cb53"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -577,14 +604,17 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb55"><html><body><pre class="r"><span class="no">p12a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12a"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb55"><pre class="downlit"> +<span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance ## matrix</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb59"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb59"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb60"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb60"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -627,7 +657,8 @@ <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb62"><html><body><pre class="r"><span class="no">p12b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12b"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb62"><pre class="downlit"> +<span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre> <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre> @@ -638,9 +669,11 @@ ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb72"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb72"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb73"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb73"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -683,12 +716,15 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb75"><html><body><pre class="r"><span class="no">p13</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p13"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb75"><pre class="downlit"> +<span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb78"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p13</span>)</pre></body></html></div> +<div class="sourceCode" id="cb78"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb79"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p13</span>)</pre></body></html></div> +<div class="sourceCode" id="cb79"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -732,16 +768,19 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb81"><html><body><pre class="r"><span class="no">p14</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p14"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb81"><pre class="downlit"> +<span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb87"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p14</span>)</pre></body></html></div> +<div class="sourceCode" id="cb87"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb88"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p14</span>)</pre></body></html></div> +<div class="sourceCode" id="cb88"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -785,16 +824,19 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb90"><html><body><pre class="r"><span class="no">p15a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15a"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb90"><pre class="downlit"> +<span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb96"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb96"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb97"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb97"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -833,16 +875,19 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb99"><html><body><pre class="r"><span class="no">p15b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15b"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb99"><pre class="downlit"> +<span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb105"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb105"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb106"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb106"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -886,14 +931,17 @@ <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb108"><html><body><pre class="r"><span class="no">p16</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p16"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb108"><pre class="downlit"> +<span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb113"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p16</span>)</pre></body></html></div> +<div class="sourceCode" id="cb113"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb114"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p16</span>)</pre></body></html></div> +<div class="sourceCode" id="cb114"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -966,7 +1014,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png Binary files differindex 291b48e1..3e9c743f 100644 --- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png +++ 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title="In-development version">0.9.50.4</span> </span> </div> @@ -171,7 +171,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/index.html b/docs/dev/index.html