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Diffstat (limited to 'docs')
132 files changed, 3369 insertions, 1357 deletions
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index 02701431..e526b3a7 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.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> @@ -95,15 +95,16 @@ - </header><div class="row"> + </header><link href="FOCUS_D_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> +<script src="FOCUS_D_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-10-08</h4> + <h4 class="date">2020-11-19</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.rmd</code></div> </div> @@ -111,8 +112,9 @@ <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look at the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</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="no">mkin</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>) -<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">FOCUS_2006_D</span>)</pre></body></html></div> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><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="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></code></pre></div> <pre><code>## name time value ## 1 parent 0 99.46 ## 2 parent 0 102.04 @@ -160,31 +162,35 @@ ## 44 m1 120 33.31</code></pre> <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p> <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> -<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></div> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></code></pre></div> <pre><code>## parent ## "d_parent = - k_parent * parent" ## m1 ## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> -<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">fit</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value ## of zero were removed from the data</code></pre> -<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Shapiro-Wilk test for -## standardized residuals: p = 0.0165</code></pre> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p> -<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">fit</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>))</pre></body></html></div> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</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="op">)</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> -<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">fit</span>)</pre></body></html></div> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> -<div class="sourceCode" id="cb12"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.50.3 -## R version used for fitting: 4.0.2 -## Date of fit: Thu Oct 8 09:14:03 2020 -## Date of summary: Thu Oct 8 09:14:03 2020 +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.50.4 +## R version used for fitting: 4.0.3 +## Date of fit: Thu Nov 19 15:00:06 2020 +## Date of summary: Thu Nov 19 15:00:06 2020 ## ## Equations: ## d_parent/dt = - k_parent * parent @@ -192,7 +198,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 421 model solutions performed in 0.171 s +## Fitted using 401 model solutions performed in 0.188 s ## ## Error model: Constant variance ## @@ -206,11 +212,11 @@ ## f_parent_to_m1 0.5000 deparm ## ## Starting values for the transformed parameters actually optimised: -## value lower upper -## parent_0 100.750000 -Inf Inf -## log_k_parent -2.302585 -Inf Inf -## log_k_m1 -2.301586 -Inf Inf -## f_parent_ilr_1 0.000000 -Inf Inf +## value lower upper +## parent_0 100.750000 -Inf Inf +## log_k_parent -2.302585 -Inf Inf +## log_k_m1 -2.301586 -Inf Inf +## f_parent_qlogis 0.000000 -Inf Inf ## ## Fixed parameter values: ## value type @@ -219,7 +225,6 @@ ## ## Warning(s): ## Observations with value of zero were removed from the data -## Shapiro-Wilk test for standardized residuals: p = 0.0165 ## ## Results: ## @@ -227,20 +232,20 @@ ## 204.4486 212.6365 -97.22429 ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 99.60000 1.57000 96.40000 102.8000 -## log_k_parent -2.31600 0.04087 -2.39900 -2.2330 -## log_k_m1 -5.24800 0.13320 -5.51800 -4.9770 -## f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694 -## sigma 3.12600 0.35850 2.39600 3.8550 +## Estimate Std. Error Lower Upper +## parent_0 99.60000 1.57000 96.4000 102.8000 +## log_k_parent -2.31600 0.04087 -2.3990 -2.2330 +## log_k_m1 -5.24700 0.13320 -5.5180 -4.9770 +## f_parent_qlogis 0.05792 0.08926 -0.1237 0.2395 +## sigma 3.12600 0.35850 2.3960 3.8550 ## ## Parameter correlation: -## parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma -## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.214e-07 -## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07 -## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.410e-07 -## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 5.093e-10 -## sigma -3.214e-07 3.168e-07 -1.410e-07 5.093e-10 1.000e+00 +## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma +## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.171e-06 +## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.481e-07 +## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.209e-07 +## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06 +## sigma -1.171e-06 -8.481e-07 8.209e-07 1.305e-06 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -277,10 +282,10 @@ ## 1 parent 92.50 90.23787 2.262e+00 ## 3 parent 63.23 74.07319 -1.084e+01 ## 3 parent 68.99 74.07319 -5.083e+00 -## 7 parent 52.32 49.91206 2.408e+00 -## 7 parent 55.13 49.91206 5.218e+00 -## 14 parent 27.27 25.01257 2.257e+00 -## 14 parent 26.64 25.01257 1.627e+00 +## 7 parent 52.32 49.91207 2.408e+00 +## 7 parent 55.13 49.91207 5.218e+00 +## 14 parent 27.27 25.01258 2.257e+00 +## 14 parent 26.64 25.01258 1.627e+00 ## 21 parent 11.50 12.53462 -1.035e+00 ## 21 parent 11.64 12.53462 -8.946e-01 ## 35 parent 2.85 3.14787 -2.979e-01 @@ -288,25 +293,25 @@ ## 50 parent 0.69 0.71624 -2.624e-02 ## 50 parent 0.63 0.71624 -8.624e-02 ## 75 parent 0.05 0.06074 -1.074e-02 -## 75 parent 0.06 0.06074 -7.381e-04 +## 75 parent 0.06 0.06074 -7.382e-04 ## 1 m1 4.84 4.80296 3.704e-02 ## 1 m1 5.64 4.80296 8.370e-01 ## 3 m1 12.91 13.02400 -1.140e-01 ## 3 m1 12.96 13.02400 -6.400e-02 ## 7 m1 22.97 25.04476 -2.075e+00 ## 7 m1 24.47 25.04476 -5.748e-01 -## 14 m1 41.69 36.69002 5.000e+00 -## 14 m1 33.21 36.69002 -3.480e+00 +## 14 m1 41.69 36.69003 5.000e+00 +## 14 m1 33.21 36.69003 -3.480e+00 ## 21 m1 44.37 41.65310 2.717e+00 ## 21 m1 46.44 41.65310 4.787e+00 -## 35 m1 41.22 43.31312 -2.093e+00 -## 35 m1 37.95 43.31312 -5.363e+00 -## 50 m1 41.19 41.21831 -2.831e-02 -## 50 m1 40.01 41.21831 -1.208e+00 -## 75 m1 40.09 36.44703 3.643e+00 -## 75 m1 33.85 36.44703 -2.597e+00 -## 100 m1 31.04 31.98163 -9.416e-01 -## 100 m1 33.13 31.98163 1.148e+00 +## 35 m1 41.22 43.31313 -2.093e+00 +## 35 m1 37.95 43.31313 -5.363e+00 +## 50 m1 41.19 41.21832 -2.832e-02 +## 50 m1 40.01 41.21832 -1.208e+00 +## 75 m1 40.09 36.44704 3.643e+00 +## 75 m1 33.85 36.44704 -2.597e+00 +## 100 m1 31.04 31.98162 -9.416e-01 +## 100 m1 33.13 31.98162 1.148e+00 ## 120 m1 25.15 28.78984 -3.640e+00 ## 120 m1 33.31 28.78984 4.520e+00</code></pre> </div> @@ -324,7 +329,7 @@ </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/FOCUS_D_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/FOCUS_D_files/anchor-sections-1.0/anchor-sections.css new file mode 100644 index 00000000..07aee5fc --- /dev/null +++ b/docs/dev/articles/FOCUS_D_files/anchor-sections-1.0/anchor-sections.css @@ -0,0 +1,4 @@ +/* Styles for section anchors */ +a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} +a.anchor-section::before {content: '#';} +.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/FOCUS_D_files/anchor-sections-1.0/anchor-sections.js b/docs/dev/articles/FOCUS_D_files/anchor-sections-1.0/anchor-sections.js new file mode 100644 index 00000000..570f99a0 --- /dev/null +++ b/docs/dev/articles/FOCUS_D_files/anchor-sections-1.0/anchor-sections.js @@ -0,0 +1,33 @@ +// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. +document.addEventListener('DOMContentLoaded', function() { + // Do nothing if AnchorJS is used + if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { + return; + } + + const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); + + // Do nothing if sections are already anchored + if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { + return null; + } + + // Use section id when pandoc runs with --section-divs + const section_id = function(x) { + return ((x.classList.contains('section') || (x.tagName === 'SECTION')) + ? x.id : ''); + }; + + // Add anchors + h.forEach(function(x) { + const id = x.id || section_id(x.parentElement); + if (id === '') { + return null; + } + let anchor = document.createElement('a'); + anchor.href = '#' + id; + anchor.classList = ['anchor-section']; + x.classList.add('hasAnchor'); + x.appendChild(anchor); + }); +}); diff --git a/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex 306244b3..8ddca415 100644 --- a/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex 158e3c50..f4937894 100644 --- a/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html index ffc0bebf..1fbe5c76 100644 --- a/docs/dev/articles/FOCUS_L.html +++ b/docs/dev/articles/FOCUS_L.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> @@ -95,15 +95,16 @@ - </header><div class="row"> + </header><link href="FOCUS_L_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> +<script src="FOCUS_L_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-10-08</h4> + <h4 class="date">2020-11-19</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> </div> @@ -114,28 +115,30 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l1" class="anchor"></a>Laboratory Data L1</h1> <p>The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:</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>) -<span class="no">FOCUS_2006_L1</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>( - <span class="kw">t</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></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">2</span>, <span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">30</span>), <span class="kw">each</span> <span class="kw">=</span> <span class="fl">2</span>), - <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">88.3</span>, <span class="fl">91.4</span>, <span class="fl">85.6</span>, <span class="fl">84.5</span>, <span class="fl">78.9</span>, <span class="fl">77.6</span>, +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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="va">FOCUS_2006_L1</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span> + t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></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">2</span>, <span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">30</span><span class="op">)</span>, each <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>, + parent <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">88.3</span>, <span class="fl">91.4</span>, <span class="fl">85.6</span>, <span class="fl">84.5</span>, <span class="fl">78.9</span>, <span class="fl">77.6</span>, <span class="fl">72.0</span>, <span class="fl">71.9</span>, <span class="fl">50.3</span>, <span class="fl">59.4</span>, <span class="fl">47.0</span>, <span class="fl">45.1</span>, - <span class="fl">27.7</span>, <span class="fl">27.3</span>, <span class="fl">10.0</span>, <span class="fl">10.4</span>, <span class="fl">2.9</span>, <span class="fl">4.0</span>)) -<span class="no">FOCUS_2006_L1_mkin</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(<span class="no">FOCUS_2006_L1</span>)</pre></body></html></div> + <span class="fl">27.7</span>, <span class="fl">27.3</span>, <span class="fl">10.0</span>, <span class="fl">10.4</span>, <span class="fl">2.9</span>, <span class="fl">4.0</span><span class="op">)</span><span class="op">)</span> +<span class="va">FOCUS_2006_L1_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_L1</span><span class="op">)</span></code></pre></div> <p>Here we use the assumptions of simple first order (SFO), the case of declining rate constant over time (FOMC) and the case of two different phases of the kinetics (DFOP). For a more detailed discussion of the models, please see the FOCUS kinetics report.</p> <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> -<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">m.L1.SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, <span class="no">FOCUS_2006_L1_mkin</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/summary.html">summary</a></span>(<span class="no">m.L1.SFO</span>)</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.50.3 -## R version used for fitting: 4.0.2 -## Date of fit: Thu Oct 8 09:14:05 2020 -## Date of summary: Thu Oct 8 09:14:05 2020 +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.L1.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.50.4 +## R version used for fitting: 4.0.3 +## Date of fit: Thu Nov 19 15:00:09 2020 +## Date of summary: Thu Nov 19 15:00:09 2020 ## ## Equations: ## d_parent/dt = - k_parent * parent ## ## Model predictions using solution type analytical ## -## Fitted using 133 model solutions performed in 0.032 s +## Fitted using 133 model solutions performed in 0.034 s ## ## Error model: Constant variance ## @@ -210,33 +213,38 @@ ## 30 parent 2.9 5.251 -2.3513 ## 30 parent 4.0 5.251 -1.2513</code></pre> <p>A plot of the fit is obtained with the plot function for mkinfit objects.</p> -<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">m.L1.SFO</span>, <span class="kw">show_errmin</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="kw">main</span> <span class="kw">=</span> <span class="st">"FOCUS L1 - SFO"</span>)</pre></body></html></div> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">m.L1.SFO</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - SFO"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> <p>The residual plot can be easily obtained by</p> -<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="../reference/mkinresplot.html">mkinresplot</a></span>(<span class="no">m.L1.SFO</span>, <span class="kw">ylab</span> <span class="kw">=</span> <span class="st">"Observed"</span>, <span class="kw">xlab</span> <span class="kw">=</span> <span class="st">"Time"</span>)</pre></body></html></div> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../reference/mkinresplot.html">mkinresplot</a></span><span class="op">(</span><span class="va">m.L1.SFO</span>, ylab <span class="op">=</span> <span class="st">"Observed"</span>, xlab <span class="op">=</span> <span class="st">"Time"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> -<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">m.L1.FOMC</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, <span class="no">FOCUS_2006_L1_mkin</span>, <span class="kw">quiet</span><span class="kw">=</span><span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.L1.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge: ## false convergence (8)</code></pre> -<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">m.L1.FOMC</span>, <span class="kw">show_errmin</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="kw">main</span> <span class="kw">=</span> <span class="st">"FOCUS L1 - FOMC"</span>)</pre></body></html></div> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">m.L1.FOMC</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - FOMC"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> -<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L1.FOMC</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></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>## mkin version used for fitting: 0.9.50.3 -## R version used for fitting: 4.0.2 -## Date of fit: Thu Oct 8 09:14:05 2020 -## Date of summary: Thu Oct 8 09:14:05 2020 +<pre><code>## mkin version used for fitting: 0.9.50.4 +## R version used for fitting: 4.0.3 +## Date of fit: Thu Nov 19 15:00:09 2020 +## Date of summary: Thu Nov 19 15:00:09 2020 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 380 model solutions performed in 0.088 s +## Fitted using 380 model solutions performed in 0.085 s ## ## Error model: Constant variance ## @@ -307,19 +315,21 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l2" class="anchor"></a>Laboratory Data L2</h1> <p>The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:</p> -<div class="sourceCode" id="cb14"><html><body><pre class="r"><span class="no">FOCUS_2006_L2</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>( - <span class="kw">t</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></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="kw">each</span> <span class="kw">=</span> <span class="fl">2</span>), - <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">96.1</span>, <span class="fl">91.8</span>, <span class="fl">41.4</span>, <span class="fl">38.7</span>, +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">FOCUS_2006_L2</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span> + t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></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="op">)</span>, each <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>, + parent <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">96.1</span>, <span class="fl">91.8</span>, <span class="fl">41.4</span>, <span class="fl">38.7</span>, <span class="fl">19.3</span>, <span class="fl">22.3</span>, <span class="fl">4.6</span>, <span class="fl">4.6</span>, - <span class="fl">2.6</span>, <span class="fl">1.2</span>, <span class="fl">0.3</span>, <span class="fl">0.6</span>)) -<span class="no">FOCUS_2006_L2_mkin</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(<span class="no">FOCUS_2006_L2</span>)</pre></body></html></div> + <span class="fl">2.6</span>, <span class="fl">1.2</span>, <span class="fl">0.3</span>, <span class="fl">0.6</span><span class="op">)</span><span class="op">)</span> +<span class="va">FOCUS_2006_L2_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_L2</span><span class="op">)</span></code></pre></div> <div id="sfo-fit-for-l2" class="section level2"> <h2 class="hasAnchor"> <a href="#sfo-fit-for-l2" class="anchor"></a>SFO fit for L2</h2> <p>Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument <code>show_residuals</code> to the plot command.</p> -<div class="sourceCode" id="cb15"><html><body><pre class="r"><span class="no">m.L2.SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, <span class="no">FOCUS_2006_L2_mkin</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/plot.html">plot</a></span>(<span class="no">m.L2.SFO</span>, <span class="kw">show_residuals</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="kw">show_errmin</span> <span class="kw">=</span> <span class="fl">TRUE</span>, - <span class="kw">main</span> <span class="kw">=</span> <span class="st">"FOCUS L2 - SFO"</span>)</pre></body></html></div> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.L2.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span> +<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">m.L2.SFO</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, + main <span class="op">=</span> <span class="st">"FOCUS L2 - SFO"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.</p> <p>In the FOCUS kinetics report, it is stated that there is no apparent systematic error observed from the residual plot up to the measured DT90 (approximately at day 5), and there is an underestimation beyond that point.</p> @@ -329,22 +339,24 @@ <h2 class="hasAnchor"> <a href="#fomc-fit-for-l2" class="anchor"></a>FOMC fit for L2</h2> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> -<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">m.L2.FOMC</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, <span class="no">FOCUS_2006_L2_mkin</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/plot.html">plot</a></span>(<span class="no">m.L2.FOMC</span>, <span class="kw">show_residuals</span> <span class="kw">=</span> <span class="fl">TRUE</span>, - <span class="kw">main</span> <span class="kw">=</span> <span class="st">"FOCUS L2 - FOMC"</span>)</pre></body></html></div> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.L2.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> +<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">m.L2.FOMC</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, + main <span class="op">=</span> <span class="st">"FOCUS L2 - FOMC"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> -<div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.FOMC</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.50.3 -## R version used for fitting: 4.0.2 -## Date of fit: Thu Oct 8 09:14:06 2020 -## Date of summary: Thu Oct 8 09:14:06 2020 +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.50.4 +## R version used for fitting: 4.0.3 +## Date of fit: Thu Nov 19 15:00:10 2020 +## Date of summary: Thu Nov 19 15:00:10 2020 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 239 model solutions performed in 0.049 s +## Fitted using 239 model solutions performed in 0.051 s ## ## Error model: Constant variance ## @@ -408,15 +420,17 @@ <h2 class="hasAnchor"> <a href="#dfop-fit-for-l2" class="anchor"></a>DFOP fit for L2</h2> <p>Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level.</p> -<div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">m.L2.DFOP</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"DFOP"</span>, <span class="no">FOCUS_2006_L2_mkin</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/plot.html">plot</a></span>(<span class="no">m.L2.DFOP</span>, <span class="kw">show_residuals</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="kw">show_errmin</span> <span class="kw">=</span> <span class="fl">TRUE</span>, - <span class="kw">main</span> <span class="kw">=</span> <span class="st">"FOCUS L2 - DFOP"</span>)</pre></body></html></div> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.L2.DFOP</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> +<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">m.L2.DFOP</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, + main <span class="op">=</span> <span class="st">"FOCUS L2 - DFOP"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> -<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.DFOP</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.50.3 -## R version used for fitting: 4.0.2 -## Date of fit: Thu Oct 8 09:14:06 2020 -## Date of summary: Thu Oct 8 09:14:06 2020 +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.50.4 +## R version used for fitting: 4.0.3 +## Date of fit: Thu Nov 19 15:00:10 2020 +## Date of summary: Thu Nov 19 15:00:10 2020 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -425,7 +439,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 572 model solutions performed in 0.136 s +## Fitted using 581 model solutions performed in 0.138 s ## ## Error model: Constant variance ## @@ -443,7 +457,7 @@ ## parent_0 93.950000 -Inf Inf ## log_k1 -2.302585 -Inf Inf ## log_k2 -4.605170 -Inf Inf -## g_ilr 0.000000 -Inf Inf +## g_qlogis 0.000000 -Inf Inf ## ## Fixed parameter values: ## None @@ -455,19 +469,19 @@ ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper -## parent_0 93.9500 9.998e-01 91.5900 96.3100 -## log_k1 3.1370 2.376e+03 -5615.0000 5622.0000 -## log_k2 -1.0880 6.285e-02 -1.2370 -0.9394 -## g_ilr -0.2821 7.033e-02 -0.4484 -0.1158 -## sigma 1.4140 2.886e-01 0.7314 2.0960 +## parent_0 93.950 9.998e-01 91.5900 96.3100 +## log_k1 3.117 1.929e+03 -4558.0000 4564.0000 +## log_k2 -1.088 6.285e-02 -1.2370 -0.9394 +## g_qlogis -0.399 9.946e-02 -0.6342 -0.1638 +## sigma 1.414 2.886e-01 0.7314 2.0960 ## ## Parameter correlation: -## parent_0 log_k1 log_k2 g_ilr sigma -## parent_0 1.000e+00 5.157e-07 2.376e-09 2.665e-01 -6.837e-09 -## log_k1 5.157e-07 1.000e+00 8.434e-05 -1.659e-04 -7.786e-06 -## log_k2 2.376e-09 8.434e-05 1.000e+00 -7.903e-01 -1.263e-08 -## g_ilr 2.665e-01 -1.659e-04 -7.903e-01 1.000e+00 3.248e-08 -## sigma -6.837e-09 -7.786e-06 -1.263e-08 3.248e-08 1.000e+00 +## parent_0 log_k1 log_k2 g_qlogis sigma +## parent_0 1.000e+00 6.459e-07 9.147e-11 2.665e-01 8.413e-11 +## log_k1 6.459e-07 1.000e+00 1.061e-04 -2.087e-04 -9.802e-06 +## log_k2 9.147e-11 1.061e-04 1.000e+00 -7.903e-01 -2.429e-09 +## g_qlogis 2.665e-01 -2.087e-04 -7.903e-01 1.000e+00 4.049e-09 +## sigma 8.413e-11 -9.802e-06 -2.429e-09 4.049e-09 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -475,7 +489,7 @@ ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100 -## k1 23.0400 4.303e-04 4.998e-01 0.0000 Inf +## k1 22.5800 5.303e-04 4.998e-01 0.0000 Inf ## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909 ## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591 ## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960 @@ -487,7 +501,7 @@ ## ## Estimated disappearance times: ## DT50 DT90 DT50back DT50_k1 DT50_k2 -## parent 0.5335 5.311 1.599 0.03009 2.058</code></pre> +## parent 0.5335 5.311 1.599 0.0307 2.058</code></pre> <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.</p> </div> </div> @@ -495,18 +509,20 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l3" class="anchor"></a>Laboratory Data L3</h1> <p>The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.</p> -<div class="sourceCode" id="cb22"><html><body><pre class="r"><span class="no">FOCUS_2006_L3</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>( - <span class="kw">t</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">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">30</span>, <span class="fl">60</span>, <span class="fl">91</span>, <span class="fl">120</span>), - <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">97.8</span>, <span class="fl">60</span>, <span class="fl">51</span>, <span class="fl">43</span>, <span class="fl">35</span>, <span class="fl">22</span>, <span class="fl">15</span>, <span class="fl">12</span>)) -<span class="no">FOCUS_2006_L3_mkin</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(<span class="no">FOCUS_2006_L3</span>)</pre></body></html></div> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">FOCUS_2006_L3</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span> + t <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">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">30</span>, <span class="fl">60</span>, <span class="fl">91</span>, <span class="fl">120</span><span class="op">)</span>, + parent <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">97.8</span>, <span class="fl">60</span>, <span class="fl">51</span>, <span class="fl">43</span>, <span class="fl">35</span>, <span class="fl">22</span>, <span class="fl">15</span>, <span class="fl">12</span><span class="op">)</span><span class="op">)</span> +<span class="va">FOCUS_2006_L3_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_L3</span><span class="op">)</span></code></pre></div> <div id="fit-multiple-models" class="section level2"> <h2 class="hasAnchor"> <a href="#fit-multiple-models" class="anchor"></a>Fit multiple models</h2> <p>As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function <code>mmkin</code>. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.</p> -<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="co"># Only use one core here, not to offend the CRAN checks</span> -<span class="no">mm.L3</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>), <span class="kw">cores</span> <span class="kw">=</span> <span class="fl">1</span>, - <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="st">"FOCUS L3"</span> <span class="kw">=</span> <span class="no">FOCUS_2006_L3_mkin</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/plot.html">plot</a></span>(<span class="no">mm.L3</span>)</pre></body></html></div> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="co"># Only use one core here, not to offend the CRAN checks</span> +<span class="va">mm.L3</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></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">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, + <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="st">"FOCUS L3"</span> <span class="op">=</span> <span class="va">FOCUS_2006_L3_mkin</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> +<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">mm.L3</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the <span class="math inline">\(\chi^2\)</span> test passes of 7%. Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level considerably.</p> </div> @@ -515,11 +531,12 @@ <a href="#accessing-mmkin-objects" class="anchor"></a>Accessing mmkin objects</h2> <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> -<div class="sourceCode" id="cb24"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L3</span><span class="kw">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span>]])</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.50.3 -## R version used for fitting: 4.0.2 -## Date of fit: Thu Oct 8 09:14:07 2020 -## Date of summary: Thu Oct 8 09:14:07 2020 +<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.50.4 +## R version used for fitting: 4.0.3 +## Date of fit: Thu Nov 19 15:00:11 2020 +## Date of summary: Thu Nov 19 15:00:11 2020 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -528,7 +545,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 373 model solutions performed in 0.086 s +## Fitted using 376 model solutions performed in 0.083 s ## ## Error model: Constant variance ## @@ -546,7 +563,7 @@ ## parent_0 97.800000 -Inf Inf ## log_k1 -2.302585 -Inf Inf ## log_k2 -4.605170 -Inf Inf -## g_ilr 0.000000 -Inf Inf +## g_qlogis 0.000000 -Inf Inf ## ## Fixed parameter values: ## None @@ -561,16 +578,16 @@ ## parent_0 97.7500 1.01900 94.5000 101.000000 ## log_k1 -0.6612 0.10050 -0.9812 -0.341300 ## log_k2 -4.2860 0.04322 -4.4230 -4.148000 -## g_ilr -0.1229 0.03727 -0.2415 -0.004343 +## g_qlogis -0.1739 0.05270 -0.3416 -0.006142 ## sigma 1.0170 0.25430 0.2079 1.827000 ## ## Parameter correlation: -## parent_0 log_k1 log_k2 g_ilr sigma -## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -6.868e-07 -## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 3.175e-07 -## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 7.631e-07 -## g_ilr 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -8.694e-07 -## sigma -6.868e-07 3.175e-07 7.631e-07 -8.694e-07 1.000e+00 +## parent_0 log_k1 log_k2 g_qlogis sigma +## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.671e-08 +## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.148e-07 +## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.022e-06 +## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.929e-07 +## sigma -9.671e-08 7.148e-07 1.022e-06 -7.929e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -602,7 +619,8 @@ ## 60 parent 22.0 23.26 -1.25919 ## 91 parent 15.0 15.18 -0.18181 ## 120 parent 12.0 10.19 1.81395</code></pre> -<div class="sourceCode" id="cb26"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">mm.L3</span><span class="kw">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span>]], <span class="kw">show_errmin</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="700"></p> <p>Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the <span class="math inline">\(\chi^2\)</span> error level criterion for laboratory data L3.</p> <p>This is also an example where the standard t-test for the parameter <code>g_ilr</code> is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter <code>g</code> is quite narrow.</p> @@ -612,30 +630,33 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l4" class="anchor"></a>Laboratory Data L4</h1> <p>The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:</p> -<div class="sourceCode" id="cb27"><html><body><pre class="r"><span class="no">FOCUS_2006_L4</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>( - <span class="kw">t</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">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">30</span>, <span class="fl">60</span>, <span class="fl">91</span>, <span class="fl">120</span>), - <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">96.6</span>, <span class="fl">96.3</span>, <span class="fl">94.3</span>, <span class="fl">88.8</span>, <span class="fl">74.9</span>, <span class="fl">59.9</span>, <span class="fl">53.5</span>, <span class="fl">49.0</span>)) -<span class="no">FOCUS_2006_L4_mkin</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(<span class="no">FOCUS_2006_L4</span>)</pre></body></html></div> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">FOCUS_2006_L4</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span> + t <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">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">30</span>, <span class="fl">60</span>, <span class="fl">91</span>, <span class="fl">120</span><span class="op">)</span>, + parent <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">96.6</span>, <span class="fl">96.3</span>, <span class="fl">94.3</span>, <span class="fl">88.8</span>, <span class="fl">74.9</span>, <span class="fl">59.9</span>, <span class="fl">53.5</span>, <span class="fl">49.0</span><span class="op">)</span><span class="op">)</span> +<span class="va">FOCUS_2006_L4_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_L4</span><span class="op">)</span></code></pre></div> <p>Fits of the SFO and FOMC models, plots and summaries are produced below:</p> -<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="co"># Only use one core here, not to offend the CRAN checks</span> -<span class="no">mm.L4</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>), <span class="kw">cores</span> <span class="kw">=</span> <span class="fl">1</span>, - <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="st">"FOCUS L4"</span> <span class="kw">=</span> <span class="no">FOCUS_2006_L4_mkin</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/plot.html">plot</a></span>(<span class="no">mm.L4</span>)</pre></body></html></div> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="co"># Only use one core here, not to offend the CRAN checks</span> +<span class="va">mm.L4</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></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">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, + <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="st">"FOCUS L4"</span> <span class="op">=</span> <span class="va">FOCUS_2006_L4_mkin</span><span class="op">)</span>, + quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> +<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">mm.L4</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> -<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.50.3 -## R version used for fitting: 4.0.2 -## Date of fit: Thu Oct 8 09:14:07 2020 -## Date of summary: Thu Oct 8 09:14:07 2020 +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.50.4 +## R version used for fitting: 4.0.3 +## Date of fit: Thu Nov 19 15:00:12 2020 +## Date of summary: Thu Nov 19 15:00:12 2020 ## ## Equations: ## d_parent/dt = - k_parent * parent ## ## Model predictions using solution type analytical ## -## Fitted using 142 model solutions performed in 0.03 s +## Fitted using 142 model solutions performed in 0.031 s ## ## Error model: Constant variance ## @@ -688,18 +709,19 @@ ## Estimated disappearance times: ## DT50 DT90 ## parent 106 352</code></pre> -<div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.50.3 -## R version used for fitting: 4.0.2 -## Date of fit: Thu Oct 8 09:14:07 2020 -## Date of summary: Thu Oct 8 09:14:07 2020 +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.50.4 +## R version used for fitting: 4.0.3 +## Date of fit: Thu Nov 19 15:00:12 2020 +## Date of summary: Thu Nov 19 15:00:12 2020 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 224 model solutions performed in 0.046 s +## Fitted using 224 model solutions performed in 0.05 s ## ## Error model: Constant variance ## @@ -784,7 +806,7 @@ </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/FOCUS_L_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/FOCUS_L_files/anchor-sections-1.0/anchor-sections.css new file mode 100644 index 00000000..07aee5fc --- /dev/null +++ b/docs/dev/articles/FOCUS_L_files/anchor-sections-1.0/anchor-sections.css @@ -0,0 +1,4 @@ +/* Styles for section anchors */ +a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} +a.anchor-section::before {content: '#';} +.