index 76113d7c..16f903d8 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -112,7 +112,8 @@ <h2 class="hasAnchor"> <a href="#installation" class="anchor"></a>Installation</h2> <p>You can install the latest released version from <a href="https://cran.r-project.org/package=mkin">CRAN</a> from within R:</p> -<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"mkin"</span>)</pre></div> +<div class="sourceCode" id="cb1"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span></pre></div> </div> <div id="background" class="section level2"> <h2 class="hasAnchor"> @@ -238,7 +239,7 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 5851c638..190bfe87 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -141,9 +141,17 @@ <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small> </div> - <div id="mkin-0-9-50-3" class="section level1"> + <div id="mkin-0-9-50-4-unreleased" class="section level1"> +<h1 class="page-header" data-toc-text="0.9.50.4"> +<a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small> +</h1> +<ul> +<li>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</li> +</ul> +</div> + <div id="mkin-0-9-50-3-2020-10-08" class="section level1"> <h1 class="page-header" data-toc-text="0.9.50.3"> -<a href="#mkin-0-9-50-3" class="anchor"></a>mkin 0.9.50.3<small> Unreleased </small> +<a href="#mkin-0-9-50-3-2020-10-08" class="anchor"></a>mkin 0.9.50.3 (2020-10-08)<small> 2020-10-08 </small> </h1> <ul> <li><p>‘parms’: Add a method for mmkin objects</p></li> @@ -835,7 +843,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/pkgdown.css b/docs/dev/pkgdown.css index c01e5923..1273238d 100644 --- a/docs/dev/pkgdown.css +++ b/docs/dev/pkgdown.css @@ -244,14 +244,14 @@ nav[data-toggle='toc'] .nav .nav > .active:focus > a { .ref-index th {font-weight: normal;} -.ref-index td {vertical-align: top;} +.ref-index td {vertical-align: top; min-width: 100px} .ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} .ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} -.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} .ref-arguments .name {width: 20%;} .ref-arguments .desc {width: 80%;} diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 116561ef..58255596 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -1,16 +1,16 @@ pandoc: 2.2.1 -pkgdown: 1.5.1 +pkgdown: 1.6.1 pkgdown_sha: ~ articles: FOCUS_D: FOCUS_D.html FOCUS_L: FOCUS_L.html mkin: mkin.html twa: twa.html - FOCUS_Z: web_only/FOCUS_Z.html - NAFTA_examples: web_only/NAFTA_examples.html - benchmarks: web_only/benchmarks.html - compiled_models: web_only/compiled_models.html -last_built: 2020-10-08T07:50Z + web_only/FOCUS_Z: FOCUS_Z.html + web_only/NAFTA_examples: NAFTA_examples.html + web_only/benchmarks: benchmarks.html + web_only/compiled_models: compiled_models.html +last_built: 2020-10-15T09:55Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index 1858e243..5a20a34c 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -126,7 +126,7 @@ advantage that the SFORB model can also be used for metabolites." /> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -146,7 +146,7 @@ advantage that the SFORB model can also be used for metabolites." /> <div class="page-header"> <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/endpoints.R'><code>R/endpoints.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/endpoints.R'><code>R/endpoints.R</code></a></small> <div class="hidden name"><code>endpoints.Rd</code></div> </div> @@ -158,7 +158,7 @@ are equivalent to the rate constants of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites.</p> </div> - <pre class="usage"><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre> + <pre class="usage"><span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -179,20 +179,26 @@ of these SFORB models, equivalent to DFOP rate constants</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>Johannes Ranke</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $distimes + <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='output co'>#> $distimes #> DT50 DT90 DT50back #> parent 1.785233 15.1479 4.559973 #> </div><div class='input'> <span class='co'># \dontrun{</span> - <span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</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'>endpoints</span>(<span class='no'>fit_2</span>)</div><div class='output co'>#> $distimes + <span class='va'>fit_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span> +</div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 1.886925 21.25106 6.397207 1.508293 38.83438 -#> </div><div class='input'> <span class='no'>fit_3</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFORB"</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'>endpoints</span>(<span class='no'>fit_3</span>)</div><div class='output co'>#> $ff +#> </div><div class='input'> <span class='va'>fit_3</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFORB"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit_3</span><span class='op'>)</span> +</div><div class='output co'>#> $ff #> parent_free #> 1 #> @@ -203,7 +209,7 @@ of these SFORB models, equivalent to DFOP rate constants</p> #> $distimes #> DT50 DT90 DT50back DT50_parent_b1 DT50_parent_b2 #> parent 1.886925 21.25106 6.397208 1.508293 38.83438 -#> </div><div class='input'> # } +#> </div><div class='input'> <span class='co'># }</span> </div></pre> </div> @@ -221,7 +227,7 @@ of these SFORB models, equivalent to DFOP rate constants</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index a5cd6663..5d70a450 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -678,7 +678,7 @@ kinetic models fitted with mkinfit</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/reference/saemix-1.png b/docs/dev/reference/saemix-1.png Binary files differindex 0d79300d..696fa7d9 100644 --- a/docs/dev/reference/saemix-1.png +++ b/docs/dev/reference/saemix-1.png diff --git a/docs/dev/reference/saemix-2.png b/docs/dev/reference/saemix-2.png Binary files differindex 04de70b5..6525a36c 100644 --- a/docs/dev/reference/saemix-2.png +++ b/docs/dev/reference/saemix-2.png diff --git a/docs/dev/reference/saemix-3.png b/docs/dev/reference/saemix-3.png Binary files differnew file mode 100644 index 00000000..13157f91 --- /dev/null +++ b/docs/dev/reference/saemix-3.png diff --git a/docs/dev/reference/saemix-4.png b/docs/dev/reference/saemix-4.png Binary files differnew file mode 100644 index 00000000..1e717cb2 --- /dev/null +++ b/docs/dev/reference/saemix-4.png diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html index da28bff1..5b160959 100644 --- a/docs/dev/reference/saemix.html +++ b/docs/dev/reference/saemix.html @@ -75,7 +75,7 @@ a list of datasets." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -123,7 +123,7 @@ a list of datasets." /> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -142,7 +142,7 @@ a list of datasets." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create saemix models from mmkin row objects</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small> <div class="hidden name"><code>saemix.Rd</code></div> </div> @@ -153,9 +153,9 @@ list of mkinfit objects that have been obtained by fitting the same model to a list of datasets.</p> </div> - <pre class="usage"><span class='fu'>saemix_model</span>(<span class='no'>object</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span>()) + <pre class="usage"><span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'>saemix_data</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre> +<span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -187,14 +187,17 @@ mmkin. Starting variances of the random effects (argument omega.init) are the variances of the deviations of the parameters from these mean values.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>], - <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)])) -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>) -<span class='no'>sfo_sfo</span> <span class='kw'><-</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='st'>"A1"</span>), - <span class='kw'>A1</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'># \dontrun{</span> -<span class='no'>f_mmkin</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>sfo_sfo</span>), <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>saemix</span>)</div><div class='output co'>#> <span class='message'>Package saemix, version 3.1.9000</span> -#> <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='no'>m_saemix</span> <span class='kw'><-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#> + <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, + <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span> +<span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, + A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</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'># \dontrun{</span> +<span class='va'>f_mmkin</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>sfo_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Package saemix, version 3.1.9000</span> +#> <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='va'>m_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +</div><div class='output co'>#> #> #> The following SaemixModel object was successfully created: #> @@ -234,8 +237,8 @@ variances of the deviations of the parameters from these mean values.</p> #> res <- unlist(res_list) #> return(res) #> } -#> <bytecode: 0x55555bbf17c0> -#> <environment: 0x55555bbec4e0> +#> <bytecode: 0x55555c1e7720> +#> <environment: 0x55555c1eff38> #> Nb of parameters: 4 #> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> distribution: @@ -250,11 +253,12 @@ variances of the deviations of the parameters from these mean values.