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/FOCUS_L_files/anchor-sections-1.0/anchor-sections.js b/docs/dev/articles/FOCUS_L_files/anchor-sections-1.0/anchor-sections.js new file mode 100644 index 00000000..570f99a0 --- /dev/null +++ b/docs/dev/articles/FOCUS_L_files/anchor-sections-1.0/anchor-sections.js @@ -0,0 +1,33 @@ +// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. +document.addEventListener('DOMContentLoaded', function() { + // Do nothing if AnchorJS is used + if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { + return; + } + + const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); + + // Do nothing if sections are already anchored + if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { + return null; + } + + // Use section id when pandoc runs with --section-divs + const section_id = function(x) { + return ((x.classList.contains('section') || (x.tagName === 'SECTION')) + ? 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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"><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> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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="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>, @@ -143,7 +144,7 @@ <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="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> +<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></code></pre></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> diff --git a/docs/dev/articles/mkin_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/mkin_files/anchor-sections-1.0/anchor-sections.css new file mode 100644 index 00000000..07aee5fc --- /dev/null +++ b/docs/dev/articles/mkin_files/anchor-sections-1.0/anchor-sections.css @@ -0,0 +1,4 @@ +/* Styles for section anchors */ +a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} +a.anchor-section::before {content: '#';} +.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/mkin_files/anchor-sections-1.0/anchor-sections.js b/docs/dev/articles/mkin_files/anchor-sections-1.0/anchor-sections.js new file mode 100644 index 00000000..570f99a0 --- /dev/null +++ b/docs/dev/articles/mkin_files/anchor-sections-1.0/anchor-sections.js @@ -0,0 +1,33 @@ +// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. +document.addEventListener('DOMContentLoaded', function() { + // Do nothing if AnchorJS is used + if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { + return; + } + + const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); + + // Do nothing if sections are already anchored + if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { + return null; + } + + // Use section id when pandoc runs with --section-divs + const section_id = function(x) { + return ((x.classList.contains('section') || (x.tagName === 'SECTION')) + ? x.id : ''); + }; + + // Add anchors + h.forEach(function(x) { + const id = x.id || section_id(x.parentElement); + if (id === '') { + return null; + } + let anchor = document.createElement('a'); + anchor.href = '#' + id; + anchor.classList = ['anchor-section']; + x.classList.add('hasAnchor'); + x.appendChild(anchor); + }); +}); 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 2f3d7a46..9b82cd62 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/twa.html b/docs/dev/articles/twa.html index d1093e13..d778b773 100644 --- a/docs/dev/articles/twa.html +++ b/docs/dev/articles/twa.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> @@ -95,15 +95,16 @@ - </header><div class="row"> + </header><link href="twa_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> +<script src="twa_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-10-08</h4> + <h4 class="date">2020-11-19</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small> <div class="hidden name"><code>twa.rmd</code></div> </div> @@ -162,7 +163,7 @@ </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/twa_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/twa_files/anchor-sections-1.0/anchor-sections.css new file mode 100644 index 00000000..07aee5fc --- /dev/null +++ b/docs/dev/articles/twa_files/anchor-sections-1.0/anchor-sections.css @@ -0,0 +1,4 @@ +/* Styles for section anchors */ +a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} +a.anchor-section::before {content: '#';} +.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/twa_files/anchor-sections-1.0/anchor-sections.js b/docs/dev/articles/twa_files/anchor-sections-1.0/anchor-sections.js new file mode 100644 index 00000000..570f99a0 --- /dev/null +++ b/docs/dev/articles/twa_files/anchor-sections-1.0/anchor-sections.js @@ -0,0 +1,33 @@ +// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. +document.addEventListener('DOMContentLoaded', function() { + // Do nothing if AnchorJS is used + if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { + return; + } + + const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); + + // Do nothing if sections are already anchored + if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { + return null; + } + + // Use section id when pandoc runs with --section-divs + const section_id = function(x) { + return ((x.classList.contains('section') || (x.tagName === 'SECTION')) + ? x.id : ''); + }; + + // Add anchors + h.forEach(function(x) { + const id = x.id || section_id(x.parentElement); + if (id === '') { + return null; + } + let anchor = document.createElement('a'); + anchor.href = '#' + id; + anchor.classList = ['anchor-section']; + x.classList.add('hasAnchor'); + x.appendChild(anchor); + }); +}); diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html index 763ca9be..4cfe6c31 100644 --- a/docs/dev/articles/web_only/FOCUS_Z.html +++ b/docs/dev/articles/web_only/FOCUS_Z.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> @@ -95,15 +95,16 @@ - </header><div class="row"> + </header><link href="FOCUS_Z_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> +<script src="FOCUS_Z_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-10-08</h4> + <h4 class="date">2020-11-19</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> </div> @@ -115,35 +116,40 @@ <h1 class="hasAnchor"> <a href="#the-data" class="anchor"></a>The data</h1> <p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</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="no">mkin</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>) -<span class="no">LOD</span> <span class="kw">=</span> <span class="fl">0.5</span> -<span class="no">FOCUS_2006_Z</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>( - <span class="kw">t</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">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>, - <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span>), - <span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>, - <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>), - <span class="kw">Z1</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">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>, - <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> * <span class="no">LOD</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">NA</span>), - <span class="kw">Z2</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">NA</span>, <span class="fl">0.5</span> * <span class="no">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>, - <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> * <span class="no">LOD</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">NA</span>), - <span class="kw">Z3</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">NA</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">0.5</span> * <span class="no">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>, - <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>)) +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><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="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span> +<span class="va">FOCUS_2006_Z</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span> + t <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">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>, + <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>, + Z0 <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">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>, + <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>, + Z1 <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">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>, + <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, + Z2 <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="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>, + <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, + Z3 <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="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>, + <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span> -<span class="no">FOCUS_2006_Z_mkin</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(<span class="no">FOCUS_2006_Z</span>)</pre></body></html></div> +<span class="va">FOCUS_2006_Z_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></code></pre></div> </div> <div id="parent-and-one-metabolite" class="section level1"> <h1 class="hasAnchor"> <a href="#parent-and-one-metabolite" class="anchor"></a>Parent and one metabolite</h1> <p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p> -<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">Z.2a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>), - <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <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">"Z1"</span><span class="op">)</span>, + Z1 <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><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">m.Z.2a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.2a</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.2a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> -<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.2a</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642 ## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600 @@ -152,16 +158,20 @@ ## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</code></pre> <p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> <p>A similar result can be obtained when formation fractions are used in the model formulation:</p> -<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="no">Z.2a.ff</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>), - <span class="kw">Z1</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>)</pre></body></html></div> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <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">"Z1"</span><span class="op">)</span>, + Z1 <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><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="no">m.Z.2a.ff</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.2a.ff</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.2a.ff</span>)</pre></body></html></div> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> -<div class="sourceCode" id="cb14"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.2a.ff</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div> +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642 ## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600 @@ -171,15 +181,19 @@ <p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p> <p>A simplified model is obtained by removing the pathway to the sink. </p> <p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p> -<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">Z.3</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z1</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>)</pre></body></html></div> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <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">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z1 <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><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb18"><html><body><pre class="r"><span class="no">m.Z.3</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.3</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.3</span>)</pre></body></html></div> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> -<div class="sourceCode" id="cb21"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.3</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538 ## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593 @@ -191,51 +205,59 @@ <h1 class="hasAnchor"> <a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1> <p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p> -<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">Z.5</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z2</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>)</pre></body></html></div> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <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">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z1 <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">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z2 <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><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb25"><html><body><pre class="r"><span class="no">m.Z.5</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.5</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb27"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.5</span>)</pre></body></html></div> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> -<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="no">Z.FOCUS</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>), - <span class="kw">Z3</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>)</pre></body></html></div> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <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">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z1 <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">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z2 <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">"Z3"</span><span class="op">)</span>, + Z3 <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><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb30"><html><body><pre class="r"><span class="no">m.Z.FOCUS</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.FOCUS</span>, <span class="no">FOCUS_2006_Z_mkin</span>, - <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="no">m.Z.5</span>$<span class="no">bparms.ode</span>, - <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>, + parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>, + quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : ## Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge: ## false convergence (8)</code></pre> -<div class="sourceCode" id="cb33"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.FOCUS</span>)</pre></body></html></div> +<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> -<div class="sourceCode" id="cb34"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.FOCUS</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 96.838721 1.994275 48.5584 4.0283e-42 92.826878 100.850563 -## k_Z0 2.215400 0.118459 18.7019 1.0414e-23 1.989462 2.466998 -## k_Z1 0.478301 0.028257 16.9267 6.2411e-22 0.424705 0.538662 -## k_Z2 0.451623 0.042138 10.7176 1.6313e-14 0.374336 0.544867 -## k_Z3 0.058694 0.015246 3.8499 1.7804e-04 0.034809 0.098967 -## f_Z2_to_Z3 0.471510 0.058352 8.0804 9.6640e-11 0.357775 0.588283 +## Z0_0 96.839001 1.994273 48.5585 4.0276e-42 92.827060 100.850943 +## k_Z0 2.215367 0.118456 18.7021 1.0410e-23 1.989432 2.466960 +## k_Z1 0.478310 0.028258 16.9265 6.2430e-22 0.424712 0.538673 +## k_Z2 0.451628 0.042139 10.7176 1.6313e-14 0.374337 0.544877 +## k_Z3 0.058692 0.015245 3.8498 1.7806e-04 0.034806 0.098972 +## f_Z2_to_Z3 0.471498 0.058350 8.0805 9.6614e-11 0.357741 0.588294 ## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</code></pre> -<div class="sourceCode" id="cb36"><html><body><pre class="r"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span>(<span class="no">m.Z.FOCUS</span>)</pre></body></html></div> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> <pre><code>## $ff ## Z2_Z3 Z2_sink -## 0.47151 0.52849 +## 0.4715 0.5285 ## ## $distimes ## DT50 DT90 ## Z0 0.31288 1.0394 -## Z1 1.44919 4.8141 -## Z2 1.53479 5.0985 -## Z3 11.80955 39.2305</code></pre> +## Z1 1.44916 4.8140 +## Z2 1.53478 5.0984 +## Z3 11.80983 39.2314</code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> </div> <div id="using-the-sforb-model" class="section level1"> @@ -243,90 +265,101 @@ <a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1> <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> -<div class="sourceCode" id="cb38"><html><body><pre class="r"><span class="no">Z.mkin.1</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>), - <span class="kw">Z3</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</pre></body></html></div> +<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <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">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z1 <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">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z2 <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">"Z3"</span><span class="op">)</span>, + Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb40"><html><body><pre class="r"><span class="no">m.Z.mkin.1</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.1</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb42"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.1</span>)</pre></body></html></div> +<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> -<div class="sourceCode" id="cb43"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.mkin.1</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">cov.unscaled</span></pre></body></html></div> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></code></pre></div> <pre><code>## NULL</code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> -<div class="sourceCode" id="cb45"><html><body><pre class="r"><span class="no">Z.mkin.3</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z1 <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">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z2 <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><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb47"><html><body><pre class="r"><span class="no">m.Z.mkin.3</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.3</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb49"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.3</span>)</pre></body></html></div> +<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> <p>This results in a much better representation of the behaviour of the parent compound Z0.</p> <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> -<div class="sourceCode" id="cb50"><html><body><pre class="r"><span class="no">Z.mkin.4</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>), - <span class="kw">Z3</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> +<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z1 <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">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z2 <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">"Z3"</span><span class="op">)</span>, + Z3 <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><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb52"><html><body><pre class="r"><span class="no">m.Z.mkin.4</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.4</span>, <span class="no">FOCUS_2006_Z_mkin</span>, - <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="no">m.Z.mkin.3</span>$<span class="no">bparms.ode</span>, - <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>, + parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>, + quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. ## 3$bparms.ode, : Observations with value of zero were removed from the data</code></pre> -<pre><code>## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. -## 3$bparms.ode, : Shapiro-Wilk test for standardized residuals: p = 0.0449</code></pre> -<div class="sourceCode" id="cb55"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.4</span>)</pre></body></html></div> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> -<div class="sourceCode" id="cb56"><html><body><pre class="r"><span class="no">Z.mkin.5</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>), - <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>), - <span class="kw">Z3</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</pre></body></html></div> +<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z1 <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">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, + Z2 <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">"Z3"</span><span class="op">)</span>, + Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb58"><html><body><pre class="r"><span class="no">m.Z.mkin.5</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.5</span>, <span class="no">FOCUS_2006_Z_mkin</span>, - <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="no">m.Z.mkin.4</span>$<span class="no">bparms.ode</span>[<span class="fl">1</span>:<span class="fl">4</span>], - <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, + parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, + quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. ## 4$bparms.ode[1:4], : Observations with value of zero were removed from the data</code></pre> -<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. -## 4$bparms.ode[1:4], : Shapiro-Wilk test for standardized residuals: p = 0.00785</code></pre> -<div class="sourceCode" id="cb61"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.5</span>)</pre></body></html></div> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> -<div class="sourceCode" id="cb62"><html><body><pre class="r"><span class="no">m.Z.mkin.5a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.5</span>, <span class="no">FOCUS_2006_Z_mkin</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="no">m.Z.mkin.5</span>$<span class="no">bparms.ode</span>[<span class="fl">1</span>:<span class="fl">7</span>], - <span class="kw">k_Z3_bound_free</span> <span class="kw">=</span> <span class="fl">0</span>), - <span class="kw">fixed_parms</span> <span class="kw">=</span> <span class="st">"k_Z3_bound_free"</span>, - <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> +<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m.Z.mkin.5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, + parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>, + k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, + fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>, + quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin. ## 5$bparms.ode[1:7], : Observations with value of zero were removed from the data</code></pre> -<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin. -## 5$bparms.ode[1:7], : Shapiro-Wilk test for standardized residuals: p = 0.00785</code></pre> -<div class="sourceCode" id="cb65"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.5a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> <p>A graphical representation of the confidence intervals can finally be obtained.</p> -<div class="sourceCode" id="cb66"><html><body><pre class="r"><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">m.Z.mkin.5a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> <p>The endpoints obtained with this model are</p> -<div class="sourceCode" id="cb67"><html><body><pre class="r"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span>(<span class="no">m.Z.mkin.5a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> <pre><code>## $ff ## Z0_free Z2_Z3 Z2_sink Z3_free ## 1.00000 0.53656 0.46344 1.00000 ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471358 0.0075126 0.0800073 0.0000000 +## 2.4471371 0.0075126 0.0800070 0.0000000 ## ## $distimes ## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 ## Z0 0.3043 1.1848 0.35666 0.28325 92.265 NA NA ## Z1 1.5148 5.0320 NA NA NA NA NA -## Z2 1.6414 5.4526 NA NA NA NA NA +## Z2 1.6414 5.4525 NA NA NA NA NA ## Z3 NA NA NA NA NA 8.6636 Inf</code></pre> <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> </div> @@ -357,7 +390,7 @@ </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/FOCUS_Z_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/web_only/FOCUS_Z_files/anchor-sections-1.0/anchor-sections.css new file mode 100644 index 00000000..07aee5fc --- /dev/null +++ b/docs/dev/articles/web_only/FOCUS_Z_files/anchor-sections-1.0/anchor-sections.css @@ -0,0 +1,4 @@ +/* Styles for section anchors */ +a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} +a.anchor-section::before {content: '#';} +.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/anchor-sections-1.0/anchor-sections.js 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a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png Binary files differindex 7db8b07d..0acfa2a4 100644 --- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png +++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differindex 0c698299..ca191b00 100644 --- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html index ebe4b84e..c3192b37 100644 --- a/docs/dev/articles/web_only/NAFTA_examples.html +++ b/docs/dev/articles/web_only/NAFTA_examples.html @@ -95,13 +95,14 @@ - </header><div class="row"> + </header><link href="NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> +<script src="NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <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">2020-10-15</h4> + <h4 class="date">2020-11-19</h4> <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> @@ -123,15 +124,15 @@ <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"><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> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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"><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> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -157,7 +158,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.17e-12 5.00e-01 0.0000 Inf +## k2 2.42e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## @@ -166,7 +167,7 @@ ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.83e+11 3.20e+11 +## DFOP 55.5 5.22e+11 2.86e+11 ## ## Representative half-life: ## [1] 321.51</code></pre> @@ -174,15 +175,15 @@ <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"><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> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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"><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> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -208,7 +209,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 1.04e-11 5.00e-01 0.0000 Inf +## k2 1.10e-11 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -217,7 +218,7 @@ ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.09e+11 6.67e+10 +## DFOP 83.6 1.03e+11 6.29e+10 ## ## Representative half-life: ## [1] 215.87</code></pre> @@ -225,15 +226,15 @@ <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"><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> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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"><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> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -259,7 +260,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.88e-11 5.00e-01 0.0000 Inf +## k2 3.60e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## @@ -268,7 +269,7 @@ ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 8.42e+09 1.79e+10 +## DFOP 34.1 9.07e+09 1.93e+10 ## ## Representative half-life: ## [1] 53.17</code></pre> @@ -276,15 +277,15 @@ <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"><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> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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"><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> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -310,7 +311,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 2.30e-10 5.00e-01 0.0000 Inf +## k2 2.89e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## @@ -319,7 +320,7 @@ ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 5.95e+09 3.01e+09 +## DFOP 96.4 4.75e+09 2.40e+09 ## ## Representative half-life: ## [1] 454.55</code></pre> @@ -332,15 +333,15 @@ <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"><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> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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"><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> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -387,15 +388,15 @@ <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"><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> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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"><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> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -421,7 +422,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 6.69e-13 5.00e-01 0.000 Inf +## k2 9.03e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## @@ -430,7 +431,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.86e+12 1.04e+12 +## DFOP 10.5 1.38e+12 7.67e+11 ## ## Representative half-life: ## [1] 101.43</code></pre> @@ -439,15 +440,19 @@ <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"><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> +<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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="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> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -470,12 +475,12 @@ ## sigma 1.288 1.76e-04 0.7456 1.830 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 1.61e-16 93.1355 96.2891 -## k1 0.0389 1.43e-06 0.0312 0.0485 -## k2 0.0389 6.67e-03 0.0186 0.0812 -## g 0.7742 5.00e-01 0.0000 1.0000 -## sigma 1.5957 2.50e-04 0.9135 2.2779 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 NA 93.1355 96.2891 +## k1 0.0389 NA 0.0266 0.0569 +## k2 0.0389 NA 0.0255 0.0592 +## g 0.5256 NA NA NA +## sigma 1.5957 NA 0.9135 2.2779 ## ## ## DTx values: @@ -491,15 +496,16 @@ <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"><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> +<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</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="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> +<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -522,12 +528,12 @@ ## sigma 4.90 1.77e-04 2.837 6.968 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 1.41e-09 91.6534 111.810 -## k1 0.0495 6.48e-04 0.0303 0.081 -## k2 0.0495 1.67e-02 0.0201 0.122 -## g 0.6634 5.00e-01 0.0000 1.000 -## sigma 8.0152 2.50e-04 4.5886 11.442 +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 1.41e-09 91.6534 111.8097 +## k1 0.0495 5.63e-03 0.0240 0.1020 +## k2 0.0495 1.93e-03 0.0272 0.0903 +## g 0.4487 NaN 0.0000 1.0000 +## sigma 8.0152 2.50e-04 4.5886 11.4418 ## ## ## DTx values: @@ -547,15 +553,15 @@ <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"><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> +<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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"><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> +<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -581,7 +587,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 1.05e+02 9.47e-13 99.9990 109.1224 ## k1 4.41e-02 5.95e-03 0.0296 0.0658 -## k2 7.25e-13 5.00e-01 0.0000 Inf +## k2 9.94e-13 5.00e-01 0.0000 Inf ## g 3.22e-01 1.45e-03 0.2814 0.3650 ## sigma 3.22e+00 3.52e-04 1.8410 4.5906 ## @@ -590,7 +596,7 @@ ## DT50 DT90 DT50_rep ## SFO 2.16e+02 7.18e+02 2.16e+02 ## IORE 9.73e+02 1.37e+08 4.11e+07 -## DFOP 4.21e+11 2.64e+12 9.56e+11 +## DFOP 3.07e+11 1.93e+12 6.97e+11 ## ## Representative half-life: ## [1] 41148171</code></pre> @@ -604,17 +610,20 @@ <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"><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> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance +## matrix + +## 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"><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> +<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -637,12 +646,12 @@ ## sigma 3.965 NA NA NA ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 2.74e-10 92.2366 108.805 -## k1 0.124 5.75e-06 0.0958 0.161 -## k2 0.124 6.72e-02 0.0319 0.484 -## g 0.877 5.00e-01 0.0000 1.000 -## sigma 7.048 2.50e-04 4.0349 10.061 +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 2.74e-10 NA NA +## k1 0.124 2.53e-05 NA NA +## k2 0.124 2.52e-02 NA NA +## g 0.793 5.00e-01 NA NA +## sigma 7.048 2.50e-04 NA NA ## ## ## DTx values: @@ -657,23 +666,21 @@ <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb62"><pre class="downlit"> -<span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> +<div class="sourceCode" id="cb66"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre> <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> -<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$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="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> +<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb75"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -697,11 +704,11 @@ ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NaN NaN NaN -## k1 0.0589 NaN NA NA -## k2 0.0589 NaN NA NA -## g 0.6902 NaN NA NA -## sigma 3.4323 NaN NaN NaN +## parent_0 97.6840 NA NaN NaN +## k1 0.0589 NA NA NA +## k2 0.0589 NA NA NA +## g 0.6473 NA NA NA +## sigma 3.4323 NA NaN NaN ## ## ## DTx values: @@ -716,15 +723,19 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb75"><pre class="downlit"> -<span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> +<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> +<pre><code>## Warning in cov2cor(ans$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="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> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb84"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -747,12 +758,12 @@ ## sigma 3.0811 9.64e-05 1.84296 4.319 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01 -## k1 0.00258 4.28e-01 1.45e-08 4.61e+02 -## k2 0.00258 3.69e-08 2.20e-03 3.03e-03 -## g 0.00442 5.00e-01 0.00e+00 1.00e+00 -## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 NA 8.95e+01 95.92118 +## k1 0.00258 NA 4.25e-04 0.01569 +## k2 0.00258 NA 1.76e-03 0.00379 +## g 0.16452 NA NA NA +## sigma 3.41172 NA 2.02e+00 4.79960 ## ## ## DTx values: @@ -768,19 +779,19 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb81"><pre class="downlit"> -<span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> +<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$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"><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> +<div class="sourceCode" id="cb92"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb93"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -806,7 +817,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 ## k1 9.53e-03 1.20e-01 0.00638 0.0143 -## k2 7.70e-12 5.00e-01 0.00000 Inf +## k2 5.33e-12 5.00e-01 0.00000 Inf ## g 3.98e-01 2.19e-01 0.30481 0.4998 ## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## @@ -815,7 +826,7 @@ ## DT50 DT90 DT50_rep ## SFO 2.48e+02 8.25e+02 2.48e+02 ## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 2.41e+10 2.33e+11 9.00e+10 +## DFOP 3.48e+10 3.37e+11 1.30e+11 ## ## Representative half-life: ## [1] 6697.44</code></pre> @@ -824,19 +835,15 @@ <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"><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> +<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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="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> +<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -860,10 +867,10 @@ ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 97.96752 NA 94.21914 101.7159 -## k1 0.00952 NA 0.00241 0.0377 -## k2 0.00952 NA 0.00747 0.0121 -## g 0.17247 NA NA NA +## parent_0 97.96751 NA 94.21913 101.7159 +## k1 0.00952 NA 0.00221 0.0411 +## k2 0.00952 NA 0.00626 0.0145 +## g 0.21241 NA 0.00000 1.0000 ## sigma 4.18778 NA 2.39747 5.9781 ## ## @@ -875,19 +882,19 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb99"><pre class="downlit"> -<span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> +<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$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"><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> +<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb108"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -911,11 +918,11 @@ ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA 98.24464 1.04e+02 -## k1 4.86e-03 NA 0.00068 3.47e-02 -## k2 4.86e-03 NA 0.00338 6.99e-03 -## g 1.50e-01 NA NA NA -## sigma 2.76e+00 NA 1.58208 3.94e+00 +## parent_0 1.01e+02 NA 9.82e+01 1.04e+02 +## k1 4.86e-03 NA 8.63e-04 2.73e-02 +## k2 4.86e-03 NA 3.21e-03 7.35e-03 +## g 1.88e-01 NA NA NA +## sigma 2.76e+00 NA 1.58e+00 3.94e+00 ## ## ## DTx values: @@ -931,17 +938,17 @@ <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"><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> +<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></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"><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> +<div class="sourceCode" id="cb115"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb116"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -966,7 +973,7 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 88.5333 7.40e-18 79.9836 97.083 -## k1 18.5560 5.00e-01 0.0000 Inf +## k1 18.8461 5.00e-01 0.0000 Inf ## k2 0.0776 1.41e-05 0.0518 0.116 ## g 0.4733 1.41e-09 0.3674 0.582 ## sigma 7.1902 2.11e-08 5.2785 9.102 diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css new file mode 100644 index 00000000..07aee5fc --- /dev/null +++ b/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css @@ -0,0 +1,4 @@ +/* Styles for section anchors */ +a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} +a.anchor-section::before {content: '#';} +.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js b/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js new file mode 100644 index 00000000..570f99a0 --- /dev/null +++ b/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js @@ -0,0 +1,33 @@ +// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. +document.addEventListener('DOMContentLoaded', function() { + // Do nothing if AnchorJS is used + if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { + return; + } + + const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); + + // Do nothing if sections are already anchored + if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { + return null; + } + + // Use section id when pandoc runs with --section-divs + const section_id = function(x) { + return ((x.classList.contains('section') || (x.tagName === 'SECTION')) + ? x.id : ''); + }; + + // Add anchors + h.forEach(function(x) { + const id = x.id || section_id(x.parentElement); + if (id === '') { + return null; + } + let anchor = document.createElement('a'); + anchor.href = '#' + id; + anchor.classList = ['anchor-section']; + x.classList.add('hasAnchor'); + x.appendChild(anchor); + }); +}); 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 3e9c743f..38b251ea 100644 --- 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 diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png Binary files differindex 029e6a17..ce177190 100644 --- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png +++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png Binary files differindex 24cb27d8..c5759a5b 100644 --- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png +++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png Binary files differindex f3fa460e..b61f28e2 100644 --- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png +++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png Binary files differindex d6ae1fa4..515e9095 100644 --- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png +++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index 5105afcd..ff70847e 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -102,7 +102,7 @@ <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-11-06</h4> + <h4 class="date">2020-11-19</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -116,17 +116,17 @@ <h2 class="hasAnchor"> <a href="#test-cases" class="anchor"></a>Test cases</h2> <p>Parent only:</p> -<div class="sourceCode" id="cb1"><pre class="downlit"> -<span class="va">FOCUS_C</span> <span class="op"><-</span> <span class="va">FOCUS_2006_C</span> -<span class="va">FOCUS_D</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">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">FOCUS_C</span> <span class="op"><-</span> <span class="va">FOCUS_2006_C</span> +<span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="va">parent_datasets</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="va">FOCUS_C</span>, <span class="va">FOCUS_D</span><span class="op">)</span> <span class="va">t1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> <span class="va">t2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</span>, - error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></pre></div> + error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div> <p>One metabolite:</p> -<div class="sourceCode" id="cb2"><pre class="downlit"> -<span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">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="op">)</span><span class="op">)</span> <span class="va">FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span> @@ -137,18 +137,18 @@ 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="op">)</span><span class="op">)</span> <span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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="va">FOCUS_D</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> <span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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="va">FOCUS_D</span><span class="op">)</span>, - error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></pre></div> + error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: ## iteration limit reached without convergence (10) ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: ## iteration limit reached without convergence (10)</code></pre> -<div class="sourceCode" id="cb4"><pre class="downlit"> -<span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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="va">FOCUS_D</span><span class="op">)</span>, - error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></pre></div> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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="va">FOCUS_D</span><span class="op">)</span>, + error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div> <p>Two metabolites, synthetic data:</p> -<div class="sourceCode" id="cb5"><pre class="downlit"> -<span class="va">m_synth_SFO_lin</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>, +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">m_synth_SFO_lin</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> @@ -173,11 +173,11 @@ <span class="va">t10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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="va">m_synth_SFO_lin</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="va">SFO_lin_a</span><span class="op">)</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> <span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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="va">m_synth_DFOP_par</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="va">DFOP_par_c</span><span class="op">)</span>, - error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></pre></div> -<div class="sourceCode" id="cb6"><pre class="downlit"> -<span class="va">mkin_benchmarks</span><span class="op">[</span><span class="va">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"t"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">11</span><span class="op">)</span><span class="op">]</span> <span class="op"><-</span> + error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">mkin_benchmarks</span><span class="op">[</span><span class="va">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"t"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">11</span><span class="op">)</span><span class="op">]</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="va">t1</span>, <span class="va">t2</span>, <span class="va">t3</span>, <span class="va">t4</span>, <span class="va">t5</span>, <span class="va">t6</span>, <span class="va">t7</span>, <span class="va">t8</span>, <span class="va">t9</span>, <span class="va">t10</span>, <span class="va">t11</span><span class="op">)</span> -<span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span><span class="op">(</span><span class="va">mkin_benchmarks</span>, file <span class="op">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span><span class="op">)</span></pre></div> +<span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span><span class="op">(</span><span class="va">mkin_benchmarks</span>, file <span class="op">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span><span class="op">)</span></code></pre></div> </div> <div id="results" class="section level2"> <h2 class="hasAnchor"> @@ -232,8 +232,8 @@ </tr> <tr class="even"> <td align="left">0.9.50.4</td> -<td align="right">1.753</td> -<td align="right">3.791</td> +<td align="right">1.702</td> +<td align="right">3.717</td> </tr> </tbody> </table> @@ -294,9 +294,9 @@ </tr> <tr class="even"> <td align="left">0.9.50.4</td> -<td align="right">1.374</td> -<td align="right">6.974</td> -<td align="right">2.735</td> +<td align="right">1.355</td> +<td align="right">7.015</td> +<td align="right">2.729</td> </tr> </tbody> </table> @@ -381,12 +381,12 @@ </tr> <tr class="even"> <td align="left">0.9.50.4</td> -<td align="right">0.766</td> -<td align="right">1.250</td> +<td align="right">0.759</td> +<td align="right">1.245</td> <td align="right">1.436</td> -<td align="right">3.749</td> -<td align="right">1.878</td> -<td align="right">2.879</td> +<td align="right">3.687</td> +<td align="right">1.886</td> +<td align="right">3.028</td> </tr> </tbody> </table> diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index 055d0646..3d1c7fcd 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.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> @@ -95,15 +95,16 @@ - </header><div class="row"> + </header><link href="compiled_models_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> +<script src="compiled_models_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-10-08</h4> + <h4 class="date">2020-11-19</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> </div> @@ -114,79 +115,86 @@ <h2 class="hasAnchor"> <a href="#how-to-benefit-from-compiled-models" class="anchor"></a>How to benefit from compiled models</h2> <p>When using an mkin version equal to or greater than 0.9-36 and a C compiler is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. Starting from version 0.9.49.9, the <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of a compiler using</p> -<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="kw pkg">pkgbuild</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/pkgbuild/man/has_compiler.html">has_compiler</a></span>()</pre></body></html></div> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/pkgbuild/man/has_compiler.html">has_compiler</a></span><span class="op">(</span><span class="op">)</span></code></pre></div> <p>In previous versions, it used <code><a href="https://rdrr.io/r/base/Sys.which.html">Sys.which("gcc")</a></code> for this check.</p> <p>On Linux, you need to have the essential build tools like make and gcc or clang installed. On Debian based linux distributions, these will be pulled in by installing the build-essential package.</p> <p>On MacOS, which I do not use personally, I have had reports that a compiler is available by default.</p> <p>On Windows, you need to install Rtools and have the path to its bin directory in your PATH variable. You do not need to modify the PATH variable when installing Rtools. Instead, I would recommend to put the line</p> -<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html">Sys.setenv</a></span>(<span class="kw">PATH</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste</a></span>(<span class="st">"C:/Rtools/bin"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv</a></span>(<span class="st">"PATH"</span>), <span class="kw">sep</span><span class="kw">=</span><span class="st">";"</span>))</pre></body></html></div> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html">Sys.setenv</a></span><span class="op">(</span>PATH <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">"C:/Rtools/bin"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv</a></span><span class="op">(</span><span class="st">"PATH"</span><span class="op">)</span>, sep<span class="op">=</span><span class="st">";"</span><span class="op">)</span><span class="op">)</span></code></pre></div> <p>into your .Rprofile startup file. This is just a text file with some R code that is executed when your R session starts. It has to be named .Rprofile and has to be located in your home directory, which will generally be your Documents folder. You can check the location of the home directory used by R by issuing</p> -<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv</a></span>(<span class="st">"HOME"</span>)</pre></body></html></div> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv</a></span><span class="op">(</span><span class="st">"HOME"</span><span class="op">)</span></code></pre></div> </div> <div id="comparison-with-other-solution-methods" class="section level2"> <h2 class="hasAnchor"> <a href="#comparison-with-other-solution-methods" class="anchor"></a>Comparison with other solution methods</h2> <p>First, we build a simple degradation model for a parent compound with one metabolite, and we remove zero values from the dataset.</p> -<div class="sourceCode" id="cb4"><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>) -<span class="no">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>))</pre></body></html></div> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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="va">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="op">)</span><span class="op">)</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">FOCUS_D</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html">subset</a></span>(<span class="no">FOCUS_2006_D</span>, <span class="no">value</span> <span class="kw">!=</span> <span class="fl">0</span>)</pre></body></html></div> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></code></pre></div> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package. In the output of below code, the warnings about zero being removed from the FOCUS D dataset are suppressed. Since mkin version 0.9.49.11, an analytical solution is also implemented, which is included in the tests below.</p> -<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">rbenchmark</span>)) { - <span class="no">b.1</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span>( - <span class="st">"deSolve, not compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"deSolve"</span>, - <span class="kw">use_compiled</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="st">"Eigenvalue based"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"eigen"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="st">"deSolve, compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"deSolve"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="st">"analytical"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"analytical"</span>, - <span class="kw">use_compiled</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="kw">replications</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">order</span> <span class="kw">=</span> <span class="st">"relative"</span>, - <span class="kw">columns</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span>)) - <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">b.1</span>) -} <span class="kw">else</span> { - <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>) -}</pre></body></html></div> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> + <span class="va">b.1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span><span class="op">(</span> + <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, + solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, + use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, + <span class="st">"Eigenvalue based"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, + solution_type <span class="op">=</span> <span class="st">"eigen"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, + <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, + solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, + <span class="st">"analytical"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, + solution_type <span class="op">=</span> <span class="st">"analytical"</span>, + use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, + replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, + columns <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">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span><span class="op">)</span> + <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">b.1</span><span class="op">)</span> +<span class="op">}</span> <span class="kw">else</span> <span class="op">{</span> + <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span> +<span class="op">}</span></code></pre></div> <pre><code>## test replications relative elapsed -## 4 analytical 1 1.000 0.195 -## 3 deSolve, compiled 1 1.769 0.345 -## 2 Eigenvalue based 1 2.087 0.407 -## 1 deSolve, not compiled 1 42.656 8.318</code></pre> +## 4 analytical 1 1.000 0.186 +## 3 deSolve, compiled 1 1.742 0.324 +## 2 Eigenvalue based 1 2.048 0.381 +## 1 deSolve, not compiled 1 42.532 7.911</code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> <div id="model-without-analytical-solution" class="section level2"> <h2 class="hasAnchor"> <a href="#model-without-analytical-solution" class="anchor"></a>Model without analytical solution</h2> <p>This evaluation is also taken from the example section of mkinfit. No analytical solution is available for this system, and now Eigenvalue based solution is possible, so only deSolve using with or without compiled code is available.</p> -<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">rbenchmark</span>)) { - <span class="no">FOMC_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">"FOMC"</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="no">b.2</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span>( - <span class="st">"deSolve, not compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">FOMC_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">use_compiled</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="st">"deSolve, compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">FOMC_SFO</span>, <span class="no">FOCUS_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="kw">replications</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">order</span> <span class="kw">=</span> <span class="st">"relative"</span>, - <span class="kw">columns</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span>)) - <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">b.2</span>) - <span class="no">factor_FOMC_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html">round</a></span>(<span class="no">b.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>]) -} <span class="kw">else</span> { - <span class="no">factor_FOMC_SFO</span> <span class="kw"><-</span> <span class="fl">NA</span> - <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package benchmark is not available"</span>) -}</pre></body></html></div> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> + <span class="va">FOMC_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">"FOMC"</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="op">)</span><span class="op">)</span> + + <span class="va">b.2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span><span class="op">(</span> + <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, + use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, + <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, + replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, + columns <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">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span><span class="op">)</span> + <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">)</span> + <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html">round</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">[</span><span class="st">"1"</span>, <span class="st">"relative"</span><span class="op">]</span><span class="op">)</span> +<span class="op">}</span> <span class="kw">else</span> <span class="op">{</span> + <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="cn">NA</span> + <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="st">"R package benchmark is not available"</span><span class="op">)</span> +<span class="op">}</span></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications relative elapsed -## 2 deSolve, compiled 1 1.000 0.474 -## 1 deSolve, not compiled 1 30.909 14.651</code></pre> +## 2 deSolve, compiled 1 1.000 0.465 +## 1 deSolve, not compiled 1 30.852 14.346</code></pre> <p>Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.50.3 on</p> -<pre><code>## R version 4.0.2 (2020-06-22) +<p>This vignette was built with mkin 0.9.50.4 on</p> +<pre><code>## R version 4.0.3 (2020-10-10) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 10 (buster)</code></pre> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> @@ -208,7 +216,7 @@ </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/compiled_models_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/web_only/compiled_models_files/anchor-sections-1.0/anchor-sections.css new file mode 100644 index 00000000..07aee5fc --- /dev/null +++ b/docs/dev/articles/web_only/compiled_models_files/anchor-sections-1.0/anchor-sections.css @@ -0,0 +1,4 @@ +/* Styles for section anchors */ +a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} +a.anchor-section::before {content: '#';} +.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/web_only/compiled_models_files/anchor-sections-1.0/anchor-sections.js b/docs/dev/articles/web_only/compiled_models_files/anchor-sections-1.0/anchor-sections.js new file mode 100644 index 00000000..570f99a0 --- /dev/null +++ b/docs/dev/articles/web_only/compiled_models_files/anchor-sections-1.0/anchor-sections.js @@ -0,0 +1,33 @@ +// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. +document.addEventListener('DOMContentLoaded', function() { + // Do nothing if AnchorJS is used + if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { + return; + } + + const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); + + // Do nothing if sections are already anchored + if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { + return null; + } + + // Use section id when pandoc runs with --section-divs + const section_id = function(x) { + return ((x.classList.contains('section') || (x.tagName === 'SECTION')) + ? x.id : ''); + }; + + // Add anchors + h.forEach(function(x) { + const id = x.id || section_id(x.parentElement); + if (id === '') { + return null; + } + let anchor = document.createElement('a'); + anchor.href = '#' + id; + anchor.classList = ['anchor-section']; + x.classList.add('hasAnchor'); + x.appendChild(anchor); + }); +}); diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 3a868426..b8577da0 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -146,6 +146,10 @@ <a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small> </h1> <ul> +<li><p>‘f_norm_temp_focus’ generic function to normalise time intervals using the FOCUS method, with methods for numeric vectors and ‘mkindsg’ objects</p></li> +<li><p>‘mkindsg’ R6 class for groups of ‘mkinds’ datasets with metadata</p></li> +<li><p>‘D24_2014’ dataset</p></li> +<li><p>‘focus_soil_moisture’ FOCUS default soil moisture data</p></li> <li><p>‘plot.mixed.mmkin’ method used for ‘nlme.mmkin’ and ‘saem.mmkin’, both inheriting from ‘mixed.mmkin’ (currently virtual)</p></li> <li><p>‘saem’ generic function to fit saemix models, with a generator ‘saem.mmkin’, summary and plot methods</p></li> <li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li> @@ -478,7 +482,7 @@ <ul> <li><p>Add plots to <code>compiled_models</code> vignette</p></li> <li><p>Give an explanatory error message when mkinmod fails due to a missing definition of a target variable</p></li> -<li><p><code><a href="../reference/print.mkinmod.html">print.mkinmod()</a></code>: Improve formatting when printing mkinmod model definitions</p></li> +<li><p><code><a href="../reference/mkinmod.html">print.mkinmod()</a></code>: Improve formatting when printing mkinmod model definitions</p></li> </ul> </div> </div> @@ -630,7 +634,7 @@ <h2 class="hasAnchor"> <a href="#new-features-2" class="anchor"></a>New features</h2> <ul> -<li><p>Add the convenience function <code><a href="../reference/mkinsub.html">mkinsub()</a></code> for creating the lists used in <code><a href="../reference/mkinmod.html">mkinmod()</a></code></p></li> +<li><p>Add the convenience function <code><a href="../reference/mkinmod.html">mkinsub()</a></code> for creating the lists used in <code><a href="../reference/mkinmod.html">mkinmod()</a></code></p></li> <li><p>Add the possibility to fit indeterminate order rate equation (IORE) models using an analytical solution (parent only) or a numeric solution. Paths from IORE compounds to metabolites are supported when using formation fractions (use_of_ff = ‘max’). Note that the numerical solution (method.ode = ‘deSolve’) of the IORE differential equations sometimes fails due to numerical problems.</p></li> <li><p>Switch to using the Port algorithm (using a model/trust region approach) per default. While needing more iterations than the Levenberg-Marquardt algorithm previously used per default, it is less sensitive to starting parameters.</p></li> </ul> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 438c79b7..bad008d6 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-11-11T18:47Z +last_built: 2020-11-19T14:38Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/AIC.mmkin.html b/docs/dev/reference/AIC.mmkin.html index a1418b82..b332257e 100644 --- a/docs/dev/reference/AIC.mmkin.html +++ b/docs/dev/reference/AIC.mmkin.html @@ -73,7 +73,7 @@ same dataset." /> </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> @@ -121,7 +121,7 @@ same dataset." /> </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> @@ -140,7 +140,7 @@ same dataset." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the AIC for a column of an mmkin object</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/AIC.mmkin.R'><code>R/AIC.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/AIC.mmkin.R'><code>R/AIC.mmkin.R</code></a></small> <div class="hidden name"><code>AIC.mmkin.Rd</code></div> </div> @@ -150,10 +150,10 @@ same dataset.</p> </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>object</span>, <span class='no'>...</span>, <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>2</span>) +<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span>, k <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> <span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></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"> @@ -177,34 +177,45 @@ column.</p></td> <p>As in the generic method (a numeric value for single fits, or a dataframe if there are several fits in the column).</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='co'># skip, as it takes > 10 s on winbuilder</span> - <span class='no'>f</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/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), - <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS A"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_A</span>, - <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> + <span class='va'>f</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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</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'>"FOCUS A"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, + <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> #> <span class='warning'>false convergence (8)</span></div><div class='input'> <span class='co'># We get a warning because the FOMC model does not converge for the</span> <span class='co'># FOCUS A dataset, as it is well described by SFO</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[<span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span>]) <span class='co'># We get a single number for a single fit</span></div><div class='output co'>#> [1] 55.