</p> #> log_k_parent 0 1 0 0 #> log_k_A1 0 0 1 0 #> f_parent_ilr_1 0 0 0 1 -#> Error model: constant , initial values: a.1=1 +#> Error model: constant , initial values: a.1=4.97259024646577 #> No covariate in the model. #> Initial values #> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 -#> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449</div><div class='input'><span class='no'>d_saemix</span> <span class='kw'><-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#> +#> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449</div><div class='input'><span class='va'>d_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> +</div><div class='output co'>#> #> #> The following SaemixData object was successfully created: #> @@ -262,14 +266,15 @@ variances of the deviations of the parameters from these mean values.</p> #> longitudinal data for use with the SAEM algorithm #> Dataset ds_saemix #> Structured data: value ~ time + name | ds -#> X variable for graphs: time () </div><div class='input'><span class='no'>saemix_options</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>, - <span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.graphs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>displayProgress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>nbiter.saemix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>200</span>, <span class='fl'>80</span>)) -<span class='no'>f_saemix</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span>(<span class='no'>m_saemix</span>, <span class='no'>d_saemix</span>, <span class='no'>saemix_options</span>)</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed May 27 07:45:07 2020" +#> X variable for graphs: time () </div><div class='input'><span class='va'>saemix_options</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>seed <span class='op'>=</span> <span class='fl'>123456</span>, + save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span>, displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, + nbiter.saemix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>200</span>, <span class='fl'>80</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>f_saemix</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix</span>, <span class='va'>d_saemix</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Oct 15 11:55:14 2020" #> .. #> Minimisation finished -#> [1] "Wed May 27 07:51:24 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> [1] "Thu Oct 15 11:57:07 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm #> ----------------------------------- #> ---- Data ---- #> ----------------------------------- @@ -333,8 +338,8 @@ variances of the deviations of the parameters from these mean values.</p> #> res <- unlist(res_list) #> return(res) #> } -#> <bytecode: 0x55555bbf17c0> -#> <environment: 0x55555bbec4e0> +#> <bytecode: 0x55555c1e7720> +#> <environment: 0x55555c1eff38> #> Nb of parameters: 4 #> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> distribution: @@ -349,7 +354,7 @@ variances of the deviations of the parameters from these mean values.</p> #> log_k_parent 0 1 0 0 #> log_k_A1 0 0 1 0 #> f_parent_ilr_1 0 0 0 1 -#> Error model: constant , initial values: a.1=1 +#> Error model: constant , initial values: a.1=4.97259024646577 #> No covariate in the model. #> Initial values #> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 @@ -375,20 +380,20 @@ variances of the deviations of the parameters from these mean values.</p> #> ---------------------------------------------------- #> ----------------- Fixed effects ------------------ #> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> [1,] parent_0 86.14 1.61 1.9 -#> [2,] log_k_parent -3.21 0.59 18.5 -#> [3,] log_k_A1 -4.66 0.30 6.4 -#> [4,] f_parent_ilr_1 -0.33 0.30 91.7 -#> [5,] a.1 4.68 0.27 5.8 +#> Parameter Estimate SE CV(%) +#> parent_0 86.09 1.57 1.8 +#> log_k_parent -3.21 0.59 18.5 +#> log_k_A1 -4.69 0.31 6.6 +#> f_parent_ilr_1 -0.34 0.30 89.2 +#> a a.1 4.69 0.27 5.8 #> ---------------------------------------------------- #> ----------- Variance of random effects ----------- #> ---------------------------------------------------- #> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 7.71 8.14 106 -#> log_k_parent omega2.log_k_parent 1.76 1.12 63 -#> log_k_A1 omega2.log_k_A1 0.26 0.26 101 -#> f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.28 71 +#> parent_0 omega2.parent_0 7.07 7.72 109 +#> log_k_parent omega2.log_k_parent 1.75 1.11 63 +#> log_k_A1 omega2.log_k_A1 0.28 0.28 99 +#> f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.27 71 #> ---------------------------------------------------- #> ------ Correlation matrix of random effects ------ #> ---------------------------------------------------- @@ -406,15 +411,245 @@ variances of the deviations of the parameters from these mean values.</p> #> --------------- Statistical criteria ------------- #> ---------------------------------------------------- #> Likelihood computed by linearisation -#> -2LL= 1064.364 -#> AIC = 1082.364 -#> BIC = 1078.848 +#> -2LL= 1064.35 +#> AIC = 1082.35 +#> BIC = 1078.835 #> #> Likelihood computed by importance sampling -#> -2LL= 1063.462 -#> AIC = 1081.462 -#> BIC = 1077.947 -#> ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span>(<span class='no'>f_saemix</span>, <span class='kw'>plot.type</span> <span class='kw'>=</span> <span class='st'>"convergence"</span>)</div><div class='output co'>#> Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'># } +#> -2LL= 1063.475 +#> AIC = 1081.475 +#> BIC = 1077.96 +#> ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saemix</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> +</div><div class='output co'>#> Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +<span class='co'># Synthetic data with two-component error</span> +<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> +<span class='va'>dt50_sfo_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>800</span>, <span class='fl'>900</span>, <span class='fl'>1000</span>, <span class='fl'>1111.11</span>, <span class='fl'>1250</span><span class='op'>)</span> +<span class='va'>k_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in</span> + +<span class='va'>SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> + +<span class='va'>pred_sfo</span> <span class='op'><-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><span class='op'>)</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> +<span class='op'>}</span> + +<span class='va'>ds_sfo_mean</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456L</span><span class='op'>)</span> +<span class='va'>ds_sfo_syn</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>, + n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> + <span class='op'>}</span><span class='op'>)</span> +<span class='va'>f_mmkin_syn</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>m_saemix_tc</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +</div><div class='output co'>#> +#> +#> The following SaemixModel object was successfully created: +#> +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> uid <- unique(id) +#> res_list <- parallel::mclapply(uid, function(i) { +#> transparms_optim <- psi[i, ] +#> names(transparms_optim) <- names(degparms_optim) +#> odeini_optim <- transparms_optim[odeini_optim_parm_names] +#> names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names) +#> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] +#> ode_transparms_optim_names <- setdiff(names(transparms_optim), +#> odeini_optim_parm_names) +#> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], +#> mkin_model, transform_rates = object[[1]]$transform_rates, +#> transform_fractions = object[[1]]$transform_fractions) +#> odeparms <- c(odeparms_optim, odeparms_fixed) +#> xidep_i <- subset(xidep, id == i) +#> if (analytical) { +#> out_values <- mkin_model$deg_func(xidep_i, odeini, +#> odeparms) +#> } +#> else { +#> i_time <- xidep_i$time +#> i_name <- xidep_i$name +#> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, +#> odeini = odeini, solution_type = object[[1]]$solution_type, +#> outtimes = sort(unique(i_time))) +#> out_index <- cbind(as.character(i_time), as.character(i_name)) +#> out_values <- out_wide[out_index] +#> } +#> return(out_values) +#> }, mc.cores = cores) +#> res <- unlist(res_list) +#> return(res) +#> } +#> <bytecode: 0x55555c1e7720> +#> <environment: 0x55555be5b848> +#> Nb of parameters: 2 +#> parameter names: parent_0 log_k_parent +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_parent normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_k_parent +#> parent_0 1 0 +#> log_k_parent 0 1 +#> Error model: combined , initial values: a.1=2.4206146215511 b.1=0.03831266409084 +#> No covariate in the model. +#> Initial values +#> parent_0 log_k_parent +#> Pop.CondInit 100.2498 -9.33922</div><div class='input'><span class='va'>d_saemix_tc</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span><span class='op'>)</span> +</div><div class='output co'>#> +#> +#> The following SaemixData object was successfully created: +#> +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_tc</span>, <span class='va'>d_saemix_tc</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Oct 15 11:57:25 2020" +#> .. +#> Minimisation finished +#> [1] "Thu Oct 15 11:58:16 2020" +#> Error in solve.default(Fth) : +#> Lapack routine dgesv: system is exactly singular: U[2,2] = 0 +#> Error computing the Fisher Information Matrix: singular system. +#> Error in solve.default(FO) : +#> Lapack routine dgesv: system is exactly singular: U[2,2] = 0 +#> Error computing the Fisher Information Matrix: singular system.