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span>]]) <span class='co'># or when extracting an mkinfit object</span></div><div class='output co'>#> [1] 55.28197</div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># We get a single number for a single fit</span> +</div><div class='output co'>#> [1] 55.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># or when extracting an mkinfit object</span> +</div><div class='output co'>#> [1] 55.28197</div><div class='input'> <span class='co'># For FOCUS A, the models fit almost equally well, so the higher the number</span> <span class='co'># of parameters, the higher (worse) the AIC</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#> df AIC + <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> +</div><div class='output co'>#> df AIC #> SFO 3 55.28197 #> FOMC 4 57.28211 -#> DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>], <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>0</span>) <span class='co'># If we do not penalize additional parameters, we get nearly the same</span></div><div class='output co'>#> df AIC +#> DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span>, k <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># If we do not penalize additional parameters, we get nearly the same</span> +</div><div class='output co'>#> df AIC #> SFO 3 49.28197 #> FOMC 4 49.28211 -#> DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>]) <span class='co'># Comparing the BIC gives a very similar picture</span></div><div class='output co'>#> df BIC +#> DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Comparing the BIC gives a very similar picture</span> +</div><div class='output co'>#> df BIC #> SFO 3 55.52030 #> FOMC 4 57.59987 #> DFOP 5 59.67918</div><div class='input'> <span class='co'># For FOCUS C, the more complex models fit better</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> df AIC + <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> +</div><div class='output co'>#> df AIC #> SFO 3 59.29336 #> FOMC 4 44.68652 -#> DFOP 5 29.02372</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> df BIC +#> DFOP 5 29.02372</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> +</div><div class='output co'>#> df BIC #> SFO 3 59.88504 #> FOMC 4 45.47542 #> DFOP 5 30.00984</div><div class='input'> @@ -225,7 +236,7 @@ dataframe if there are several fits in the column).</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/D24_2014.html b/docs/dev/reference/D24_2014.html new file mode 100644 index 00000000..ba768186 --- /dev/null +++ b/docs/dev/reference/D24_2014.html @@ -0,0 +1,251 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014 • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> + +<!-- Font Awesome icons --> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> + +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + + + + +<meta property="og:title" content="Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014" /> +<meta property="og:description" content="The five datasets were extracted from the active substance evaluation dossier +published by EFSA. Kinetic evaluations shown for these datasets are intended +to illustrate and advance kinetic modelling. The fact that these data and +some results are shown here does not imply a license to use them in the +context of pesticide registrations, as the use of the data may be +constrained by data protection regulations." /> + + +<meta name="robots" content="noindex"> + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + + </head> + + <body data-spy="scroll" data-target="#toc"> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </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">0.9.50.4</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/D24_2014.R'><code>R/D24_2014.R</code></a></small> + <div class="hidden name"><code>D24_2014.Rd</code></div> + </div> + + <div class="ref-description"> + <p>The five datasets were extracted from the active substance evaluation dossier +published by EFSA. Kinetic evaluations shown for these datasets are intended +to illustrate and advance kinetic modelling. The fact that these data and +some results are shown here does not imply a license to use them in the +context of pesticide registrations, as the use of the data may be +constrained by data protection regulations.</p> + </div> + + <pre class="usage"><span class='va'>D24_2014</span></pre> + + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>An <a href='mkindsg.html'>mkindsg</a> object grouping five datasets</p> + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>Hellenic Ministry of Rural Development and Agriculture (2014) +Final addendum to the Renewal Assessment Report - public version - 2,4-D +Volume 3 Annex B.8 Fate and behaviour in the environment +<a href='http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812'>http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812</a></p> + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>Data for the first dataset are from p. 685. Data for the other four +datasets were used in the preprocessed versions given in the kinetics +section (p. 761ff.), with the exception of residues smaller than 1 for DCP +in the soil from Site I2, where the values given on p. 694 were used.</p> +<p>The R code used to create this data object is installed with this package +in the 'dataset_generation' directory. In the code, page numbers are given for +specific pieces of information in the comments.</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>D24_2014</span><span class='op'>)</span> +</div><div class='output co'>#> <mkindsg> holding 5 mkinds objects +#> Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 +#> Occurrene of observed compounds $observed_n: +#> D24 DCP DCA +#> 5 4 4 +#> Meta information $meta: +#> study usda_soil_type study_moisture_ref_type rel_moisture +#> 1 Cohen 1991 Silt loam <NA> NA +#> 2 Liu and Adelfinskaya 2011 Silt loam pF1 0.5 +#> 3 Liu and Adelfinskaya 2011 Loam pF1 0.5 +#> 4 Liu and Adelfinskaya 2011 Loam pF1 0.5 +#> 5 Liu and Adelfinskaya 2011 Loamy sand pF1 0.5 +#> temperature +#> 1 25 +#> 2 20 +#> 3 20 +#> 4 20 +#> 5 20</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>D24_2014</span><span class='op'>$</span><span class='va'>ds</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <mkinds> with $title: Mississippi +#> Observed compounds $observed: D24 +#> Sampling times $sampling_times: +#> 0, 2, 4, 7, 15, 24, 35, 56, 71, 114, 183, 273, 365 +#> With a maximum of 1 replicates +#> time D24 +#> 1 0 96.8 +#> 2 2 81.0 +#> 3 4 81.7 +#> 4 7 88.2 +#> 5 15 66.3 +#> 6 24 72.9 +#> 7 35 62.6 +#> 8 56 54.6 +#> 9 71 35.2 +#> 10 114 18.0 +#> 11 183 11.3 +#> 12 273 9.9 +#> 13 365 6.3</div><div class='input'><span class='va'>m_D24</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>D24 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCP"</span><span class='op'>)</span>, + DCP <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCA"</span><span class='op'>)</span>, + DCA <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></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/dev/reference/DFOP.solution-1.png b/docs/dev/reference/DFOP.solution-1.png Binary files differindex a2d75ccc..616e19d5 100644 --- a/docs/dev/reference/DFOP.solution-1.png +++ b/docs/dev/reference/DFOP.solution-1.png diff --git a/docs/dev/reference/DFOP.solution.html b/docs/dev/reference/DFOP.solution.html index e7c69fc3..22b28732 100644 --- a/docs/dev/reference/DFOP.solution.html +++ b/docs/dev/reference/DFOP.solution.html @@ -73,7 +73,7 @@ two exponential decline functions." /> </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> @@ -121,7 +121,7 @@ two exponential decline functions." /> </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> @@ -140,7 +140,7 @@ two exponential decline functions." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Double First-Order in Parallel kinetics</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> <div class="hidden name"><code>DFOP.solution.Rd</code></div> </div> @@ -149,7 +149,7 @@ two exponential decline functions." /> two exponential decline functions.</p> </div> - <pre class="usage"><span class='fu'>DFOP.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>)</pre> + <pre class="usage"><span class='fu'>DFOP.solution</span><span class='op'>(</span><span class='va'>t</span>, <span class='va'>parent_0</span>, <span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>g</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -204,7 +204,8 @@ Version 1.1, 18 December 2014 <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</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'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>DFOP.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fl'>0</span>, <span class='fl'>4</span>, ylim <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'>100</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='img'><img src='DFOP.solution-1.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"> @@ -221,7 +222,7 @@ Version 1.1, 18 December 2014 </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/FOMC.solution-1.png b/docs/dev/reference/FOMC.solution-1.png Binary files differindex aa41a253..1d32355a 100644 --- a/docs/dev/reference/FOMC.solution-1.png +++ b/docs/dev/reference/FOMC.solution-1.png diff --git a/docs/dev/reference/FOMC.solution.html b/docs/dev/reference/FOMC.solution.html index f89f87c9..ed5c4d21 100644 --- a/docs/dev/reference/FOMC.solution.html +++ b/docs/dev/reference/FOMC.solution.html @@ -73,7 +73,7 @@ a decreasing rate constant." /> </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> @@ -121,7 +121,7 @@ a decreasing rate constant." /> </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> @@ -140,7 +140,7 @@ a decreasing rate constant." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>First-Order Multi-Compartment kinetics</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> <div class="hidden name"><code>FOMC.solution.Rd</code></div> </div> @@ -149,7 +149,7 @@ a decreasing rate constant." /> a decreasing rate constant.</p> </div> - <pre class="usage"><span class='fu'>FOMC.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>)</pre> + <pre class="usage"><span class='fu'>FOMC.solution</span><span class='op'>(</span><span class='va'>t</span>, <span class='va'>parent_0</span>, <span class='va'>alpha</span>, <span class='va'>beta</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -213,7 +213,8 @@ Technology</em> <b>24</b>, 1032-1038</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</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'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>FOMC.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span><span class='op'>)</span>, <span class='fl'>0</span>, <span class='fl'>2</span>, ylim <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'>100</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='img'><img src='FOMC.solution-1.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"> @@ -230,7 +231,7 @@ Technology</em> <b>24</b>, 1032-1038</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/HS.solution-1.png b/docs/dev/reference/HS.solution-1.png Binary files differindex ae056d9b..32d04b2d 100644 --- a/docs/dev/reference/HS.solution-1.png +++ b/docs/dev/reference/HS.solution-1.png diff --git a/docs/dev/reference/HS.solution.html b/docs/dev/reference/HS.solution.html index 4622ac80..8cf5c7f9 100644 --- a/docs/dev/reference/HS.solution.html +++ b/docs/dev/reference/HS.solution.html @@ -73,7 +73,7 @@ between them." /> </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> @@ -121,7 +121,7 @@ between them." /> </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> @@ -140,7 +140,7 @@ between them." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Hockey-Stick kinetics</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> <div class="hidden name"><code>HS.solution.Rd</code></div> </div> @@ -149,7 +149,7 @@ between them." /> between them.</p> </div> - <pre class="usage"><span class='fu'>HS.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>)</pre> + <pre class="usage"><span class='fu'>HS.solution</span><span class='op'>(</span><span class='va'>t</span>, <span class='va'>parent_0</span>, <span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>tb</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -205,7 +205,8 @@ Version 1.1, 18 December 2014 <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</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'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>HS.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span><span class='op'>)</span>, <span class='fl'>0</span>, <span class='fl'>2</span>, ylim<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'>100</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='img'><img src='HS.solution-1.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"> @@ -222,7 +223,7 @@ Version 1.1, 18 December 2014 </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/IORE.solution-1.png b/docs/dev/reference/IORE.solution-1.png Binary files differindex 00e28460..42643a58 100644 --- a/docs/dev/reference/IORE.solution-1.png +++ b/docs/dev/reference/IORE.solution-1.png diff --git a/docs/dev/reference/IORE.solution.html b/docs/dev/reference/IORE.solution.html index 26a34c73..29d615dc 100644 --- a/docs/dev/reference/IORE.solution.html +++ b/docs/dev/reference/IORE.solution.html @@ -73,7 +73,7 @@ a concentration dependent rate constant." /> </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> @@ -121,7 +121,7 @@ a concentration dependent rate constant." /> </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> @@ -140,7 +140,7 @@ a concentration dependent rate constant." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Indeterminate order rate equation kinetics</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> <div class="hidden name"><code>IORE.solution.Rd</code></div> </div> @@ -149,7 +149,7 @@ a concentration dependent rate constant." /> a concentration dependent rate constant.</p> </div> - <pre class="usage"><span class='fu'>IORE.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k__iore</span>, <span class='no'>N</span>)</pre> + <pre class="usage"><span class='fu'>IORE.solution</span><span class='op'>(</span><span class='va'>t</span>, <span class='va'>parent_0</span>, <span class='va'>k__iore</span>, <span class='va'>N</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -198,21 +198,24 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</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'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># \dontrun{</span> - <span class='no'>fit.fomc</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='no'>fit.iore</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='no'>fit.iore.deS</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</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/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='no'>fit.fomc</span>$<span class='no'>par</span>, <span class='no'>fit.iore</span>$<span class='no'>par</span>, <span class='no'>fit.iore.deS</span>$<span class='no'>par</span>, - <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>4</span>)))</div><div class='output co'>#> fit.fomc.par fit.iore.par fit.iore.deS.par + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>IORE.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span><span class='op'>)</span>, <span class='fl'>0</span>, <span class='fl'>2</span>, ylim <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'>100</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># \dontrun{</span> + <span class='va'>fit.fomc</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='va'>fit.iore</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"IORE"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='va'>fit.iore.deS</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"IORE"</span>, <span class='va'>FOCUS_2006_C</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + + <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span><span class='va'>fit.fomc</span><span class='op'>$</span><span class='va'>par</span>, <span class='va'>fit.iore</span><span class='op'>$</span><span class='va'>par</span>, <span class='va'>fit.iore.deS</span><span class='op'>$</span><span class='va'>par</span>, + row.names <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"model par"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> fit.fomc.par fit.iore.par fit.iore.deS.par #> model par 1 85.87489063 85.874890 85.874890 #> model par 2 0.05192238 -4.826631 -4.826631 #> model par 3 0.65096665 1.949403 1.949403 -#> model par 4 1.85744396 1.857444 1.857444</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/cbind.html'>rbind</a></span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, - <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back +#> model par 4 1.85744396 1.857444 1.857444</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/cbind.html'>rbind</a></span><span class='op'>(</span>fomc <span class='op'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.fomc</span><span class='op'>)</span><span class='op'>$</span><span class='va'>distimes</span>, iore <span class='op'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.iore</span><span class='op'>)</span><span class='op'>$</span><span class='va'>distimes</span>, + iore.deS <span class='op'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.iore</span><span class='op'>)</span><span class='op'>$</span><span class='va'>distimes</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> DT50 DT90 DT50back #> fomc 1.785233 15.1479 4.559973 #> iore 1.785233 15.1479 4.559973 -#> iore.deS 1.785233 15.1479 4.559973</div><div class='input'> # } +#> iore.deS 1.785233 15.1479 4.559973</div><div class='input'> <span class='co'># }</span> </div></pre> </div> @@ -230,7 +233,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</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/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 17a35806..f001da49 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 9b97a634..c6c75f42 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png Binary files differindex ff6bc722..41711ba6 100644 --- a/docs/dev/reference/Rplot003.png +++ b/docs/dev/reference/Rplot003.png diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png Binary files differindex 98dd019e..875d6daf 100644 --- a/docs/dev/reference/Rplot004.png +++ b/docs/dev/reference/Rplot004.png diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png Binary files differindex 5e675828..91c7777b 100644 --- a/docs/dev/reference/Rplot005.png +++ b/docs/dev/reference/Rplot005.png diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png Binary files differindex 511c6b00..921e0394 100644 --- a/docs/dev/reference/Rplot006.png +++ b/docs/dev/reference/Rplot006.png diff --git a/docs/dev/reference/Rplot007.png b/docs/dev/reference/Rplot007.png Binary files differindex a0d6336e..fcca232c 100644 --- a/docs/dev/reference/Rplot007.png +++ b/docs/dev/reference/Rplot007.png diff --git a/docs/dev/reference/SFO.solution-1.png b/docs/dev/reference/SFO.solution-1.png Binary files differindex b0b854bb..56d27ef6 100644 --- a/docs/dev/reference/SFO.solution-1.png +++ b/docs/dev/reference/SFO.solution-1.png diff --git a/docs/dev/reference/SFO.solution.html b/docs/dev/reference/SFO.solution.html index 930c2a97..b3e7ef9a 100644 --- a/docs/dev/reference/SFO.solution.html +++ b/docs/dev/reference/SFO.solution.html @@ -72,7 +72,7 @@ </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> @@ -120,7 +120,7 @@ </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> @@ -139,7 +139,7 @@ <div class="col-md-9 contents"> <div class="page-header"> <h1>Single First-Order kinetics</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> <div class="hidden name"><code>SFO.solution.Rd</code></div> </div> @@ -147,7 +147,7 @@ <p>Function describing exponential decline from a defined starting value.</p> </div> - <pre class="usage"><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k</span>)</pre> + <pre class="usage"><span class='fu'>SFO.solution</span><span class='op'>(</span><span class='va'>t</span>, <span class='va'>parent_0</span>, <span class='va'>k</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -193,7 +193,8 @@ Version 1.1, 18 December 2014 <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>SFO.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span><span class='op'>)</span>, <span class='fl'>0</span>, <span class='fl'>2</span><span class='op'>)</span> +</div><div class='img'><img src='SFO.solution-1.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"> @@ -210,7 +211,7 @@ Version 1.1, 18 December 2014 </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/SFORB.solution-1.png b/docs/dev/reference/SFORB.solution-1.png Binary files differindex cd58caec..4eeb0d41 100644 --- a/docs/dev/reference/SFORB.solution-1.png +++ b/docs/dev/reference/SFORB.solution-1.png diff --git a/docs/dev/reference/SFORB.solution.html b/docs/dev/reference/SFORB.solution.html index 845377a2..9310212f 100644 --- a/docs/dev/reference/SFORB.solution.html +++ b/docs/dev/reference/SFORB.solution.html @@ -76,7 +76,7 @@ and no substance in the bound fraction." /> </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> @@ -124,7 +124,7 @@ and no substance in the bound fraction." /> </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> @@ -143,7 +143,7 @@ and no substance in the bound fraction." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Single First-Order Reversible Binding kinetics</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> <div class="hidden name"><code>SFORB.solution.Rd</code></div> </div> @@ -155,7 +155,7 @@ fraction. The initial condition is a defined amount in the free fraction and no substance in the bound fraction.</p> </div> - <pre class="usage"><span class='fu'>SFORB.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k_12</span>, <span class='no'>k_21</span>, <span class='no'>k_1output</span>)</pre> + <pre class="usage"><span class='fu'>SFORB.solution</span><span class='op'>(</span><span class='va'>t</span>, <span class='va'>parent_0</span>, <span class='va'>k_12</span>, <span class='va'>k_21</span>, <span class='va'>k_1output</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -211,7 +211,8 @@ Version 1.1, 18 December 2014 <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>SFORB.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span><span class='op'>)</span>, <span class='fl'>0</span>, <span class='fl'>2</span><span class='op'>)</span> +</div><div class='img'><img src='SFORB.solution-1.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"> @@ -228,7 +229,7 @@ Version 1.1, 18 December 2014 </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/add_err-1.png b/docs/dev/reference/add_err-1.png Binary files differindex f5686754..d2ce797f 100644 --- a/docs/dev/reference/add_err-1.png +++ b/docs/dev/reference/add_err-1.png diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html index e362ab7a..ae10e863 100644 --- a/docs/dev/reference/add_err.html +++ b/docs/dev/reference/add_err.html @@ -222,8 +222,8 @@ https://jrwb.de/posters/piacenza_2015.pdf</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># The kinetic model</span> -<span class='va'>m_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'>"M1"</span><span class='op'>)</span>, - M1 <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>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> +<span class='va'>m_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='mkinmod.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='mkinmod.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><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'># Generate a prediction for a specific set of parameters</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> diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index 5b683355..745f2dc4 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> </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> @@ -127,7 +127,7 @@ method of Venzon and Moolgavkar (1988)." /> </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 @@ method of Venzon and Moolgavkar (1988)." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Confidence intervals for parameters of mkinfit objects</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/confint.mkinfit.R'><code>R/confint.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/confint.mkinfit.R'><code>R/confint.mkinfit.R</code></a></small> <div class="hidden name"><code>confint.mkinfit.Rd</code></div> </div> @@ -162,20 +162,20 @@ method of Venzon and Moolgavkar (1988).</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>( - <span class='no'>object</span>, - <span class='no'>parm</span>, - <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, - <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> - <span class='no'>level</span>, - <span class='no'>cutoff</span>, - <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"quadratic"</span>, <span class='st'>"profile"</span>), - <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>(), - <span class='kw'>rel_tol</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='no'>...</span> -)</pre> +<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span> + <span class='va'>object</span>, + <span class='va'>parm</span>, + level <span class='op'>=</span> <span class='fl'>0.95</span>, + alpha <span class='op'>=</span> <span class='fl'>1</span> <span class='op'>-</span> <span class='va'>level</span>, + <span class='va'>cutoff</span>, + method <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'>"quadratic"</span>, <span class='st'>"profile"</span><span class='op'>)</span>, + transformed <span class='op'>=</span> <span class='cn'>TRUE</span>, + backtransform <span class='op'>=</span> <span class='cn'>TRUE</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>, + rel_tol <span class='op'>=</span> <span class='fl'>0.01</span>, + quiet <span class='op'>=</span> <span class='cn'>FALSE</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"> @@ -257,68 +257,79 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, 87–94.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</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'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% + <pre class="examples"><div class='input'><span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</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'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% #> parent_0 71.8242430 93.1600766 #> k_parent 0.2109541 0.4440528 #> sigma 1.9778868 7.3681380</div><div class='input'> <span class='co'># \dontrun{</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> 2.5% 97.5% +<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f</span>, method <span class='op'>=</span> <span class='st'>"profile"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> 2.5% 97.5% #> parent_0 73.0641834 92.1392181 #> k_parent 0.2170293 0.4235348 #> sigma 3.1307772 8.0628314</div><div class='input'> <span class='co'># Set the number of cores for the profiling method for further examples</span> -<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span>(<span class='st'>"NOT_CRAN"</span>), <span class='st'>"true"</span>)) { - <span class='no'>n_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>() - <span class='fl'>1</span> -} <span class='kw'>else</span> { - <span class='no'>n_cores</span> <span class='kw'><-</span> <span class='fl'>1</span> -} -<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span>(<span class='st'>"TRAVIS"</span>) <span class='kw'>!=</span> <span class='st'>""</span>) <span class='no'>n_cores</span> <span class='kw'>=</span> <span class='fl'>1</span> -<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span>()[<span class='st'>"sysname"</span>] <span class='kw'>==</span> <span class='st'>"Windows"</span>) <span class='no'>n_cores</span> <span class='kw'>=</span> <span class='fl'>1</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'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>SFO_SFO.ff</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'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), - <span class='kw'>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='no'>f_d_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> user system elapsed -#> 3.810 0.964 3.430 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> +<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"NOT_CRAN"</span><span class='op'>)</span>, <span class='st'>"true"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> + <span class='va'>n_cores</span> <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='fl'>1</span> +<span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span> + <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fl'>1</span> +<span class='op'>}</span> +<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>!=</span> <span class='st'>""</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span> +<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</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'>"m1"</span><span class='op'>)</span>, m1 <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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>SFO_SFO.ff</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'>"m1"</span><span class='op'>)</span>, m1 <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>, + 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='va'>f_d_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> user system elapsed +#> 3.829 1.000 3.519 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> <span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> <span class='co'># minor interest), we get a nice performance improvement from about 50</span> <span class='co'># seconds to about 12 seconds if we use at least four cores</span> -<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile_no_parent_0</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#> <span class='error'>Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.015 0.029 0.198</span></div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#> 2.5% 97.5% +<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#> <span class='error'>Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.011 0.029 0.241</span></div><div class='input'><span class='va'>ci_profile</span> +</div><div class='output co'>#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent 0.090911032 1.071578e-01 -#> k_m1 0.003892605 6.702778e-03 +#> k_m1 0.003892606 6.702775e-03 #> f_parent_to_m1 0.471328495 5.611550e-01 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) -<span class='no'>ci_quadratic_transformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403839460 1.027931e+02 -#> k_parent 0.090823790 1.072543e-01 -#> k_m1 0.004012216 6.897547e-03 -#> f_parent_to_m1 0.469118713 5.595960e-01 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) -<span class='no'>ci_quadratic_untransformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403839413 1.027931e+02 -#> k_parent 0.090491931 1.069035e-01 -#> k_m1 0.003835483 6.685819e-03 -#> f_parent_to_m1 0.469113365 5.598386e-01 +#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +<span class='va'>ci_quadratic_transformed</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403833585 102.79311650 +#> k_parent 0.090823771 0.10725430 +#> k_m1 0.004012219 0.00689755 +#> f_parent_to_m1 0.469118824 0.55959615 +#> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +<span class='va'>ci_quadratic_untransformed</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403833589 1.027931e+02 +#> k_parent 0.090491913 1.069035e-01 +#> k_m1 0.003835485 6.685823e-03 +#> f_parent_to_m1 0.469113477 5.598387e-01 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> <span class='co'># intervals based on the internal parameter transformation are less</span> <span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span> <span class='co'># interval based on the untransformed fit for k_m1_sink</span> -<span class='no'>rel_diffs_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>) -<span class='no'>rel_diffs_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>) -<span class='no'>rel_diffs_transformed</span> <span class='kw'><</span> <span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 TRUE TRUE +<span class='va'>rel_diffs_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_transformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span> +<span class='va'>rel_diffs_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_untransformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span> +<span class='va'>rel_diffs_transformed</span> <span class='op'><</span> <span class='va'>rel_diffs_untransformed</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 FALSE FALSE #> k_parent TRUE TRUE #> k_m1 FALSE FALSE #> f_parent_to_m1 TRUE FALSE -#> sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> 2.5% 97.5% +#> sigma TRUE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% #> parent_0 0.000541 0.000222 #> k_parent 0.000960 0.000900 #> k_m1 0.030700 0.029100 #> f_parent_to_m1 0.004690 0.002780 -#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_untransformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> 2.5% 97.5% +#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% #> parent_0 0.000541 0.000222 #> k_parent 0.004610 0.002370 #> k_m1 0.014700 0.002530 @@ -326,66 +337,76 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> sigma 0.055000 0.032700</div><div class='input'> <span class='co'># Investigate a case with formation fractions</span> -<span class='no'>f_d_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>ci_profile_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>)</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='no'>ci_profile_ff</span></div><div class='output co'>#> 2.5% 97.5% +<span class='va'>f_d_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>ci_profile_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='va'>ci_profile_ff</span> +</div><div class='output co'>#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent 0.090911032 1.071578e-01 -#> k_m1 0.003892605 6.702778e-03 +#> k_m1 0.003892606 6.702775e-03 #> f_parent_to_m1 0.471328495 5.611550e-01 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) -<span class='no'>ci_quadratic_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403839460 1.027931e+02 -#> k_parent 0.090823790 1.072543e-01 -#> k_m1 0.004012216 6.897547e-03 -#> f_parent_to_m1 0.469118713 5.595960e-01 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) -<span class='no'>ci_quadratic_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403839413 1.027931e+02 -#> k_parent 0.090491931 1.069035e-01 -#> k_m1 0.003835483 6.685819e-03 -#> f_parent_to_m1 0.469113365 5.598386e-01 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>) -<span class='no'>rel_diffs_untransformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>) +#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +<span class='va'>ci_quadratic_transformed_ff</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403833585 102.79311650 +#> k_parent 0.090823771 0.10725430 +#> k_m1 0.004012219 0.00689755 +#> f_parent_to_m1 0.469118824 0.55959615 +#> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +<span class='va'>ci_quadratic_untransformed_ff</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403833589 1.027931e+02 +#> k_parent 0.090491913 1.069035e-01 +#> k_m1 0.003835485 6.685823e-03 +#> f_parent_to_m1 0.469113477 5.598387e-01 +#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'>-</span> <span class='va'>ci_profile_ff</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile_ff</span><span class='op'>)</span> +<span class='va'>rel_diffs_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'>-</span> <span class='va'>ci_profile_ff</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile_ff</span><span class='op'>)</span> <span class='co'># While the confidence interval for the parent rate constant is closer to</span> <span class='co'># the profile based interval when using the internal parameter</span> <span class='co'># transformation, the interval for the metabolite rate constant is 'better</span> <span class='co'># without internal parameter transformation.</span> -<span class='no'>rel_diffs_transformed_ff</span> <span class='kw'><</span> <span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 TRUE TRUE +<span class='va'>rel_diffs_transformed_ff</span> <span class='op'><</span> <span class='va'>rel_diffs_untransformed_ff</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 FALSE FALSE #> k_parent TRUE TRUE #> k_m1 FALSE FALSE #> f_parent_to_m1 TRUE FALSE -#> sigma FALSE FALSE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408080 0.0002217794 -#> k_parent 0.0009596417 0.0009003876 -#> k_m1 0.0307277370 0.0290579182 -#> f_parent_to_m1 0.0046884130 0.0027782556 -#> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408085 0.0002217799 -#> k_parent 0.0046100096 0.0023730229 -#> k_m1 0.0146746469 0.0025301011 -#> f_parent_to_m1 0.0046997599 0.0023460223 +#> sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.0005408689 0.0002217234 +#> k_parent 0.0009598532 0.0009001864 +#> k_m1 0.0307283044 0.0290588365 +#> f_parent_to_m1 0.0046881768 0.0027780063 +#> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.0005408689 0.0002217233 +#> k_parent 0.0046102155 0.0023732281 +#> k_m1 0.0146740688 0.0025291817 +#> f_parent_to_m1 0.0046995211 0.0023457712 #> sigma 0.0550252516 0.0327066836</div><div class='input'> <span class='co'># The profiling for the following fit does not finish in a reasonable time,</span> <span class='co'># therefore we use the quadratic approximation</span> -<span class='no'>m_synth_DFOP_par</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'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>DFOP_par_c</span> <span class='kw'><-</span> <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span> -<span class='no'>f_tc_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, <span class='no'>DFOP_par_c</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, - <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='st'>"direct"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59613833 106.19939215 -#> k_M1 0.03760542 0.04490759 -#> k_M2 0.00856874 0.01087675 -#> f_parent_to_M1 0.02146166 0.62023888 -#> f_parent_to_M2 0.01516502 0.37975343 -#> k1 0.27389751 0.33388078 -#> k2 0.01861456 0.02250379 -#> g 0.67194349 0.73583256 -#> sigma_low 0.25128383 0.83992146 -#> rsd_high 0.04041100 0.07662001</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59614 106.1994</div><div class='input'># } +<span class='va'>m_synth_DFOP_par</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'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, + M1 <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>, + M2 <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>, + 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='va'>DFOP_par_c</span> <span class='op'><-</span> <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span> +<span class='va'>f_tc_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, <span class='va'>DFOP_par_c</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, + error_model_algorithm <span class='op'>=</span> <span class='st'>"direct"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 94.596126334 106.19944007 +#> k_M1 0.037605408 0.04490759 +#> k_M2 0.008568739 0.01087675 +#> f_parent_to_M1 0.021463787 0.62023881 +#> f_parent_to_M2 0.015166531 0.37975349 +#> k1 0.273897467 0.33388084 +#> k2 0.018614555 0.02250379 +#> g 0.671943606 0.73583278 +#> sigma_low 0.251283766 0.83992113 +#> rsd_high 0.040411014 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 94.59613 106.1994</div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -402,7 +423,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, </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/create_deg_func.html b/docs/dev/reference/create_deg_func.html index a25fa165..9f2e4deb 100644 --- a/docs/dev/reference/create_deg_func.html +++ b/docs/dev/reference/create_deg_func.html @@ -72,7 +72,7 @@ </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> @@ -120,7 +120,7 @@ </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> @@ -139,7 +139,7 @@ <div class="col-md-9 contents"> <div class="page-header"> <h1>Create degradation functions for known analytical solutions</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/create_deg_func.R'><code>R/create_deg_func.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/create_deg_func.R'><code>R/create_deg_func.R</code></a></small> <div class="hidden name"><code>create_deg_func.Rd</code></div> </div> @@ -147,7 +147,7 @@ <p>Create degradation functions for known analytical solutions</p> </div> - <pre class="usage"><span class='fu'>create_deg_func</span>(<span class='no'>spec</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"min"</span>, <span class='st'>"max"</span>))</pre> + <pre class="usage"><span class='fu'>create_deg_func</span><span class='op'>(</span><span class='va'>spec</span>, use_of_ff <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'>"min"</span>, <span class='st'>"max"</span><span class='op'>)</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -168,30 +168,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> -<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'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>FOCUS_D</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>) <span class='co'># to avoid warnings</span> -<span class='no'>fit_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='co'># \dontrun{</span> -<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) - <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>( - <span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.423 1.000 0.423 0 0 -#> 2 deSolve 2 0.716 1.693 0.715 0 0 +<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'>"m1"</span><span class='op'>)</span>, + m1 <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='va'>FOCUS_D</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'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># to avoid warnings</span> +<span class='va'>fit_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<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='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='co'># \dontrun{</span> +<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> + <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span> + analytical <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, + deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, + replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child +#> 1 analytical 2 0.397 1.000 0.397 0.001 0 +#> 2 deSolve 2 0.684 1.723 0.683 0.000 0 #> sys.child #> 1 0 -#> 2 0</div><div class='input'> <span class='no'>DFOP_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'>"DFOP"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</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='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>( - <span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>DFOP_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>DFOP_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.910 1.000 0.909 0 0 -#> 2 deSolve 2 1.734 1.905 1.733 0 0 +#> 2 0</div><div class='input'> <span class='va'>DFOP_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'>"DFOP"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, + m1 <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='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span> + analytical <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, + deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, + replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> +</div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child +#> 1 analytical 2 0.834 1.000 0.833 0.001 0 +#> 2 deSolve 2 1.545 1.853 1.541 0.001 0 #> sys.child #> 1 0 -#> 2 0</div><div class='input'># } +#> 2 0</div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -208,7 +214,7 @@ </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/reference/experimental_data_for_UBA-1.png b/docs/dev/reference/experimental_data_for_UBA-1.png Binary files differindex b316a5db..24cb54c5 100644 --- a/docs/dev/reference/experimental_data_for_UBA-1.png +++ b/docs/dev/reference/experimental_data_for_UBA-1.png diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html index d49924c7..cd098b7d 100644 --- a/docs/dev/reference/experimental_data_for_UBA.html +++ b/docs/dev/reference/experimental_data_for_UBA.html @@ -60,11 +60,11 @@ Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate (Austria, 2015, p. 16). Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate - (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling, + (Germany, 2013, pages 8, 28, 50, 51). For the initial sampling, the residues given for the metabolite were added to the parent value, following the recommendation of the FOCUS kinetics workgroup. Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D - (Germany, 2013b, p. 644). Values reported as zero were set to NA, with + (Hellas, 2013, p. 644). Values reported as zero were set to NA, with the exception of the day three sampling of metabolite A2, which was set to one half of the LOD reported to be 1% AR. Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl @@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-danger" 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> @@ -148,7 +148,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </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> @@ -192,24 +192,24 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <p>Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate (Austria, 2015, p. 16).</p> <p>Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate - (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling, + (Germany, 2013, pages 8, 28, 50, 51). For the initial sampling, the residues given for the metabolite were added to the parent value, following the recommendation of the FOCUS kinetics workgroup.</p> <p>Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D - (Germany, 2013b, p. 644). Values reported as zero were set to NA, with + (Hellas, 2013, p. 644). Values reported as zero were set to NA, with the exception of the day three sampling of metabolite A2, which was set to one half of the LOD reported to be 1% AR.</p> <p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81).</p> </div> - <pre class="usage"><span class='no'>experimental_data_for_UBA_2019</span></pre> + <pre class="usage"><span class='va'>experimental_data_for_UBA_2019</span></pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, - each containing, among others, the following components</p><dl'> + each containing, among others, the following components</p><dl> <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd> <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> @@ -227,9 +227,9 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> -<p>Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate +<p>Germany (2013). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate and Behaviour</p> -<p>Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the +<p>Hellas (2013). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the environment</p> <p>Ranke (2019) Documentation of results obtained for the error model expertise written for the German Umweltbundesamt.</p> @@ -241,35 +241,40 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> <span class='co'># Model definitions</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='kw'>to</span> <span class='kw'>=</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>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span> -)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='no'>dfop_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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</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>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span> -)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='no'>sfo_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='kw'>to</span> <span class='kw'>=</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>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), - <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span> -)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='no'>dfop_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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</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>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), - <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span> -)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>d_1_2</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'>1</span>:<span class='fl'>2</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>) -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>d_1_2</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Soil"</span>, <span class='fl'>1</span>:<span class='fl'>2</span>) - - -<span class='no'>f_1_2_tc</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'>"DFOP-SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>dfop_sfo_sfo</span>), <span class='no'>d_1_2</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>) - -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_1_2_tc</span>, <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'> -# }</div></pre> +<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>, to <span class='op'>=</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>, + use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>dfop_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'>"DFOP"</span>, to <span class='op'>=</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>, + use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>sfo_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>, to <span class='op'>=</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>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>, + A2 <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>, + use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>dfop_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'>"DFOP"</span>, to <span class='op'>=</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>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>, + A2 <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>, + use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>d_1_2</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'>1</span><span class='op'>:</span><span class='fl'>2</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='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/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_1_2</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'>"Soil"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>)</span> + + +<span class='va'>f_1_2_tc</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'>"DFOP-SFO-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo_sfo</span><span class='op'>)</span>, <span class='va'>d_1_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> + +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_1_2_tc</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span> +</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='co'># }</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"> @@ -285,7 +290,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </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/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html new file mode 100644 index 00000000..a95234a7 --- /dev/null +++ b/docs/dev/reference/f_time_norm_focus.html @@ -0,0 +1,283 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Normalisation factors for aerobic soil degradation 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class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> + +<span class='co'># S3 method for numeric</span> +<span class='fu'>f_time_norm_focus</span><span class='op'>(</span> + <span class='va'>object</span>, + moisture <span class='op'>=</span> <span class='cn'>NA</span>, + field_moisture <span class='op'>=</span> <span class='cn'>NA</span>, + temperature <span class='op'>=</span> <span class='va'>object</span>, + Q10 <span class='op'>=</span> <span class='fl'>2.58</span>, + walker <span class='op'>=</span> <span class='fl'>0.7</span>, + f_na <span class='op'>=</span> <span class='cn'>NA</span>, + <span class='va'>...</span> +<span class='op'>)</span> + +<span class='co'># S3 method for mkindsg</span> +<span class='fu'>f_time_norm_focus</span><span class='op'>(</span> + <span class='va'>object</span>, + study_moisture_ref_source <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'>"meta"</span>, <span class='st'>"focus"</span><span class='op'>)</span>, + Q10 <span class='op'>=</span> <span class='fl'>2.58</span>, + walker <span class='op'>=</span> <span class='fl'>0.7</span>, + f_na <span class='op'>=</span> <span class='cn'>NA</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"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>An object containing information used for the calculations</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Currently not used</p></td> + </tr> + <tr> + <th>moisture</th> + <td><p>Numeric vector of moisture contents in \% w/w</p></td> + </tr> + <tr> + <th>field_moisture</th> + <td><p>Numeric vector of moisture contents at field capacity +(pF2) in \% w/w</p></td> + </tr> + <tr> + <th>temperature</th> + <td><p>Numeric vector of temperatures in °C</p></td> + </tr> + <tr> + <th>Q10</th> + <td><p>The Q10 value used for temperature normalisation</p></td> + </tr> + <tr> + <th>walker</th> + <td><p>The Walker exponent used for moisture normalisation</p></td> + </tr> + <tr> + <th>f_na</th> + <td><p>The factor to use for NA values. If set to NA, only factors +for complete cases will be returned.</p></td> + </tr> + <tr> + <th>study_moisture_ref_source</th> + <td><p>Source for the reference value +used to calculate the study moisture</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a> +FOCUS (2014) “Generic guidance for Estimating Persistence +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <div class='dont-index'><p><a href='focus_soil_moisture.html'>focus_soil_moisture</a></p></div> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='fl'>25</span>, <span class='fl'>20</span>, <span class='fl'>25</span><span class='op'>)</span> <span class='co'># 1.37, compare FOCUS 2014 p. 184</span> +</div><div class='output co'>#> [1] 1.373956</div><div class='input'> +<span class='va'>D24_2014</span><span class='op'>$</span><span class='va'>meta</span> +</div><div class='output co'>#> study usda_soil_type study_moisture_ref_type rel_moisture +#> 1 Cohen 1991 Silt loam <NA> NA +#> 2 Liu and Adelfinskaya 2011 Silt loam pF1 0.5 +#> 3 Liu and Adelfinskaya 2011 Loam pF1 0.5 +#> 4 Liu and Adelfinskaya 2011 Loam pF1 0.5 +#> 5 Liu and Adelfinskaya 2011 Loamy sand pF1 0.5 +#> temperature +#> 1 25 +#> 2 20 +#> 3 20 +#> 4 20 +#> 5 20</div><div class='input'><span class='co'># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span> +<span class='co'># temperature only normalisation as in the EU evaluation</span> +<span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='va'>D24_2014</span>, study_moisture_ref_source <span class='op'>=</span> <span class='st'>"focus"</span>, f_na <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +</div><div class='output co'>#> $time_norm was set to +#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div><div class='output co'>#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/dev/reference/focus_soil_moisture.html b/docs/dev/reference/focus_soil_moisture.html new file mode 100644 index 00000000..c46fd69a --- /dev/null +++ b/docs/dev/reference/focus_soil_moisture.html @@ -0,0 +1,206 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture • mkin</title> + + +<!-- jquery --> 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capacity, MWHC and 1/3 bar — focus_soil_moisture" /> +<meta property="og:description" content="The value were transcribed from p. 36. The table assumes field capacity +corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> + + +<meta name="robots" content="noindex"> + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + + </head> + + <body data-spy="scroll" data-target="#toc"> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </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">0.9.50.4</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/focus_soil_moisture.R'><code>R/focus_soil_moisture.R</code></a></small> + <div class="hidden name"><code>focus_soil_moisture.Rd</code></div> + </div> + + <div class="ref-description"> + <p>The value were transcribed from p. 36. The table assumes field capacity +corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.</p> + </div> + + <pre class="usage"><span class='va'>focus_soil_moisture</span></pre> + + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A matrix with upper case USDA soil classes as row names, and water tension +('pF1', 'pF2', 'pF 2.5') as column names</p> + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>Anonymous (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessment +Version 2.2, May 2014 <a href='https://esdac.jrc.ec.europa.eu/projects/ground-water'>https://esdac.jrc.ec.europa.eu/projects/ground-water</a></p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='va'>focus_soil_moisture</span> +</div><div class='output co'>#> pF1 pF2 pF2.5 +#> Sand 24 12 7 +#> Loamy sand 24 14 9 +#> Sandy loam 27 19 15 +#> Sandy clay loam 28 22 18 +#> Clay loam 32 28 25 +#> Loam 31 25 21 +#> Silt loam 32 26 21 +#> Silty clay loam 34 30 27 +#> Silt 31 27 21 +#> Sandy clay 41 35 31 +#> Silty clay 44 40 36 +#> Clay 53 48 43</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/dev/reference/ilr.html b/docs/dev/reference/ilr.html index 8f58949e..98e51211 100644 --- a/docs/dev/reference/ilr.html +++ b/docs/dev/reference/ilr.html @@ -73,7 +73,7 @@ transformations." /> </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> @@ -121,7 +121,7 @@ transformations." /> </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> @@ -140,7 +140,7 @@ transformations." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to perform isometric log-ratio transformation</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/ilr.R'><code>R/ilr.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/ilr.R'><code>R/ilr.R</code></a></small> <div class="hidden name"><code>ilr.Rd</code></div> </div> @@ -149,9 +149,9 @@ transformations." /> transformations.</p> </div> - <pre class="usage"><span class='fu'>ilr</span>(<span class='no'>x</span>) + <pre class="usage"><span class='fu'>ilr</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> -<span class='fu'>invilr</span>(<span class='no'>x</span>)</pre> +<span class='fu'>invilr</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -176,19 +176,33 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> <div class='dont-index'><p>Another implementation can be found in R package <code>robCompositions</code>.</p></div> + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>René Lehmann and Johannes Ranke</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Order matters</span> -<span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#> [1] 1.628174 2.820079</div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> -<span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#> [1] 0 0</div><div class='input'><span class='co'># Almost equal entries give small numbers</span> -<span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#> [1] -0.2034219 0.1174457</div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> -<span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fl'>2.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> -<span class='fu'>invilr</span>(-<span class='fl'>10</span>)</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01</div><div class='input'><span class='fu'>invilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(-<span class='fl'>10</span>, <span class='fl'>0</span>))</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04</div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> -<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='fu'>invilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#> [1] 1</div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> -<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>) -<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>invilr</span>(<span class='no'>a</span>) -<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#> [1] 4</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#> [1] 0.1 0.3 0.5</div><div class='input'> +<span class='fu'>ilr</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'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</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'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> [1] 1.628174 2.820079</div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> +<span class='fu'>ilr</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'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> [1] 0 0</div><div class='input'><span class='co'># Almost equal entries give small numbers</span> +<span class='fu'>ilr</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'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> [1] -0.2034219 0.1174457</div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> +<span class='fu'>invilr</span><span class='op'>(</span><span class='fu'>ilr</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'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'>ilr</span><span class='op'>(</span><span class='fl'>2.1</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'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> +<span class='fu'>invilr</span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span><span class='op'>)</span> +</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01</div><div class='input'><span class='fu'>invilr</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='op'>-</span><span class='fl'>10</span>, <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04</div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> +<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>invilr</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='op'>-</span><span class='fl'>10</span>, <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> [1] 1</div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> +<span class='va'>a</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'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span><span class='op'>)</span> +<span class='va'>b</span> <span class='op'><-</span> <span class='fu'>invilr</span><span class='op'>(</span><span class='va'>a</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>)</span> <span class='co'># Four elements</span> +</div><div class='output co'>#> [1] 4</div><div class='input'><span class='fu'>ilr</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='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, <span class='fl'>1</span> <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># Gives c(0.1, 0.3, 0.5)</span> +</div><div class='output co'>#> [1] 0.1 0.3 0.5</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -205,7 +219,7 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248</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 36c10225..cb37f9a6 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -163,7 +163,7 @@ <tr> <td> - <p><code><a href="mkinmod.html">mkinmod()</a></code> </p> + <p><code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i><mkinmod></i>)</a></code> <code><a href="mkinmod.html">mkinsub()</a></code> </p> </td> <td><p>Function to set up a kinetic model with one or more state variables</p></td> </tr><tr> @@ -374,6 +374,18 @@ of an mmkin object</p></td> <tr> <td> + <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p> + </td> + <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td> + </tr><tr> + + <td> + <p><code><a href="D24_2014.html">D24_2014</a></code> </p> + </td> + <td><p>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</p></td> + </tr><tr> + + <td> <p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> </p> </td> <td><p>Datasets A to F from the FOCUS Kinetics report from 2006</p></td> @@ -446,15 +458,15 @@ of an mmkin object</p></td> </tr><tr> <td> - <p><code><a href="mkinds.html">mkinds</a></code> </p> + <p><code><a href="mkinds.html">print(<i><mkinds></i>)</a></code> </p> </td> <td><p>A dataset class for mkin</p></td> </tr><tr> <td> - <p><code><a href="print.mkinds.html">print(<i><mkinds></i>)</a></code> </p> + <p><code><a href="mkindsg.html">print(<i><mkindsg></i>)</a></code> </p> </td> - <td><p>Print mkinds objects</p></td> + <td><p>A class for dataset groups for mkin</p></td> </tr> </tbody><tbody> <tr> @@ -484,7 +496,7 @@ of an mmkin object</p></td> </tbody><tbody> <tr> <th colspan="2"> - <h2 id="section-helper-functions-mainly-used-internally" class="hasAnchor"><a href="#section-helper-functions-mainly-used-internally" class="anchor"></a>Helper functions mainly used internally</h2> + <h2 id="section-utility-functions" class="hasAnchor"><a href="#section-utility-functions" class="anchor"></a>Utility functions</h2> <p class="section-desc"></p> </th> </tr> @@ -496,9 +508,9 @@ of an mmkin object</p></td> <tr> <td> - <p><code><a href="mkinsub.html">mkinsub()</a></code> </p> + <p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p> </td> - <td><p>Function to set up a kinetic submodel for one state variable</p></td> + <td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td> </tr><tr> <td> @@ -509,12 +521,6 @@ kinetic models fitted with mkinfit</p></td> </tr><tr> <td> - <p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p> - </td> - <td><p>Produce predictions from a kinetic model using specific parameters</p></td> - </tr><tr> - - <td> <p><code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> </p> </td> <td><p>Convert a dataframe with observations over time into long format</p></td> @@ -524,12 +530,25 @@ kinetic models fitted with mkinfit</p></td> <p><code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> </p> </td> <td><p>Convert a dataframe from long to wide format</p></td> - </tr><tr> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-helper-functions-mainly-used-internally" class="hasAnchor"><a href="#section-helper-functions-mainly-used-internally" class="anchor"></a>Helper functions mainly used internally</h2> + <p class="section-desc"></p> + </th> + </tr> + + + </tbody><tbody> + + + <tr> <td> - <p><code><a href="print.mkinmod.html">print(<i><mkinmod></i>)</a></code> </p> + <p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p> </td> - <td><p>Print mkinmod objects</p></td> + <td><p>Produce predictions from a kinetic model using specific parameters</p></td> </tr><tr> <td> @@ -545,12 +564,6 @@ kinetic models fitted with mkinfit</p></td> </tr><tr> <td> - <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p> - </td> - <td><p>Two-component error model</p></td> - </tr><tr> - - <td> <p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p> </td> <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td> @@ -664,6 +677,12 @@ kinetic models fitted with mkinfit</p></td> <p><code><a href="add_err.html">add_err()</a></code> </p> </td> <td><p>Add normally distributed errors to simulated kinetic degradation data</p></td> + </tr><tr> + + <td> + <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p> + </td> + <td><p>Two-component error model</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html index 7ab36f0d..dbeeef60 100644 --- a/docs/dev/reference/logLik.mkinfit.html +++ b/docs/dev/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error model." /> </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> @@ -124,7 +124,7 @@ the error model." /> </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> @@ -143,7 +143,7 @@ the error model." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculated the log-likelihood of a fitted mkinfit object</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/logLik.mkinfit.R'><code>R/logLik.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/logLik.mkinfit.R'><code>R/logLik.mkinfit.R</code></a></small> <div class="hidden name"><code>logLik.mkinfit.Rd</code></div> </div> @@ -156,7 +156,7 @@ the error model.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></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"> @@ -185,18 +185,26 @@ and the fitted error model parameters.</p> <div class='dont-index'><p>Compare the AIC of columns of <code><a href='mmkin.html'>mmkin</a></code> objects using <code><a href='AIC.mmkin.html'>AIC.mmkin</a></code>.</p></div> + <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='co'># \dontrun{</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>) - )</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>d_t</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> - <span class='no'>f_nw</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># no weighting (weights are unity)</span></div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'> <span class='no'>f_obs</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='no'>f_tc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>)</div><div class='output co'>#> df AIC + <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>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, + m1 <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='va'>d_t</span> <span class='op'><-</span> <span class='va'>FOCUS_2006_D</span> + <span class='va'>f_nw</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># no weighting (weights are unity)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='va'>f_obs</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='va'>f_tc</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</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> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nw</span>, <span class='va'>f_obs</span>, <span class='va'>f_tc</span><span class='op'>)</span> +</div><div class='output co'>#> df AIC #> f_nw 5 204.4486 #> f_obs 6 205.8727 -#> f_tc 6 141.9656</div><div class='input'> # } +#> f_tc 6 141.9656</div><div class='input'> <span class='co'># }</span> </div></pre> </div> @@ -214,7 +222,7 @@ and the fitted error model parameters.</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/logistic.solution-1.png b/docs/dev/reference/logistic.solution-1.png Binary files differindex fd11d0c0..84d8e722 100644 --- a/docs/dev/reference/logistic.solution-1.png +++ b/docs/dev/reference/logistic.solution-1.png diff --git a/docs/dev/reference/logistic.solution-2.png b/docs/dev/reference/logistic.solution-2.png Binary files differindex 78a31f93..764996df 100644 --- a/docs/dev/reference/logistic.solution-2.png +++ b/docs/dev/reference/logistic.solution-2.png diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html index 248edcda..86be11a7 100644 --- a/docs/dev/reference/logistic.solution.html +++ b/docs/dev/reference/logistic.solution.html @@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> </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> @@ -121,7 +121,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> </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> @@ -140,7 +140,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Logistic kinetics</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> <div class="hidden name"><code>logistic.solution.Rd</code></div> </div> @@ -149,7 +149,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> an increasing rate constant, supposedly caused by microbial growth</p> </div> - <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre> + <pre class="usage"><span class='fu'>logistic.solution</span><span class='op'>(</span><span class='va'>t</span>, <span class='va'>parent_0</span>, <span class='va'>kmax</span>, <span class='va'>k0</span>, <span class='va'>r</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -208,30 +208,38 @@ Version 1.1, 18 December 2014 <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>), - <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</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'>100</span>), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>), - <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>), - <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>), - <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>), - <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, - <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>), - <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)), - <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>)</div><div class='img'><img src='logistic.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>logistic.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span><span class='op'>)</span>, + from <span class='op'>=</span> <span class='fl'>0</span>, to <span class='op'>=</span> <span class='fl'>100</span>, ylim <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'>100</span><span class='op'>)</span>, + xlab <span class='op'>=</span> <span class='st'>"Time"</span>, ylab <span class='op'>=</span> <span class='st'>"Residue"</span><span class='op'>)</span> +</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>logistic.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span><span class='op'>)</span>, + from <span class='op'>=</span> <span class='fl'>0</span>, to <span class='op'>=</span> <span class='fl'>100</span>, add <span class='op'>=</span> <span class='cn'>TRUE</span>, lty <span class='op'>=</span> <span class='fl'>2</span>, col <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> +</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>logistic.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span><span class='op'>)</span>, + from <span class='op'>=</span> <span class='fl'>0</span>, to <span class='op'>=</span> <span class='fl'>100</span>, add <span class='op'>=</span> <span class='cn'>TRUE</span>, lty <span class='op'>=</span> <span class='fl'>3</span>, col <span class='op'>=</span> <span class='fl'>3</span><span class='op'>)</span> +</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>logistic.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span><span class='op'>)</span>, + from <span class='op'>=</span> <span class='fl'>0</span>, to <span class='op'>=</span> <span class='fl'>100</span>, add <span class='op'>=</span> <span class='cn'>TRUE</span>, lty <span class='op'>=</span> <span class='fl'>4</span>, col <span class='op'>=</span> <span class='fl'>4</span><span class='op'>)</span> +</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></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'>logistic.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span><span class='op'>)</span>, + from <span class='op'>=</span> <span class='fl'>0</span>, to <span class='op'>=</span> <span class='fl'>100</span>, add <span class='op'>=</span> <span class='cn'>TRUE</span>, lty <span class='op'>=</span> <span class='fl'>5</span>, col <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span> +</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span><span class='op'>(</span><span class='st'>"topright"</span>, inset <span class='op'>=</span> <span class='fl'>0.05</span>, + legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span><span class='op'>)</span>, + <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span><span class='op'>)</span><span class='op'>)</span>, + lty <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span>, col <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span> +</div><div class='img'><img src='logistic.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Fit with synthetic data</span> - <span class='no'>logistic</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'>"logistic"</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'>parms_logistic</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>kmax</span> <span class='kw'>=</span> <span class='fl'>0.08</span>, <span class='kw'>k0</span> <span class='kw'>=</span> <span class='fl'>0.0001</span>, <span class='kw'>r</span> <span class='kw'>=</span> <span class='fl'>0.2</span>) - <span class='no'>d_logistic</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>logistic</span>, - <span class='no'>parms_logistic</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='no'>sampling_times</span>) - <span class='no'>d_2_1</span> <span class='kw'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_logistic</span>, - <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>), - <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]] - - <span class='no'>m</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower + <span class='va'>logistic</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'>"logistic"</span><span class='op'>)</span><span class='op'>)</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'>parms_logistic</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>kmax <span class='op'>=</span> <span class='fl'>0.08</span>, k0 <span class='op'>=</span> <span class='fl'>0.0001</span>, r <span class='op'>=</span> <span class='fl'>0.2</span><span class='op'>)</span> + <span class='va'>d_logistic</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>logistic</span>, + <span class='va'>parms_logistic</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='va'>d_2_1</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_logistic</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='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span><span class='op'>)</span>, + n <span class='op'>=</span> <span class='fl'>1</span>, reps <span class='op'>=</span> <span class='fl'>2</span>, digits <span class='op'>=</span> <span class='fl'>5</span>, LOD <span class='op'>=</span> <span class='fl'>0.1</span>, seed <span class='op'>=</span> <span class='fl'>123456</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> + + <span class='va'>m</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"logistic"</span>, <span class='va'>d_2_1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span> +</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower #> parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02 #> kmax 6.398190e-02 0.0143201031 4.467978 3.841829e-04 3.929235e-02 #> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08 @@ -242,7 +250,8 @@ Version 1.1, 18 December 2014 #> kmax 0.1041853 #> k0 0.4448749 #> r 1.1821120 -#> sigma 7.3256566</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#> DT50 DT90 DT50_k0 DT50_kmax +#> sigma 7.3256566</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span><span class='op'>$</span><span class='va'>distimes</span> +</div><div class='output co'>#> DT50 DT90 DT50_k0 DT50_kmax #> parent 36.86533 62.41511 4297.853 10.83349</div><div class='input'> </div></pre> </div> @@ -260,7 +269,7 @@ Version 1.1, 18 December 2014 </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/max_twa_parent.html b/docs/dev/reference/max_twa_parent.html index 01aab55d..25f745e9 100644 --- a/docs/dev/reference/max_twa_parent.html +++ b/docs/dev/reference/max_twa_parent.html @@ -78,7 +78,7 @@ soil section of the FOCUS guidance." /> </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 @@ soil section of the FOCUS guidance." /> </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 @@ soil section of the FOCUS guidance." /> <div class="page-header"> <h1>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/max_twa_parent.R'><code>R/max_twa_parent.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/max_twa_parent.R'><code>R/max_twa_parent.R</code></a></small> <div class="hidden name"><code>max_twa_parent.Rd</code></div> </div> @@ -158,15 +158,15 @@ FOMC, DFOP and HS models, using the analytical formulas given in the PEC soil section of the FOCUS guidance.</p> </div> - <pre class="usage"><span class='fu'>max_twa_parent</span>(<span class='no'>fit</span>, <span class='no'>windows</span>) + <pre class="usage"><span class='fu'>max_twa_parent</span><span class='op'>(</span><span class='va'>fit</span>, <span class='va'>windows</span><span class='op'>)</span> -<span class='fu'>max_twa_sfo</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k</span>, <span class='no'>t</span>) +<span class='fu'>max_twa_sfo</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k</span>, <span class='va'>t</span><span class='op'>)</span> -<span class='fu'>max_twa_fomc</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>, <span class='no'>t</span>) +<span class='fu'>max_twa_fomc</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>alpha</span>, <span class='va'>beta</span>, <span class='va'>t</span><span class='op'>)</span> -<span class='fu'>max_twa_dfop</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>, <span class='no'>t</span>) +<span class='fu'>max_twa_dfop</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>g</span>, <span class='va'>t</span><span class='op'>)</span> -<span class='fu'>max_twa_hs</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>, <span class='no'>t</span>)</pre> +<span class='fu'>max_twa_hs</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>tb</span>, <span class='va'>t</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -233,11 +233,15 @@ and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></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'>max_twa_parent</span>(<span class='no'>fit</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>))</div><div class='output co'>#> 7 21 + <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'>max_twa_parent</span><span class='op'>(</span><span class='va'>fit</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>7</span>, <span class='fl'>21</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> 7 21 #> 34.71343 18.22124 </div><div class='input'> </div></pre> </div> @@ -255,7 +259,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </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/mkinds.html b/docs/dev/reference/mkinds.html index a8641375..907f8ad3 100644 --- a/docs/dev/reference/mkinds.html +++ b/docs/dev/reference/mkinds.html @@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." /> </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 @@ provided by this package come as mkinds objects nevertheless." /> </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 @@ provided by this package come as mkinds objects nevertheless." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>A dataset class for mkin</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinds.R'><code>R/mkinds.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinds.R'><code>R/mkinds.R</code></a></small> <div class="hidden name"><code>mkinds.Rd</code></div> </div> @@ -153,14 +153,29 @@ such as the on contained in the data field of mkinds objects. Some datasets provided by this package come as mkinds objects nevertheless.</p> </div> + <pre class="usage"><span class='co'># S3 method for mkinds</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, data <span class='op'>=</span> <span class='cn'>FALSE</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"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>An mkinds object.</p></td> + </tr> + <tr> + <th>data</th> + <td><p>Should the data be printed?</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Not used.</p></td> + </tr> + </table> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>The S3 printing method <code><a href='print.mkinds.html'>print.mkinds</a></code></p></div> <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> - <p><div class="r6-fields"></p><dl'> + <p><div class="r6-fields"></p><dl> <dt><code>title</code></dt><dd><p>A full title for the dataset</p></dd> <dt><code>sampling_times</code></dt><dd><p>The sampling times</p></dd> @@ -180,19 +195,19 @@ and value in order to be compatible with mkinfit</p></dd> <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> -<h3>Public methods</h3> +<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3> <ul> <li><p><a href='#method-new'><code>mkinds$new()</code></a></p></li> <li><p><a href='#method-clone'><code>mkinds$clone()</code></a></p></li> </ul> <p><hr> -<a id="method-new"></a></p><h3>Method <code>new()</code></h3> -<p>Create a new mkinds object</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='no'>data</span>, <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>unit</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre><p></div></p> +<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3> +<p>Create a new mkinds object</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> +<p><div class="r"></p><pre><span class='va'>mkinds</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>title <span class='op'>=</span> <span class='st'>""</span>, <span class='va'>data</span>, time_unit <span class='op'>=</span> <span class='cn'>NA</span>, unit <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre><p></div></p> -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> +<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4> +<p><div class="arguments"></p><dl> <dt><code>title</code></dt><dd><p>The dataset title</p></dd> <dt><code>data</code></dt><dd><p>The data</p></dd> @@ -203,12 +218,12 @@ and value in order to be compatible with mkinfit</p></dd> </dl><p></div></p> <p><hr> -<a id="method-clone"></a></p><h3>Method <code>clone()</code></h3> -<p>The objects of this class are cloneable with this method.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>mkinds</span>$<span class='fu'>clone</span>(<span class='kw'>deep</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> +<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3> +<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> +<p><div class="r"></p><pre><span class='va'>mkinds</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p> -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> +<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4> +<p><div class="arguments"></p><dl> <dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> </dl><p></div></p> @@ -217,10 +232,12 @@ and value in order to be compatible with mkinfit</p></dd> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> -<span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>) -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>mds</span>)</div><div class='output co'>#> <mkinds> with $title: FOCUS A +<span class='va'>mds</span> <span class='op'><-</span> <span class='va'>mkinds</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"FOCUS A"</span>, <span class='va'>FOCUS_2006_A</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mds</span><span class='op'>)</span> +</div><div class='output co'>#> <mkinds> with $title: FOCUS A #> Observed compounds $observed: parent -#> Sampling times $sampling_times: 0, 3, 7, 14, 30, 62, 90, 118 +#> Sampling times $sampling_times: +#> 0, 3, 7, 14, 30, 62, 90, 118 #> With a maximum of 1 replicates</div><div class='input'> </div></pre> </div> @@ -238,7 +255,7 @@ and value in order to be compatible with mkinfit</p></dd> </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/mkindsg.html b/docs/dev/reference/mkindsg.html new file mode 100644 index 00000000..3e4dfb39 --- /dev/null +++ b/docs/dev/reference/mkindsg.html @@ -0,0 +1,460 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>A class for dataset groups for mkin — mkindsg • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" 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for each +dataset if no data are supplied." /> + + +<meta name="robots" content="noindex"> + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + + </head> + + <body data-spy="scroll" data-target="#toc"> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </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">0.9.50.4</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>A class for dataset groups for mkin</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinds.R'><code>R/mkinds.R</code></a></small> + <div class="hidden name"><code>mkindsg.Rd</code></div> + </div> + + <div class="ref-description"> + <p>A container for working with datasets that share at least one compound, +so that combined evaluations are desirable.</p> +<p>Time normalisation factors are initialised with a value of 1 for each +dataset if no data are supplied.</p> + </div> + + <pre class="usage"><span class='co'># S3 method for mkindsg</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='va'>data</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"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>An mkindsg object.</p></td> + </tr> + <tr> + <th>data</th> + <td><p>Should the mkinds objects be printed with their data?</p></td> + </tr> + <tr> + <th>verbose</th> + <td><p>Should the mkinds objects be printed?</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Not used.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> + + <p><div class="r6-fields"></p><dl> +<dt><code>title</code></dt><dd><p>A title for the dataset group</p></dd> + +<dt><code>ds</code></dt><dd><p>A list of mkinds objects</p></dd> + +<dt><code>observed_n</code></dt><dd><p>Occurrence counts of compounds in datasets</p></dd> + +<dt><code>f_time_norm</code></dt><dd><p>Time normalisation factors</p></dd> + +<dt><code>meta</code></dt><dd><p>A data frame with a row for each dataset, +containing additional information in the form +of categorical data (factors) or numerical data +(e.g. temperature, moisture, +or covariates like soil pH).</p></dd> + +</dl><p></div></p> + <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> + + +<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3> + +<ul> +<li><p><a href='#method-new'><code>mkindsg$new()</code></a></p></li> +<li><p><a href='#method-clone'><code>mkindsg$clone()</code></a></p></li> +</ul> +<p><hr> +<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3> +<p>Create a new mkindsg object</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> +<p><div class="r"></p><pre><span class='va'>mkindsg</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>title <span class='op'>=</span> <span class='st'>""</span>, <span class='va'>ds</span>, f_time_norm <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>meta</span><span class='op'>)</span></pre><p></div></p> + +<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4> +<p><div class="arguments"></p><dl> +<dt><code>title</code></dt><dd><p>The title</p></dd> + +<dt><code>ds</code></dt><dd><p>A list of mkinds objects</p></dd> + +<dt><code>f_time_norm</code></dt><dd><p>Time normalisation factors</p></dd> + +<dt><code>meta</code></dt><dd><p>The meta data</p></dd> + +</dl><p></div></p> +<p><hr> +<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3> +<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> +<p><div class="r"></p><pre><span class='va'>mkindsg</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p> + +<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4> +<p><div class="arguments"></p><dl> +<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> + +</dl><p></div></p> + + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> +<span class='va'>mdsg</span> <span class='op'><-</span> <span class='va'>mkindsg</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"Experimental X"</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='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span><span class='op'>)</span> +</div><div class='output co'>#> <mkindsg> holding 5 mkinds objects +#> Title $title: Experimental X +#> Occurrene of observed compounds $observed_n: +#> parent A1 +#> 5 5 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <mkindsg> holding 5 mkinds objects +#> Title $title: Experimental X +#> Occurrene of observed compounds $observed_n: +#> parent A1 +#> 5 5 +#> +#> Datasets $ds: +#> <mkinds> with $title: Soil 6 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> +#> <mkinds> with $title: Soil 7 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 3, 7, 14, 30, 60, 90, 120, 180 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> +#> <mkinds> with $title: Soil 8 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 1, 3, 8, 14, 27, 48, 70 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> +#> <mkinds> with $title: Soil 9 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> +#> <mkinds> with $title: Soil 10 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 8, 14, 21, 41, 63, 91, 120 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <mkindsg> holding 5 mkinds objects +#> Title $title: Experimental X +#> Occurrene of observed compounds $observed_n: +#> parent A1 +#> 5 5 +#> +#> Datasets $ds: +#> <mkinds> with $title: Soil 6 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> time parent A1 +#> 1 0 97.2 NA +#> 2 0 96.4 NA +#> 3 3 71.1 4.3 +#> 4 3 69.2 4.6 +#> 5 6 58.1 7.0 +#> 6 6 56.6 7.2 +#> 7 10 44.4 8.2 +#> 8 10 43.4 8.0 +#> 9 20 33.3 11.0 +#> 10 20 29.2 13.7 +#> 11 34 17.6 11.5 +#> 12 34 18.0 12.7 +#> 13 55 10.5 14.9 +#> 14 55 9.3 14.5 +#> 15 90 4.5 12.1 +#> 16 90 4.7 12.3 +#> 17 112 3.0 9.9 +#> 18 112 3.4 10.2 +#> 19 132 2.3 8.8 +#> 20 132 2.7 7.8 +#> +#> <mkinds> with $title: Soil 7 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 3, 7, 14, 30, 60, 90, 120, 180 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> time parent A1 +#> 1 0 93.6 NA +#> 2 0 92.3 NA +#> 3 3 87.0 3.9 +#> 4 3 82.2 3.1 +#> 5 7 74.0 6.9 +#> 6 7 73.9 6.6 +#> 7 14 64.2 10.4 +#> 8 14 69.5 8.3 +#> 9 30 54.0 14.4 +#> 10 30 54.6 13.7 +#> 11 60 41.1 22.1 +#> 12 60 38.4 22.3 +#> 13 90 32.5 27.5 +#> 14 90 35.5 25.4 +#> 15 120 28.1 28.0 +#> 16 120 29.0 26.6 +#> 17 180 26.5 25.8 +#> 18 180 27.6 25.3 +#> +#> <mkinds> with $title: Soil 8 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 1, 3, 8, 14, 27, 48, 70 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> time parent A1 +#> 1 0 91.9 NA +#> 2 0 90.8 NA +#> 3 1 64.9 9.6 +#> 4 1 66.2 7.7 +#> 5 3 43.5 15.0 +#> 6 3 44.1 15.1 +#> 7 8 18.3 21.2 +#> 8 8 18.1 21.1 +#> 9 14 10.2 19.7 +#> 10 14 10.8 18.9 +#> 11 27 4.9 17.5 +#> 12 27 3.3 15.9 +#> 13 48 1.6 9.5 +#> 14 48 1.5 9.8 +#> 15 70 1.1 6.2 +#> 16 70 0.9 6.1 +#> +#> <mkinds> with $title: Soil 9 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> time parent A1 +#> 1 0 99.8 NA +#> 2 0 98.3 NA +#> 3 1 77.1 4.2 +#> 4 1 77.2 3.9 +#> 5 3 59.0 7.4 +#> 6 3 58.1 7.9 +#> 7 8 27.4 14.5 +#> 8 8 29.2 13.7 +#> 9 14 19.1 14.2 +#> 10 14 29.6 12.2 +#> 11 27 10.1 13.7 +#> 12 27 18.2 13.2 +#> 13 48 4.5 13.6 +#> 14 48 9.1 15.4 +#> 15 70 2.3 10.4 +#> 16 70 2.9 11.6 +#> 17 91 2.0 10.0 +#> 18 91 1.8 9.5 +#> 19 120 2.0 9.1 +#> 20 120 2.2 9.0 +#> +#> <mkinds> with $title: Soil 10 +#> Observed compounds $observed: parent, A1 +#> Sampling times $sampling_times: +#> 0, 8, 14, 21, 41, 63, 91, 120 +#> With a maximum of 2 replicates +#> Time unit: days +#> Observation unit: \%AR +#> time parent A1 +#> 1 0 96.1 NA +#> 2 0 94.3 NA +#> 3 8 73.9 3.3 +#> 4 8 73.9 3.4 +#> 5 14 69.4 3.9 +#> 6 14 73.1 2.9 +#> 7 21 65.6 6.4 +#> 8 21 65.3 7.2 +#> 9 41 55.9 9.1 +#> 10 41 54.4 8.5 +#> 11 63 47.0 11.7 +#> 12 63 49.3 12.0 +#> 13 91 44.7 13.3 +#> 14 91 46.7 13.2 +#> 15 120 42.1 14.3 +#> 16 120 41.3 12.1</div><div class='input'> +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/dev/reference/mkinerrplot-1.png b/docs/dev/reference/mkinerrplot-1.png Binary files differindex c5d3495f..bae6071d 100644 --- a/docs/dev/reference/mkinerrplot-1.png +++ b/docs/dev/reference/mkinerrplot-1.png diff --git a/docs/dev/reference/mkinerrplot.html b/docs/dev/reference/mkinerrplot.html index 104d1e3a..48d20ca8 100644 --- a/docs/dev/reference/mkinerrplot.html +++ b/docs/dev/reference/mkinerrplot.html @@ -76,7 +76,7 @@ using the argument show_errplot = TRUE." /> </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> @@ -124,7 +124,7 @@ using the argument show_errplot = TRUE." /> </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> @@ -143,7 +143,7 @@ using the argument show_errplot = TRUE." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot squared residuals and the error model for an mkin object</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinerrplot.R'><code>R/mkinerrplot.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinerrplot.R'><code>R/mkinerrplot.R</code></a></small> <div class="hidden name"><code>mkinerrplot.Rd</code></div> </div> @@ -155,20 +155,20 @@ and this error model plot can be obtained with <code><a href='plot.mkinfit.html' using the argument <code>show_errplot = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinerrplot</span>( - <span class='no'>object</span>, - <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>predicted</span>)), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Predicted"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Squared residual"</span>, - <span class='kw'>maxy</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, - <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='no'>...</span> -)</pre> + <pre class="usage"><span class='fu'>mkinerrplot</span><span class='op'>(</span> + <span class='va'>object</span>, + obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, + xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>predicted</span><span class='op'>)</span><span class='op'>)</span>, + xlab <span class='op'>=</span> <span class='st'>"Predicted"</span>, + ylab <span class='op'>=</span> <span class='st'>"Squared residual"</span>, + maxy <span class='op'>=</span> <span class='st'>"auto"</span>, + legend <span class='op'>=</span> <span class='cn'>TRUE</span>, + lpos <span class='op'>=</span> <span class='st'>"topright"</span>, + col_obs <span class='op'>=</span> <span class='st'>"auto"</span>, + pch_obs <span class='op'>=</span> <span class='st'>"auto"</span>, + frame <span class='op'>=</span> <span class='cn'>TRUE</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"> @@ -223,7 +223,7 @@ be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a </tr> <tr> <th>...</th> - <td><p>further arguments passed to <code><a href='https://rdrr.io/r/base/plot.html'>plot</a></code>.</p></td> + <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> </tr> </table> @@ -235,11 +235,17 @@ effect, namely to produce a plot.</p> <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the mkinfit object.</p></div> + <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='co'># \dontrun{</span> -<span class='no'>model</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'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinerrplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'># } +<span class='va'>model</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'>"m1"</span><span class='op'>)</span>, m1 <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='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</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> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinerrplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> @@ -257,7 +263,7 @@ lines of the mkinfit object.</p></div> </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/mkinfit.html b/docs/dev/reference/mkinfit.html index b46c2cce..f5a913b2 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -432,15 +432,15 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='output co'>#> mkin version used for fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Thu Nov 5 23:14:40 2020 -#> Date of summary: Thu Nov 5 23:14:40 2020 +#> Date of fit: Thu Nov 19 14:49:38 2020 +#> Date of summary: Thu Nov 19 14:49:38 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.05 s +#> Fitted using 222 model solutions performed in 0.045 s #> #> Error model: Constant variance #> @@ -573,10 +573,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 analytical <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>}</span> -</div><div class='output co'>#> <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#> test relative elapsed -#> 3 analytical 1.000 0.532 -#> 1 deSolve_compiled 1.765 0.939 -#> 2 eigen 2.229 1.186</div><div class='input'><span class='co'># }</span> +</div><div class='output co'>#> test relative elapsed +#> 3 analytical 1.000 0.534 +#> 1 deSolve_compiled 1.908 1.019 +#> 2 eigen 2.238 1.195</div><div class='input'><span class='co'># }</span> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span> <span class='co'># \dontrun{</span> @@ -600,8 +600,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.FOMC_SFO.tc</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> </div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Thu Nov 5 23:14:51 2020 -#> Date of summary: Thu Nov 5 23:14:51 2020 +#> Date of fit: Thu Nov 19 14:49:49 2020 +#> Date of summary: Thu Nov 19 14:49:49 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -610,7 +610,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> #> Model predictions using solution type deSolve #> -#> Fitted using 4273 model solutions performed in 3.081 s +#> Fitted using 4273 model solutions performed in 3.1 s #> #> Error model: Two-component variance function #> diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index 42529747..979e653a 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -42,7 +42,11 @@ <meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" /> <meta property="og:description" content="This function is usually called using a call to mkinsub() for each observed variable, specifying the corresponding submodel as well as outgoing pathways -(see examples)." /> +(see examples). +Print mkinmod objects in a way that the user finds his way to get to its +components. +This is a convenience function to set up the lists used as arguments for +mkinmod." /> <meta name="robots" content="noindex"> @@ -74,7 +78,7 @@ variable, specifying the corresponding submodel as well as outgoing pathways </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> @@ -122,7 +126,7 @@ variable, specifying the corresponding submodel as well as outgoing pathways </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> @@ -141,50 +145,60 @@ variable, specifying the corresponding submodel as well as outgoing pathways <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to set up a kinetic model with one or more state variables</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinmod.R'><code>R/mkinmod.