</div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> ----------------------------------- +#> ---- Data ---- +#> ----------------------------------- +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () +#> Dataset characteristics: +#> number of subjects: 5 +#> number of observations: 90 +#> average/min/max nb obs: 18.00 / 18 / 18 +#> First 10 lines of data: +#> ds time name value mdv cens occ ytype +#> 1 1 0 parent 105.9 0 0 1 1 +#> 2 1 0 parent 98.0 0 0 1 1 +#> 3 1 1 parent 97.4 0 0 1 1 +#> 4 1 1 parent 100.5 0 0 1 1 +#> 5 1 3 parent 115.6 0 0 1 1 +#> 6 1 3 parent 105.6 0 0 1 1 +#> 7 1 7 parent 108.6 0 0 1 1 +#> 8 1 7 parent 117.0 0 0 1 1 +#> 9 1 14 parent 107.0 0 0 1 1 +#> 10 1 14 parent 95.8 0 0 1 1 +#> ----------------------------------- +#> ---- Model ---- +#> ----------------------------------- +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> uid <- unique(id) +#> res_list <- parallel::mclapply(uid, function(i) { +#> transparms_optim <- psi[i, ] +#> names(transparms_optim) <- names(degparms_optim) +#> odeini_optim <- transparms_optim[odeini_optim_parm_names] +#> names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names) +#> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] +#> ode_transparms_optim_names <- setdiff(names(transparms_optim), +#> odeini_optim_parm_names) +#> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], +#> mkin_model, transform_rates = object[[1]]$transform_rates, +#> transform_fractions = object[[1]]$transform_fractions) +#> odeparms <- c(odeparms_optim, odeparms_fixed) +#> xidep_i <- subset(xidep, id == i) +#> if (analytical) { +#> out_values <- mkin_model$deg_func(xidep_i, odeini, +#> odeparms) +#> } +#> else { +#> i_time <- xidep_i$time +#> i_name <- xidep_i$name +#> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, +#> odeini = odeini, solution_type = object[[1]]$solution_type, +#> outtimes = sort(unique(i_time))) +#> out_index <- cbind(as.character(i_time), as.character(i_name)) +#> out_values <- out_wide[out_index] +#> } +#> return(out_values) +#> }, mc.cores = cores) +#> res <- unlist(res_list) +#> return(res) +#> } +#> <bytecode: 0x55555c1e7720> +#> <environment: 0x55555be5b848> +#> Nb of parameters: 2 +#> parameter names: parent_0 log_k_parent +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_parent normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_k_parent +#> parent_0 1 0 +#> log_k_parent 0 1 +#> Error model: combined , initial values: a.1=2.4206146215511 b.1=0.03831266409084 +#> No covariate in the model. +#> Initial values +#> parent_0 log_k_parent +#> Pop.CondInit 100.2498 -9.33922 +#> ----------------------------------- +#> ---- Key algorithm options ---- +#> ----------------------------------- +#> Estimation of individual parameters (MAP) +#> Estimation of standard errors and linearised log-likelihood +#> Estimation of log-likelihood by importance sampling +#> Number of iterations: K1=200, K2=80 +#> Number of chains: 10 +#> Seed: 123456 +#> Number of MCMC iterations for IS: 5000 +#> Simulations: +#> nb of simulated datasets used for npde: 1000 +#> nb of simulated datasets used for VPC: 100 +#> Input/output +#> save the results to a file: FALSE +#> save the graphs to files: FALSE +#> ---------------------------------------------------- +#> ---- Results ---- +#> ---------------------------------------------------- +#> ----------------- Fixed effects ------------------ +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 97.44 <NA> <NA> +#> log_k_parent -56.97 <NA> <NA> +#> a a.1 -7.12 <NA> <NA> +#> b b.1 0.15 <NA> <NA> +#> ---------------------------------------------------- +#> ----------- Variance of random effects ----------- +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 omega2.parent_0 2.8 NA NA +#> log_k_parent omega2.log_k_parent 750.3 NA NA +#> ---------------------------------------------------- +#> ------ Correlation matrix of random effects ------ +#> ---------------------------------------------------- +#> omega2.parent_0 omega2.log_k_parent +#> omega2.parent_0 1 0 +#> omega2.log_k_parent 0 1 +#> ---------------------------------------------------- +#> --------------- Statistical criteria ------------- +#> ---------------------------------------------------- +#> Likelihood computed by linearisation +#> -2LL= 623.7744 +#> AIC = 635.7744 +#> BIC = 633.431 +#> +#> Likelihood computed by importance sampling +#> -2LL= 621.1909 +#> AIC = 633.1909 +#> BIC = 630.8475 +#> ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saemix_tc</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> +</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> Plotting convergence plots</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -431,7 +666,7 @@ variances of the deviations of the parameters from these mean values.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index 81368436..e284abf6 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -172,6 +172,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/residuals.mkinfit.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/saemix.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html</loc> </url> <url> |