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinmod.R'><code>R/mkinmod.R</code></a>, <a href='https://github.com/jranke/mkin/blob/master/R/mkinsub.R'><code>R/mkinsub.R</code></a></small> <div class="hidden name"><code>mkinmod.Rd</code></div> </div> <div class="ref-description"> - <p>This function is usually called using a call to <code><a href='mkinsub.html'>mkinsub()</a></code> for each observed + <p>This function is usually called using a call to <code>mkinsub()</code> for each observed variable, specifying the corresponding submodel as well as outgoing pathways (see examples).</p> +<p>Print mkinmod objects in a way that the user finds his way to get to its +components.</p> +<p>This is a convenience function to set up the lists used as arguments for +<code>mkinmod</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinmod</span>( - <span class='no'>...</span>, - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, - <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> -)</pre> + <pre class="usage"><span class='fu'>mkinmod</span><span class='op'>(</span> + <span class='va'>...</span>, + use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, + speclist <span class='op'>=</span> <span class='cn'>NULL</span>, + quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, + verbose <span class='op'>=</span> <span class='cn'>FALSE</span> +<span class='op'>)</span> + +<span class='co'># S3 method for mkinmod</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span> + +<span class='fu'>mkinsub</span><span class='op'>(</span><span class='va'>submodel</span>, to <span class='op'>=</span> <span class='cn'>NULL</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span>, full_name <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> <th>...</th> - <td><p>For each observed variable, a list as obtained by <code><a href='mkinsub.html'>mkinsub()</a></code> + <td><p>For each observed variable, a list as obtained by <code>mkinsub()</code> has to be specified as an argument (see examples). Currently, single first order kinetics "SFO", indeterminate order rate equation kinetics "IORE", or single first order with reversible binding "SFORB" are implemented for all variables, while "FOMC", "DFOP", "HS" and "logistic" can additionally be chosen for the first variable which is assumed to be the source compartment. -Additionally, <code><a href='mkinsub.html'>mkinsub()</a></code> has an argument <code>to</code>, specifying names of +Additionally, <code>mkinsub()</code> has an argument <code>to</code>, specifying names of variables to which a transfer is to be assumed in the model. If the argument <code>use_of_ff</code> is set to "min" (default) and the model for the compartment is "SFO" or "SFORB", an -additional <code><a href='mkinsub.html'>mkinsub()</a></code> argument can be <code>sink = FALSE</code>, effectively -fixing the flux to sink to zero.</p></td> +additional <code>mkinsub()</code> argument can be <code>sink = FALSE</code>, effectively +fixing the flux to sink to zero. +In print.mkinmod, this argument is currently not used.</p></td> </tr> <tr> <th>use_of_ff</th> <td><p>Specification of the use of formation fractions in the -model equations and, if applicable, the coefficient matrix. If "min", a -minimum use of formation fractions is made in order to avoid fitting the -product of formation fractions and rate constants. If "max", formation -fractions are always used.</p></td> +model equations and, if applicable, the coefficient matrix. If "max", +formation fractions are always used (default). If "min", a minimum use of +formation fractions is made, i.e. each pathway to a metabolite has its +own rate constant.</p></td> </tr> <tr> <th>speclist</th> @@ -201,6 +215,32 @@ argument. Default is NULL.</p></td> <td><p>If <code>TRUE</code>, passed to <code><a href='https://rdrr.io/pkg/inline/man/cfunction.html'>inline::cfunction()</a></code> if applicable to give detailed information about the C function being built.</p></td> </tr> + <tr> + <th>x</th> + <td><p>An <code>mkinmod</code> object.</p></td> + </tr> + <tr> + <th>submodel</th> + <td><p>Character vector of length one to specify the submodel type. +See <code>mkinmod</code> for the list of allowed submodel names.</p></td> + </tr> + <tr> + <th>to</th> + <td><p>Vector of the names of the state variable to which a +transformation shall be included in the model.</p></td> + </tr> + <tr> + <th>sink</th> + <td><p>Should a pathway to sink be included in the model in addition to +the pathways to other state variables?</p></td> + </tr> + <tr> + <th>full_name</th> + <td><p>An optional name to be used e.g. for plotting fits +performed with the model. You can use non-ASCII characters here, but then +your R code will not be portable, <em>i.e.</em> may produce unintended plot +results on other operating systems or system configurations.</p></td> + </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -219,6 +259,8 @@ represented by one.</p></dd> <dt>cf</dt><dd><p>If generated, a compiled function calculating the derivatives as returned by cfunction.</p></dd> +A list for use with mkinmod. + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>For the definition of model types and their parameters, the equations given @@ -244,27 +286,36 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</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='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> -<span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)) +<span class='va'>SFO</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># One parent compound, one metabolite, both single first order</span> -<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</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='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> + parent <span class='op'>=</span> <span class='fu'>mkinsub</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'>mkinsub</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='co'># Now supplying full names used for plotting</span> + <span class='va'>SFO_SFO.2</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> + parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</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'># The above model used to be specified like this, before the advent of mkinsub()</span> -<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> + parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <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'># Show details of creating the C function</span> -<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file306f74383fd2.c 2> file306f74383fd2.c.err.txt -#> Program source: +<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> + parent <span class='op'>=</span> <span class='fu'>mkinsub</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'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> Program source: #> 1: #include <R.h> #> 2: #> 3: @@ -286,7 +337,8 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> #> 19: }</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'># The symbolic solution which is available in this case is not</span> <span class='co'># made for human reading but for speed of computation</span> -<span class='no'>SFO_SFO</span>$<span class='no'>deg_func</span></div><div class='output co'>#> function (observed, odeini, odeparms) +<span class='va'>SFO_SFO</span><span class='op'>$</span><span class='va'>deg_func</span> +</div><div class='output co'>#> function (observed, odeini, odeparms) #> { #> predicted <- numeric(0) #> with(as.list(odeparms), { @@ -301,19 +353,41 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> #> }) #> return(predicted) #> } -#> <environment: 0x55555ad56ea0></div><div class='input'> +#> <environment: 0x55555cb0b088></div><div class='input'> <span class='co'># If we have several parallel metabolites</span> <span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> -<span class='no'>m_synth_DFOP_par</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - -<span class='no'>fit_DFOP_par_c</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, - <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.000174</span></div><div class='input'># } - +<span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> + parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, + M1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, + M2 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, + quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + +<span class='va'>fit_DFOP_par_c</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, + <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, + quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='co'># }</span> + + + <span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, + M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, + M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <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><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='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span><span class='op'>)</span> +</div><div class='output co'>#> <mkinmod> model generated with +#> Use of formation fractions $use_of_ff: max +#> Specification $spec: +#> $parent +#> $type: SFO; $to: M1; $sink: TRUE +#> $M1 +#> $type: SFO; $to: M2; $sink: TRUE +#> $M2 +#> $type: SFO; $sink: TRUE +#> Coefficient matrix $coefmat available +#> Compiled model $cf available +#> Differential equations: +#> d_parent/dt = - k_parent * parent +#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 +#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -330,7 +404,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</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/mkinparplot-1.png b/docs/dev/reference/mkinparplot-1.png Binary files differindex 6853a4ba..dcf3e4b5 100644 --- a/docs/dev/reference/mkinparplot-1.png +++ b/docs/dev/reference/mkinparplot-1.png diff --git a/docs/dev/reference/mkinparplot.html b/docs/dev/reference/mkinparplot.html index 027d8ae9..e237ecae 100644 --- a/docs/dev/reference/mkinparplot.html +++ b/docs/dev/reference/mkinparplot.html @@ -73,7 +73,7 @@ mkinfit." /> </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> @@ -121,7 +121,7 @@ mkinfit." /> </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> @@ -140,7 +140,7 @@ mkinfit." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot the confidence intervals obtained using mkinfit</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinparplot.R'><code>R/mkinparplot.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinparplot.R'><code>R/mkinparplot.R</code></a></small> <div class="hidden name"><code>mkinparplot.Rd</code></div> </div> @@ -149,7 +149,7 @@ mkinfit." /> <code><a href='mkinfit.html'>mkinfit</a></code>.</p> </div> - <pre class="usage"><span class='fu'>mkinparplot</span>(<span class='no'>object</span>)</pre> + <pre class="usage"><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -164,14 +164,20 @@ mkinfit." /> <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</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='co'># \dontrun{</span> -<span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( - <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), - <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"anisole"</span>)), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'># } +<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> + T245 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <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'>"phenol"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, + phenol <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <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'>"anisole"</span><span class='op'>)</span><span class='op'>)</span>, + anisole <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>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -188,7 +194,7 @@ effect, namely to produce a plot.</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/mkinpredict.html b/docs/dev/reference/mkinpredict.html index 7d522eb1..d3a86276 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -407,11 +407,11 @@ as these always return mapped output.</p></td> <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><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span><span class='op'>)</span> <span class='op'>}</span> -</div><div class='output co'>#> <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#> test relative elapsed +</div><div class='output co'>#> test relative elapsed #> 2 deSolve_compiled 1.0 0.005 +#> 4 analytical 1.0 0.005 #> 1 eigen 4.0 0.020 -#> 4 analytical 4.0 0.020 -#> 3 deSolve 45.6 0.228</div><div class='input'> +#> 3 deSolve 44.6 0.223</div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> diff --git a/docs/dev/reference/mkinresplot-1.png b/docs/dev/reference/mkinresplot-1.png Binary files differindex bb9657b4..ffd34f6f 100644 --- a/docs/dev/reference/mkinresplot-1.png +++ b/docs/dev/reference/mkinresplot-1.png diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html index 5591d26f..38c52425 100644 --- a/docs/dev/reference/mkinresplot.html +++ b/docs/dev/reference/mkinresplot.html @@ -75,7 +75,7 @@ argument show_residuals = TRUE." /> </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 @@ argument show_residuals = TRUE." /> </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 @@ argument show_residuals = TRUE." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot residuals stored in an mkin object</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinresplot.R'><code>R/mkinresplot.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinresplot.R'><code>R/mkinresplot.R</code></a></small> <div class="hidden name"><code>mkinresplot.Rd</code></div> </div> @@ -153,21 +153,21 @@ the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinf argument <code>show_residuals = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinresplot</span>( - <span class='no'>object</span>, - <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)), - <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>standardized</span>, <span class='st'>"Standardized residual"</span>, <span class='st'>"Residual"</span>), - <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, - <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='no'>...</span> -)</pre> + <pre class="usage"><span class='fu'>mkinresplot</span><span class='op'>(</span> + <span class='va'>object</span>, + obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, + xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span><span class='op'>)</span>, + standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, + xlab <span class='op'>=</span> <span class='st'>"Time"</span>, + ylab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>standardized</span>, <span class='st'>"Standardized residual"</span>, <span class='st'>"Residual"</span><span class='op'>)</span>, + maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, + legend <span class='op'>=</span> <span class='cn'>TRUE</span>, + lpos <span class='op'>=</span> <span class='st'>"topright"</span>, + col_obs <span class='op'>=</span> <span class='st'>"auto"</span>, + pch_obs <span class='op'>=</span> <span class='st'>"auto"</span>, + frame <span class='op'>=</span> <span class='cn'>TRUE</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"> @@ -227,7 +227,7 @@ be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a </tr> <tr> <th>...</th> - <td><p>further arguments passed to <code><a href='https://rdrr.io/r/base/plot.html'>plot</a></code>.</p></td> + <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> </tr> </table> @@ -240,10 +240,16 @@ effect, namely to produce a plot.</p> <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the mkinfit object, and <code><a href='plot.mkinfit.html'>plot_res</a></code> for a function combining the plot of the fit and the residual plot.</p></div> + <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'>model</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'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='va'>model</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'>"m1"</span><span class='op'>)</span>, m1 <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='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinresplot</span><span class='op'>(</span><span class='va'>fit</span>, <span class='st'>"m1"</span><span class='op'>)</span> +</div><div class='img'><img src='mkinresplot-1.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"> @@ -260,7 +266,7 @@ combining the plot of the fit and the residual plot.</p></div> </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/mkinsub.html b/docs/dev/reference/mkinsub.html index 585e1840..68fd6268 100644 --- a/docs/dev/reference/mkinsub.html +++ b/docs/dev/reference/mkinsub.html @@ -73,7 +73,7 @@ mkinmod." /> </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> @@ -121,7 +121,7 @@ mkinmod." /> </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> @@ -140,7 +140,7 @@ mkinmod." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to set up a kinetic submodel for one state variable</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinsub.R'><code>R/mkinsub.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinsub.R'><code>R/mkinsub.R</code></a></small> <div class="hidden name"><code>mkinsub.Rd</code></div> </div> @@ -149,7 +149,7 @@ mkinmod." /> <code><a href='mkinmod.html'>mkinmod</a></code>.</p> </div> - <pre class="usage"><span class='fu'>mkinsub</span>(<span class='no'>submodel</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> + <pre class="usage"><span class='fu'>mkinsub</span><span class='op'>(</span><span class='va'>submodel</span>, to <span class='op'>=</span> <span class='cn'>NULL</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span>, full_name <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -181,22 +181,28 @@ results on other operating systems or system configurations.</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list for use with <code><a href='mkinmod.html'>mkinmod</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='co'># One parent compound, one metabolite, both single first order.</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='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <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'># The same model using mkinsub</span> -<span class='no'>SFO_SFO.2</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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</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='va'>SFO_SFO.2</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'>mkinsub</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'>mkinsub</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='co'># Now supplying full names</span> - <span class='no'>SFO_SFO.2</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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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='va'>SFO_SFO.2</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'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</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'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -213,7 +219,7 @@ results on other operating systems or system configurations.</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/mmkin.html b/docs/dev/reference/mmkin.html index b0ca90f0..4786b02e 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -227,9 +227,9 @@ plotting.</p></div> <span class='va'>time_default</span> </div><div class='output co'>#> user system elapsed -#> 4.706 0.488 1.375 </div><div class='input'><span class='va'>time_1</span> +#> 4.664 0.433 1.317 </div><div class='input'><span class='va'>time_1</span> </div><div class='output co'>#> user system elapsed -#> 5.232 0.005 5.238 </div><div class='input'> +#> 5.326 0.001 5.330 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink @@ -252,7 +252,29 @@ plotting.</p></div> <span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> <span class='co'># allow to plot the observed variables separately</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='co'># On Windows, we can use multiple cores by making a cluster using the parallel</span> +<span class='co'># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span> +<span class='va'>cl</span> <span class='op'><-</span> <span class='fu'>makePSOCKcluster</span><span class='op'>(</span><span class='fl'>12</span><span class='op'>)</span> +<span class='va'>f</span> <span class='op'><-</span> <span class='fu'>mmkin</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'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, + <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>A <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span>, D <span class='op'>=</span> <span class='va'>FOCUS_2006_D</span><span class='op'>)</span>, + cluster <span class='op'>=</span> <span class='va'>cl</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> +</div><div class='output co'>#> <mmkin> object +#> Status of individual fits: +#> +#> dataset +#> model A B C D +#> SFO OK OK OK OK +#> FOMC C OK OK OK +#> DFOP OK OK OK OK +#> +#> OK: No warnings +#> C: Optimisation did not converge: +#> false convergence (8)</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> +<span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span> +<span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span> +<span class='co'># }</span> </div></pre> </div> diff --git a/docs/dev/reference/nafta-1.png b/docs/dev/reference/nafta-1.png Binary files differindex 9025f2bb..4d823d77 100644 --- a/docs/dev/reference/nafta-1.png +++ b/docs/dev/reference/nafta-1.png diff --git a/docs/dev/reference/nafta.html b/docs/dev/reference/nafta.html index 690e4827..bbc8797d 100644 --- a/docs/dev/reference/nafta.html +++ b/docs/dev/reference/nafta.html @@ -76,7 +76,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> </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> @@ -124,7 +124,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> </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> @@ -143,7 +143,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Evaluate parent kinetics using the NAFTA guidance</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small> <div class="hidden name"><code>nafta.Rd</code></div> </div> @@ -155,10 +155,10 @@ and plotting.</p> order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.</p> </div> - <pre class="usage"><span class='fu'>nafta</span>(<span class='no'>ds</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>) + <pre class="usage"><span class='fu'>nafta</span><span class='op'>(</span><span class='va'>ds</span>, title <span class='op'>=</span> <span class='cn'>NA</span>, quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span> <span class='co'># S3 method for nafta</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, digits <span class='op'>=</span> <span class='fl'>3</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"> @@ -211,10 +211,15 @@ Degradation <code><a href='mmkin.html'>mmkin</a></code> object containing the fits of the three models. The list element named "title" contains the title of the dataset used. The list element "data" contains the dataset used in the fits.</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'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00192</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00258</span></div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: + <span class='va'>nafta_evaluation</span> <span class='op'><-</span> <span class='fu'>nafta</span><span class='op'>(</span><span class='va'>NAFTA_SOP_Appendix_D</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> +</div><div class='output co'>#> Sums of squares: #> SFO IORE DFOP #> 1378.6832 615.7730 517.8836 #> @@ -251,7 +256,8 @@ list element "data" contains the dataset used in the fits.</p> #> DFOP 429 2380 841 #> #> Representative half-life: -#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'> +#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> +</div><div class='img'><img src='nafta-1.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"> @@ -268,7 +274,7 @@ list element "data" contains the dataset used in the fits.</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/nlme-1.png b/docs/dev/reference/nlme-1.png Binary files differindex 0b34db8f..193722c7 100644 --- a/docs/dev/reference/nlme-1.png +++ b/docs/dev/reference/nlme-1.png diff --git a/docs/dev/reference/nlme-2.png b/docs/dev/reference/nlme-2.png Binary files differindex ce932c86..7129c580 100644 --- a/docs/dev/reference/nlme-2.png +++ b/docs/dev/reference/nlme-2.png diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html index e21074e7..e109b34e 100644 --- a/docs/dev/reference/nlme.html +++ b/docs/dev/reference/nlme.html @@ -226,28 +226,28 @@ nlme for the case of a single grouping variable ds.</p> #> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) #> Data: grouped_data #> AIC BIC logLik -#> 298.2781 307.7372 -144.1391 +#> 252.7798 262.1358 -121.3899 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k_parent_sink Residual -#> StdDev: 0.9374733 0.7098105 3.83543 +#> parent_0 log_k_parent_sink Residual +#> StdDev: 0.0006768135 0.6800777 2.489397 #> #> Fixed effects: parent_0 + log_k_parent_sink ~ 1 -#> Value Std.Error DF t-value p-value -#> parent_0 101.76838 1.1445444 45 88.91606 0 -#> log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0 +#> Value Std.Error DF t-value p-value +#> parent_0 101.74884 0.6456014 44 157.60321 0 +#> log_k_parent_sink -3.05575 0.4015811 44 -7.60929 0 #> Correlation: #> prnt_0 -#> log_k_parent_sink 0.034 +#> log_k_parent_sink 0.026 #> #> Standardized Within-Group Residuals: #> Min Q1 Med Q3 Max -#> -2.6169360 -0.2185329 0.0574070 0.5720937 3.0459868 +#> -2.1317488 -0.6878121 0.0828385 0.8592270 2.9529864 #> -#> Number of Observations: 49 +#> Number of Observations: 48 #> Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span><span class='op'>(</span><span class='va'>m_nlme</span>, level <span class='op'>=</span> <span class='fl'>0</span><span class='op'>:</span><span class='fl'>1</span><span class='op'>)</span>, layout <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'>3</span>, <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span> </div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># augPred does not work on fits with more than one state</span> <span class='co'># variable</span> diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index 05edbde5..84990521 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -332,12 +332,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> StdDev: 0.002417 21.63 #> </div><div class='input'> <span class='va'>ds_2</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='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='va'>m_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>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='va'>m_sfo_sfo_ff</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>, 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='va'>m_dfop_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'>"DFOP"</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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='va'>m_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='mkinmod.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='mkinmod.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'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='va'>m_sfo_sfo_ff</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='mkinmod.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='mkinmod.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='va'>m_dfop_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='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, + A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_2</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'>m_sfo_sfo</span>, <span class='st'>"SFO-SFO-ff"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo_ff</span>, diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index bd35d3c1..ba0e89bb 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." /> </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> @@ -122,7 +122,7 @@ considering the error structure that was assumed for the fit." /> </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> @@ -141,7 +141,7 @@ considering the error structure that was assumed for the fit." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Extract model parameters from mkinfit models</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parms.mkinfit.R'><code>R/parms.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parms.mkinfit.R'><code>R/parms.mkinfit.R</code></a></small> <div class="hidden name"><code>parms.Rd</code></div> </div> @@ -151,13 +151,13 @@ model parameters, in order to avoid working with a fitted model without considering the error structure that was assumed for the fit.</p> </div> - <pre class="usage"><span class='fu'>parms</span>(<span class='no'>object</span>, <span class='no'>...</span>) + <pre class="usage"><span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> <span class='co'># S3 method for mkinfit</span> -<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>) +<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span> <span class='co'># S3 method for mmkin</span> -<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> +<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</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"> @@ -187,19 +187,24 @@ such matrices is returned.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># mkinfit objects</span> -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</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'>parms</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 k_parent sigma -#> 82.4921598 0.3060633 4.6730124 </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fit</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> parent_0 log_k_parent sigma +<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'>"SFO"</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'>parms</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='output co'>#> parent_0 k_parent sigma +#> 82.4921598 0.3060633 4.6730124 </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> parent_0 log_k_parent sigma #> 82.492160 -1.183963 4.673012 </div><div class='input'> <span class='co'># mmkin objects</span> -<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>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)])) -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>) +<span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, + <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</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='co'># \dontrun{</span> -<span class='no'>fits</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/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0195</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00408</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0492</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00985</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00815</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.011</span></div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>[<span class='st'>"SFO"</span>, ])</div><div class='output co'>#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +<span class='va'>fits</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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +<span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +</div><div class='output co'>#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450 #> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421 -#> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>[, <span class='fl'>2</span>])</div><div class='output co'>#> $SFO +#> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>)</span> +</div><div class='output co'>#> $SFO #> Dataset 7 #> parent_0 82.666781678 #> k_parent 0.009647805 @@ -214,12 +219,13 @@ such matrices is returned.</p> #> #> $DFOP #> Dataset 7 -#> parent_0 91.058971503 +#> parent_0 91.058971597 #> k1 0.044946770 #> k2 0.002868336 -#> g 0.526942415 +#> g 0.526942414 #> sigma 2.221302196 -#> </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>)</div><div class='output co'>#> $SFO +#> </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span> +</div><div class='output co'>#> $SFO #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450 #> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421 @@ -234,12 +240,13 @@ such matrices is returned.</p> #> #> $DFOP #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 96.55213663 91.058971503 90.34509469 98.14858850 94.311323409 -#> k1 0.21954589 0.044946770 0.41232289 0.31697588 0.080663853 -#> k2 0.02957934 0.002868336 0.07581767 0.03260384 0.003425417 -#> g 0.44845068 0.526942415 0.66091965 0.65322767 0.342652880 +#> parent_0 96.55213663 91.058971597 90.34509493 98.14858820 94.311323733 +#> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857 +#> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417 +#> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880 #> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831 -#> </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> $SFO +#> </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> $SFO #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094 #> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090 @@ -253,13 +260,13 @@ such matrices is returned.</p> #> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278 #> #> $DFOP -#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 96.5521366 91.05897150 90.3450947 98.1485885 94.311323 -#> log_k1 -1.5161940 -3.10227638 -0.8859485 -1.1489296 -2.517465 -#> log_k2 -3.5206791 -5.85402317 -2.5794240 -3.4233253 -5.676532 -#> g_ilr -0.1463234 0.07627854 0.4719196 0.4477805 -0.460676 -#> sigma 1.3569047 2.22130220 1.3416908 2.8715985 1.942068 -#> </div><div class='input'># } +#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +#> parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237 +#> log_k1 -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647 +#> log_k2 -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322 +#> g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943 +#> sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678 +#> </div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -276,7 +283,7 @@ such matrices is returned.</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/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png Binary files differindex 67058e6c..d58b9c69 100644 --- a/docs/dev/reference/plot.mixed.mmkin-3.png +++ b/docs/dev/reference/plot.mixed.mmkin-3.png diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 4108aea3..6ed7cbba 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -277,10 +277,10 @@ corresponding model prediction lines for the different datasets.</p></td> </div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='va'>f_saem</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 17:18:17 2020" +#> [1] "Thu Nov 19 14:51:14 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 17:18:26 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span> +#> [1] "Thu Nov 19 14:51:24 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span> </div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> diff --git a/docs/dev/reference/plot.mkinfit-1.png b/docs/dev/reference/plot.mkinfit-1.png Binary files differindex c6a415d7..fc195031 100644 --- a/docs/dev/reference/plot.mkinfit-1.png +++ b/docs/dev/reference/plot.mkinfit-1.png diff --git a/docs/dev/reference/plot.mkinfit-2.png b/docs/dev/reference/plot.mkinfit-2.png Binary files differindex 5dd3731e..fa99f680 100644 --- a/docs/dev/reference/plot.mkinfit-2.png +++ b/docs/dev/reference/plot.mkinfit-2.png diff --git a/docs/dev/reference/plot.mkinfit-3.png b/docs/dev/reference/plot.mkinfit-3.png Binary files differindex 59cf8f8d..28789544 100644 --- a/docs/dev/reference/plot.mkinfit-3.png +++ b/docs/dev/reference/plot.mkinfit-3.png diff --git a/docs/dev/reference/plot.mkinfit-4.png b/docs/dev/reference/plot.mkinfit-4.png Binary files differindex d9867952..77b3422f 100644 --- a/docs/dev/reference/plot.mkinfit-4.png +++ b/docs/dev/reference/plot.mkinfit-4.png diff --git a/docs/dev/reference/plot.mkinfit-5.png b/docs/dev/reference/plot.mkinfit-5.png Binary files differindex 1109c8df..b4b6528b 100644 --- a/docs/dev/reference/plot.mkinfit-5.png +++ b/docs/dev/reference/plot.mkinfit-5.png diff --git a/docs/dev/reference/plot.mkinfit-6.png b/docs/dev/reference/plot.mkinfit-6.png Binary files differindex 230c90e9..f71f1769 100644 --- a/docs/dev/reference/plot.mkinfit-6.png +++ b/docs/dev/reference/plot.mkinfit-6.png diff --git a/docs/dev/reference/plot.mkinfit-7.png b/docs/dev/reference/plot.mkinfit-7.png Binary files differindex b23427b5..98fee908 100644 --- a/docs/dev/reference/plot.mkinfit-7.png +++ b/docs/dev/reference/plot.mkinfit-7.png diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html index ffbd1206..3a05a02d 100644 --- a/docs/dev/reference/plot.mkinfit.html +++ b/docs/dev/reference/plot.mkinfit.html @@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." /> </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> @@ -122,7 +122,7 @@ observed data together with the solution of the fitted model." /> </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> @@ -141,7 +141,7 @@ observed data together with the solution of the fitted model." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the observed data and the fitted model of an mkinfit object</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><code>R/plot.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><code>R/plot.mkinfit.R</code></a></small> <div class="hidden name"><code>plot.mkinfit.Rd</code></div> </div> @@ -152,49 +152,49 @@ observed data together with the solution of the fitted model.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>, - <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Observed"</span>, - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>), - <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), - <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>, - <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)), - <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>, - <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, - <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, - <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), - <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='no'>...</span> -) - -<span class='fu'>plot_sep</span>( - <span class='no'>fit</span>, - <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>TRUE</span>, <span class='st'>"standardized"</span>), - <span class='no'>...</span> -) - -<span class='fu'>plot_res</span>( - <span class='no'>fit</span>, - <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, - <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>FALSE</span>, <span class='fl'>TRUE</span>), - <span class='no'>...</span> -) - -<span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> + <span class='va'>x</span>, + fit <span class='op'>=</span> <span class='va'>x</span>, + obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, + xlab <span class='op'>=</span> <span class='st'>"Time"</span>, + ylab <span class='op'>=</span> <span class='st'>"Observed"</span>, + xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>, + ylim <span class='op'>=</span> <span class='st'>"default"</span>, + col_obs <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>obs_vars</span><span class='op'>)</span>, + pch_obs <span class='op'>=</span> <span class='va'>col_obs</span>, + lty_obs <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>obs_vars</span><span class='op'>)</span><span class='op'>)</span>, + add <span class='op'>=</span> <span class='cn'>FALSE</span>, + legend <span class='op'>=</span> <span class='op'>!</span><span class='va'>add</span>, + show_residuals <span class='op'>=</span> <span class='cn'>FALSE</span>, + show_errplot <span class='op'>=</span> <span class='cn'>FALSE</span>, + maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, + sep_obs <span class='op'>=</span> <span class='cn'>FALSE</span>, + rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>, + row_layout <span class='op'>=</span> <span class='cn'>FALSE</span>, + lpos <span class='op'>=</span> <span class='st'>"topright"</span>, + inset <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'>0.05</span>, <span class='fl'>0.05</span><span class='op'>)</span>, + show_errmin <span class='op'>=</span> <span class='cn'>FALSE</span>, + errmin_digits <span class='op'>=</span> <span class='fl'>3</span>, + frame <span class='op'>=</span> <span class='cn'>TRUE</span>, + <span class='va'>...</span> +<span class='op'>)</span> + +<span class='fu'>plot_sep</span><span class='op'>(</span> + <span class='va'>fit</span>, + show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>, + show_residuals <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>err_mod</span>, <span class='st'>"const"</span><span class='op'>)</span>, <span class='cn'>TRUE</span>, <span class='st'>"standardized"</span><span class='op'>)</span>, + <span class='va'>...</span> +<span class='op'>)</span> + +<span class='fu'>plot_res</span><span class='op'>(</span> + <span class='va'>fit</span>, + sep_obs <span class='op'>=</span> <span class='cn'>FALSE</span>, + show_errmin <span class='op'>=</span> <span class='va'>sep_obs</span>, + standardized <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>err_mod</span>, <span class='st'>"const"</span><span class='op'>)</span>, <span class='cn'>FALSE</span>, <span class='cn'>TRUE</span><span class='op'>)</span>, + <span class='va'>...</span> +<span class='op'>)</span> + +<span class='fu'>plot_err</span><span class='op'>(</span><span class='va'>fit</span>, sep_obs <span class='op'>=</span> <span class='cn'>FALSE</span>, show_errmin <span class='op'>=</span> <span class='va'>sep_obs</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"> @@ -314,7 +314,7 @@ chi2 error percentage.</p></td> </tr> <tr> <th>...</th> - <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/base/plot.html'>plot</a></code>.</p></td> + <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> </tr> <tr> <th>standardized</th> @@ -331,22 +331,35 @@ standardized in the residual plot?</p></td> <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then latex is being used for the formatting of the chi2 error level, if <code>show_errmin = TRUE</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='co'># One parent compound, one metabolite, both single first order, path from</span> <span class='co'># parent to sink included</span> <span class='co'># \dontrun{</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'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> +<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'>"m1"</span>, full <span class='op'>=</span> <span class='st'>"Parent"</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, full <span class='op'>=</span> <span class='st'>"Metabolite M1"</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='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><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='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span><span class='op'>(</span><span class='va'>fit</span>, standardized <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately, with residuals</span> -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span>, sep_obs <span class='op'>=</span> <span class='cn'>TRUE</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</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='op'>)</span>, + show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span> -<span class='fu'>plot_sep</span>(<span class='no'>fit</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>))</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='fu'>plot_sep</span><span class='op'>(</span><span class='va'>fit</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='op'>)</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately, with the error model</span> -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-7.png' alt='' width='700' height='433' /></div><div class='input'># } +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span>, sep_obs <span class='op'>=</span> <span class='cn'>TRUE</span>, show_errplot <span class='op'>=</span> <span class='cn'>TRUE</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='op'>)</span>, + show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mkinfit-7.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> @@ -364,7 +377,7 @@ latex is being used for the formatting of the chi2 error level, if </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/plot.mmkin-1.png b/docs/dev/reference/plot.mmkin-1.png Binary files differindex 24fa6ca7..438d5a53 100644 --- a/docs/dev/reference/plot.mmkin-1.png +++ b/docs/dev/reference/plot.mmkin-1.png diff --git a/docs/dev/reference/plot.mmkin-2.png b/docs/dev/reference/plot.mmkin-2.png Binary files differindex 377e50b5..ee04b3c4 100644 --- a/docs/dev/reference/plot.mmkin-2.png +++ b/docs/dev/reference/plot.mmkin-2.png diff --git a/docs/dev/reference/plot.mmkin-3.png b/docs/dev/reference/plot.mmkin-3.png Binary files differindex 3ea7b38a..e06ed002 100644 --- a/docs/dev/reference/plot.mmkin-3.png +++ b/docs/dev/reference/plot.mmkin-3.png diff --git a/docs/dev/reference/plot.mmkin-4.png b/docs/dev/reference/plot.mmkin-4.png Binary files differindex 017fbd1d..5869df55 100644 --- a/docs/dev/reference/plot.mmkin-4.png +++ b/docs/dev/reference/plot.mmkin-4.png diff --git a/docs/dev/reference/plot.mmkin-5.png b/docs/dev/reference/plot.mmkin-5.png Binary files differindex e7463916..927c573b 100644 --- a/docs/dev/reference/plot.mmkin-5.png +++ b/docs/dev/reference/plot.mmkin-5.png diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html index f02e2ea6..32da836d 100644 --- a/docs/dev/reference/plot.mmkin.html +++ b/docs/dev/reference/plot.mmkin.html @@ -76,7 +76,7 @@ the fit of at least one model to the same dataset is shown." /> </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> @@ -124,7 +124,7 @@ the fit of at least one model to the same dataset is shown." /> </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> @@ -144,31 +144,31 @@ the fit of at least one model to the same dataset is shown." /> <div class="page-header"> <h1>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.mmkin.R'><code>R/plot.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mmkin.R'><code>R/plot.mmkin.R</code></a></small> <div class="hidden name"><code>plot.mmkin.Rd</code></div> </div> <div class="ref-description"> - <p>When x is a row selected from an mmkin object (<code><a href='Extract.mmkin.html'>[.mmkin</a></code>), the + <p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the same model fitted for at least one dataset is shown. When it is a column, the fit of at least one model to the same dataset is shown.</p> </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), - <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, - <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, - <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, - <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='no'>...</span> -)</pre> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> + <span class='va'>x</span>, + main <span class='op'>=</span> <span class='st'>"auto"</span>, + legends <span class='op'>=</span> <span class='fl'>1</span>, + resplot <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'>"time"</span>, <span class='st'>"errmod"</span><span class='op'>)</span>, + standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, + show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>, + errmin_var <span class='op'>=</span> <span class='st'>"All data"</span>, + errmin_digits <span class='op'>=</span> <span class='fl'>3</span>, + cex <span class='op'>=</span> <span class='fl'>0.7</span>, + rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>, + ymax <span class='op'>=</span> <span class='st'>"auto"</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"> @@ -240,21 +240,30 @@ than two rows of plots are shown.</p></td> <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then latex is being used for the formatting of the chi2 error level.</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='co'># \dontrun{</span> <span class='co'># Only use one core not to offend CRAN checks</span> - <span class='no'>fits</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/c.html'>c</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), - <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</span> - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='va'>fits</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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"HS"</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'>"FOCUS B"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, <span class='co'># named list for titles</span> + cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> +#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, show_errmin <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span> <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span> <span class='co'># generated by pkgdown, as far as I know).</span> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># same as plot(fits[1, 2])</span> +</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the error models</span> - <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='plot.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> # } + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span> </div></pre> </div> @@ -272,7 +281,7 @@ latex is being used for the formatting of the chi2 error level.</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/saem-5.png b/docs/dev/reference/saem-5.png Binary files differindex 6e6e0f91..a12f8383 100644 --- a/docs/dev/reference/saem-5.png +++ b/docs/dev/reference/saem-5.png diff --git a/docs/dev/reference/saem-6.png b/docs/dev/reference/saem-6.png Binary files differnew file mode 100644 index 00000000..314f9cd9 --- /dev/null +++ b/docs/dev/reference/saem-6.png diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index d0c3495a..948e1378 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -247,27 +247,27 @@ using <a href='mmkin.html'>mmkin</a>.</p> state.ini <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>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:47:58 2020" +#> [1] "Thu Nov 19 14:51:31 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:00 2020"</div><div class='input'> +#> [1] "Thu Nov 19 14:51:33 2020"</div><div class='input'> <span class='va'>f_mmkin_parent</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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</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='va'>f_saem_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:01 2020" +#> [1] "Thu Nov 19 14:51:34 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:03 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Thu Nov 19 14:51:36 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:03 2020" +#> [1] "Thu Nov 19 14:51:36 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:05 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Thu Nov 19 14:51:38 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:06 2020" +#> [1] "Thu Nov 19 14:51:39 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:08 2020"</div><div class='input'> +#> [1] "Thu Nov 19 14:51:42 2020"</div><div class='input'> <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span> <span class='co'># functions from saemix</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> @@ -313,10 +313,10 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:11 2020" +#> [1] "Thu Nov 19 14:51:44 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:16 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Thu Nov 19 14:51:49 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC #> 1 467.7096 464.9757 #> 2 469.5208 466.3963</div><div class='input'> @@ -327,7 +327,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> </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='va'>dfop_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'>"DFOP"</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'># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span> -<span class='co'># and compiled ODEs for FOMC, both are fast</span> +<span class='co'># and compiled ODEs for FOMC that are much slower</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='st'>"FOMC-SFO"</span> <span class='op'>=</span> <span class='va'>fomc_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_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> @@ -336,15 +336,15 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='co'># solutions written for mkin this took around four minutes</span> <span class='va'>f_saem_sfo_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:18 2020" +#> [1] "Thu Nov 19 14:51:52 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:23 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Thu Nov 19 14:51:57 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:23 2020" +#> [1] "Thu Nov 19 14:51:57 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:32 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Thu Nov 19 14:52:06 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -359,8 +359,6 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> 170 observations of 2 variable(s) grouped in 5 datasets #> #> Likelihood computed by importance sampling -#> -#> LL by is "-407.78 (df=13)" #> AIC BIC logLik #> 841.6 836.5 -407.8 #> @@ -385,13 +383,12 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> SD.log_k1 1.42027 0.52714 2.3134 #> SD.log_k2 1.90634 0.70934 3.1033 #> SD.g_qlogis 0.44771 -0.86417 1.7596</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_saem_dfop_sfo</span><span class='op'>)</span> -</div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -</div><div class='output co'>#> -#> LL by is "-407.78 (df=13)"</div><div class='output co'>#> saemix version used for fitting: 3.1.9000 +</div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Nov 11 19:48:33 2020 -#> Date of summary: Wed Nov 11 19:48:33 2020 +#> Date of fit: Thu Nov 19 14:52:07 2020 +#> Date of summary: Thu Nov 19 14:52:07 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -406,7 +403,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.564 s using 300, 100 iterations +#> Fitted in 10.034 s using 300, 100 iterations #> #> Variance model: Constant variance #> @@ -472,11 +469,206 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 14.11 59.53 17.92 8.717 25.03 -#> A1 319.21 1060.38 NA NA NA</div><div class='input'> +#> A1 319.21 1060.38 NA NA NA +#> +#> Data: +#> ds name time observed predicted residual std standardized +#> Dataset 6 parent 0 97.2 95.79523 -1.40477 1.883 -0.745888 +#> Dataset 6 parent 0 96.4 95.79523 -0.60477 1.883 -0.321114 +#> Dataset 6 parent 3 71.1 71.32042 0.22042 1.883 0.117035 +#> Dataset 6 parent 3 69.2 71.32042 2.12042 1.883 1.125873 +#> Dataset 6 parent 6 58.1 56.45256 -1.64744 1.883 -0.874739 +#> Dataset 6 parent 6 56.6 56.45256 -0.14744 1.883 -0.078288 +#> Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045256 +#> Dataset 6 parent 10 43.4 44.48523 1.08523 1.883 0.576224 +#> Dataset 6 parent 20 33.3 29.75774 -3.54226 1.883 -1.880826 +#> Dataset 6 parent 20 29.2 29.75774 0.55774 1.883 0.296141 +#> Dataset 6 parent 34 17.6 19.35710 1.75710 1.883 0.932966 +#> Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720578 +#> Dataset 6 parent 55 10.5 10.48443 -0.01557 1.883 -0.008266 +#> Dataset 6 parent 55 9.3 10.48443 1.18443 1.883 0.628895 +#> Dataset 6 parent 90 4.5 3.78622 -0.71378 1.883 -0.378995 +#> Dataset 6 parent 90 4.7 3.78622 -0.91378 1.883 -0.485188 +#> Dataset 6 parent 112 3.0 1.99608 -1.00392 1.883 -0.533048 +#> Dataset 6 parent 112 3.4 1.99608 -1.40392 1.883 -0.745435 +#> Dataset 6 parent 132 2.3 1.11539 -1.18461 1.883 -0.628990 +#> Dataset 6 parent 132 2.7 1.11539 -1.58461 1.883 -0.841377 +#> Dataset 6 A1 3 4.3 4.66132 0.36132 1.883 0.191849 +#> Dataset 6 A1 3 4.6 4.66132 0.06132 1.883 0.032559 +#> Dataset 6 A1 6 7.0 7.41087 0.41087 1.883 0.218157 +#> Dataset 6 A1 6 7.2 7.41087 0.21087 1.883 0.111964 +#> Dataset 6 A1 10 8.2 9.50878 1.30878 1.883 0.694921 +#> Dataset 6 A1 10 8.0 9.50878 1.50878 1.883 0.801114 +#> Dataset 6 A1 20 11.0 11.69902 0.69902 1.883 0.371157 +#> Dataset 6 A1 20 13.7 11.69902 -2.00098 1.883 -1.062455 +#> Dataset 6 A1 34 11.5 12.67784 1.17784 1.883 0.625396 +#> Dataset 6 A1 34 12.7 12.67784 -0.02216 1.883 -0.011765 +#> Dataset 6 A1 55 14.9 12.78556 -2.11444 1.883 -1.122701 +#> Dataset 6 A1 55 14.5 12.78556 -1.71444 1.883 -0.910314 +#> Dataset 6 A1 90 12.1 11.52954 -0.57046 1.883 -0.302898 +#> Dataset 6 A1 90 12.3 11.52954 -0.77046 1.883 -0.409092 +#> Dataset 6 A1 112 9.9 10.43825 0.53825 1.883 0.285793 +#> Dataset 6 A1 112 10.2 10.43825 0.23825 1.883 0.126503 +#> Dataset 6 A1 132 8.8 9.42830 0.62830 1.883 0.333609 +#> Dataset 6 A1 132 7.8 9.42830 1.62830 1.883 0.864577 +#> Dataset 7 parent 0 93.6 90.91477 -2.68523 1.883 -1.425772 +#> Dataset 7 parent 0 92.3 90.91477 -1.38523 1.883 -0.735514 +#> Dataset 7 parent 3 87.0 84.76874 -2.23126 1.883 -1.184726 +#> Dataset 7 parent 3 82.2 84.76874 2.56874 1.883 1.363919 +#> Dataset 7 parent 7 74.0 77.62735 3.62735 1.883 1.926003 +#> Dataset 7 parent 7 73.9 77.62735 3.72735 1.883 1.979100 +#> Dataset 7 parent 14 64.2 67.52266 3.32266 1.883 1.764224 +#> Dataset 7 parent 14 69.5 67.52266 -1.97734 1.883 -1.049904 +#> Dataset 7 parent 30 54.0 52.41949 -1.58051 1.883 -0.839202 +#> Dataset 7 parent 30 54.6 52.41949 -2.18051 1.883 -1.157783 +#> Dataset 7 parent 60 41.1 39.36582 -1.73418 1.883 -0.920794 +#> Dataset 7 parent 60 38.4 39.36582 0.96582 1.883 0.512818 +#> Dataset 7 parent 90 32.5 33.75388 1.25388 1.883 0.665771 +#> Dataset 7 parent 90 35.5 33.75388 -1.74612 1.883 -0.927132 +#> Dataset 7 parent 120 28.1 30.41716 2.31716 1.883 1.230335 +#> Dataset 7 parent 120 29.0 30.41716 1.41716 1.883 0.752464 +#> Dataset 7 parent 180 26.5 25.66046 -0.83954 1.883 -0.445767 +#> Dataset 7 parent 180 27.6 25.66046 -1.93954 1.883 -1.029832 +#> Dataset 7 A1 3 3.9 2.69355 -1.20645 1.883 -0.640585 +#> Dataset 7 A1 3 3.1 2.69355 -0.40645 1.883 -0.215811 +#> Dataset 7 A1 7 6.9 5.81807 -1.08193 1.883 -0.574470 +#> Dataset 7 A1 7 6.6 5.81807 -0.78193 1.883 -0.415180 +#> Dataset 7 A1 14 10.4 10.22529 -0.17471 1.883 -0.092767 +#> Dataset 7 A1 14 8.3 10.22529 1.92529 1.883 1.022265 +#> Dataset 7 A1 30 14.4 16.75484 2.35484 1.883 1.250345 +#> Dataset 7 A1 30 13.7 16.75484 3.05484 1.883 1.622022 +#> Dataset 7 A1 60 22.1 22.22540 0.12540 1.883 0.066583 +#> Dataset 7 A1 60 22.3 22.22540 -0.07460 1.883 -0.039610 +#> Dataset 7 A1 90 27.5 24.38799 -3.11201 1.883 -1.652376 +#> Dataset 7 A1 90 25.4 24.38799 -1.01201 1.883 -0.537344 +#> Dataset 7 A1 120 28.0 25.53294 -2.46706 1.883 -1.309927 +#> Dataset 7 A1 120 26.6 25.53294 -1.06706 1.883 -0.566572 +#> Dataset 7 A1 180 25.8 26.94943 1.14943 1.883 0.610309 +#> Dataset 7 A1 180 25.3 26.94943 1.64943 1.883 0.875793 +#> Dataset 8 parent 0 91.9 91.53246 -0.36754 1.883 -0.195151 +#> Dataset 8 parent 0 90.8 91.53246 0.73246 1.883 0.388914 +#> Dataset 8 parent 1 64.9 67.73197 2.83197 1.883 1.503686 +#> Dataset 8 parent 1 66.2 67.73197 1.53197 1.883 0.813428 +#> Dataset 8 parent 3 43.5 41.58448 -1.91552 1.883 -1.017081 +#> Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335661 +#> Dataset 8 parent 8 18.3 19.62286 1.32286 1.883 0.702395 +#> Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808589 +#> Dataset 8 parent 14 10.2 10.77819 0.57819 1.883 0.306999 +#> Dataset 8 parent 14 10.8 10.77819 -0.02181 1.883 -0.011582 +#> Dataset 8 parent 27 4.9 3.26977 -1.63023 1.883 -0.865599 +#> Dataset 8 parent 27 3.3 3.26977 -0.03023 1.883 -0.016051 +#> Dataset 8 parent 48 1.6 0.48024 -1.11976 1.883 -0.594557 +#> Dataset 8 parent 48 1.5 0.48024 -1.01976 1.883 -0.541460 +#> Dataset 8 parent 70 1.1 0.06438 -1.03562 1.883 -0.549881 +#> Dataset 8 parent 70 0.9 0.06438 -0.83562 1.883 -0.443688 +#> Dataset 8 A1 1 9.6 7.61539 -1.98461 1.883 -1.053761 +#> Dataset 8 A1 1 7.7 7.61539 -0.08461 1.883 -0.044923 +#> Dataset 8 A1 3 15.0 15.47954 0.47954 1.883 0.254622 +#> Dataset 8 A1 3 15.1 15.47954 0.37954 1.883 0.201525 +#> Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517076 +#> Dataset 8 A1 8 21.1 20.22616 -0.87384 1.883 -0.463979 +#> Dataset 8 A1 14 19.7 20.00067 0.30067 1.883 0.159645 +#> Dataset 8 A1 14 18.9 20.00067 1.10067 1.883 0.584419 +#> Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593929 +#> Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255619 +#> Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400123 +#> Dataset 8 A1 48 9.8 10.25357 0.45357 1.883 0.240833 +#> Dataset 8 A1 70 6.2 5.95728 -0.24272 1.883 -0.128878 +#> Dataset 8 A1 70 6.1 5.95728 -0.14272 1.883 -0.075781 +#> Dataset 9 parent 0 99.8 97.47274 -2.32726 1.883 -1.235697 +#> Dataset 9 parent 0 98.3 97.47274 -0.82726 1.883 -0.439246 +#> Dataset 9 parent 1 77.1 79.72257 2.62257 1.883 1.392500 +#> Dataset 9 parent 1 77.2 79.72257 2.52257 1.883 1.339404 +#> Dataset 9 parent 3 59.0 56.26497 -2.73503 1.883 -1.452212 +#> Dataset 9 parent 3 58.1 56.26497 -1.83503 1.883 -0.974342 +#> Dataset 9 parent 8 27.4 31.66985 4.26985 1.883 2.267151 +#> Dataset 9 parent 8 29.2 31.66985 2.46985 1.883 1.311410 +#> Dataset 9 parent 14 19.1 22.39789 3.29789 1.883 1.751071 +#> Dataset 9 parent 14 29.6 22.39789 -7.20211 1.883 -3.824090 +#> Dataset 9 parent 27 10.1 14.21758 4.11758 1.883 2.186301 +#> Dataset 9 parent 27 18.2 14.21758 -3.98242 1.883 -2.114537 +#> Dataset 9 parent 48 4.5 7.27921 2.77921 1.883 1.475671 +#> Dataset 9 parent 48 9.1 7.27921 -1.82079 1.883 -0.966780 +#> Dataset 9 parent 70 2.3 3.61470 1.31470 1.883 0.698065 +#> Dataset 9 parent 70 2.9 3.61470 0.71470 1.883 0.379485 +#> Dataset 9 parent 91 2.0 1.85303 -0.14697 1.883 -0.078038 +#> Dataset 9 parent 91 1.8 1.85303 0.05303 1.883 0.028155 +#> Dataset 9 parent 120 2.0 0.73645 -1.26355 1.883 -0.670906 +#> Dataset 9 parent 120 2.2 0.73645 -1.46355 1.883 -0.777099 +#> Dataset 9 A1 1 4.2 3.87843 -0.32157 1.883 -0.170743 +#> Dataset 9 A1 1 3.9 3.87843 -0.02157 1.883 -0.011453 +#> Dataset 9 A1 3 7.4 8.90535 1.50535 1.883 0.799291 +#> Dataset 9 A1 3 7.9 8.90535 1.00535 1.883 0.533807 +#> Dataset 9 A1 8 14.5 13.75172 -0.74828 1.883 -0.397312 +#> Dataset 9 A1 8 13.7 13.75172 0.05172 1.883 0.027462 +#> Dataset 9 A1 14 14.2 14.97541 0.77541 1.883 0.411715 +#> Dataset 9 A1 14 12.2 14.97541 2.77541 1.883 1.473650 +#> Dataset 9 A1 27 13.7 14.94728 1.24728 1.883 0.662266 +#> Dataset 9 A1 27 13.2 14.94728 1.74728 1.883 0.927750 +#> Dataset 9 A1 48 13.6 13.66078 0.06078 1.883 0.032272 +#> Dataset 9 A1 48 15.4 13.66078 -1.73922 1.883 -0.923470 +#> Dataset 9 A1 70 10.4 11.84899 1.44899 1.883 0.769365 +#> Dataset 9 A1 70 11.6 11.84899 0.24899 1.883 0.132204 +#> Dataset 9 A1 91 10.0 10.09177 0.09177 1.883 0.048727 +#> Dataset 9 A1 91 9.5 10.09177 0.59177 1.883 0.314211 +#> Dataset 9 A1 120 9.1 7.91379 -1.18621 1.883 -0.629841 +#> Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576745 +#> Dataset 10 parent 0 96.1 93.65257 -2.44743 1.883 -1.299505 +#> Dataset 10 parent 0 94.3 93.65257 -0.64743 1.883 -0.343763 +#> Dataset 10 parent 8 73.9 77.85906 3.95906 1.883 2.102132 +#> Dataset 10 parent 8 73.9 77.85906 3.95906 1.883 2.102132 +#> Dataset 10 parent 14 69.4 70.17143 0.77143 1.883 0.409606 +#> Dataset 10 parent 14 73.1 70.17143 -2.92857 1.883 -1.554974 +#> Dataset 10 parent 21 65.6 63.99188 -1.60812 1.883 -0.853862 +#> Dataset 10 parent 21 65.3 63.99188 -1.30812 1.883 -0.694572 +#> Dataset 10 parent 41 55.9 54.64292 -1.25708 1.883 -0.667467 +#> Dataset 10 parent 41 54.4 54.64292 0.24292 1.883 0.128985 +#> Dataset 10 parent 63 47.0 49.61303 2.61303 1.883 1.387433 +#> Dataset 10 parent 63 49.3 49.61303 0.31303 1.883 0.166207 +#> Dataset 10 parent 91 44.7 45.17807 0.47807 1.883 0.253839 +#> Dataset 10 parent 91 46.7 45.17807 -1.52193 1.883 -0.808096 +#> Dataset 10 parent 120 42.1 41.27970 -0.82030 1.883 -0.435552 +#> Dataset 10 parent 120 41.3 41.27970 -0.02030 1.883 -0.010778 +#> Dataset 10 A1 8 3.3 3.99294 0.69294 1.883 0.367929 +#> Dataset 10 A1 8 3.4 3.99294 0.59294 1.883 0.314832 +#> Dataset 10 A1 14 3.9 5.92756 2.02756 1.883 1.076570 +#> Dataset 10 A1 14 2.9 5.92756 3.02756 1.883 1.607538 +#> Dataset 10 A1 21 6.4 7.47313 1.07313 1.883 0.569799 +#> Dataset 10 A1 21 7.2 7.47313 0.27313 1.883 0.145025 +#> Dataset 10 A1 41 9.1 9.76819 0.66819 1.883 0.354786 +#> Dataset 10 A1 41 8.5 9.76819 1.26819 1.883 0.673367 +#> Dataset 10 A1 63 11.7 10.94733 -0.75267 1.883 -0.399643 +#> Dataset 10 A1 63 12.0 10.94733 -1.05267 1.883 -0.558933 +#> Dataset 10 A1 91 13.3 11.93773 -1.36227 1.883 -0.723321 +#> Dataset 10 A1 91 13.2 11.93773 -1.26227 1.883 -0.670224 +#> Dataset 10 A1 120 14.3 12.77666 -1.52334 1.883 -0.808847 +#> Dataset 10 A1 120 12.1 12.77666 0.67666 1.883 0.359282</div><div class='input'> <span class='co'># Using a single core, the following takes about 6 minutes as we do not have an</span> <span class='co'># analytical solution. Using 10 cores it is slower instead of faster</span> -<span class='co'>#f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)</span> -<span class='co'># }</span> +<span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Nov 19 14:52:08 2020" +#> DLSODA- At current T (=R1), MXSTEP (=I1) steps +#> taken on this call before reaching TOUT +#> In above message, I1 = 5000 +#> +#> In above message, R1 = 0.00156238 +#> +#> DLSODA- At T (=R1) and step size H (=R2), the +#> corrector convergence failed repeatedly +#> or with ABS(H) = HMIN +#> In above message, R1 = 0, R2 = 1.1373e-10 +#> +#> DLSODA- At current T (=R1), MXSTEP (=I1) steps +#> taken on this call before reaching TOUT +#> In above message, I1 = 5000 +#> +#> In above message, R1 = 2.24752e-06 +#> +#> .... +#> Minimisation finished +#> [1] "Thu Nov 19 14:59:05 2020"</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_saem_fomc</span><span class='op'>)</span> +</div><div class='img'><img src='saem-6.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index 2113a001..cd183cbc 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -238,15 +238,15 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='fu'><a href='mkinfit.html'>mkinfit</a></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'>FOCUS_2006_A</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> mkin version used for fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Nov 7 13:28:04 2020 -#> Date of summary: Sat Nov 7 13:28:04 2020 +#> Date of fit: Thu Nov 19 14:59:41 2020 +#> Date of summary: Thu Nov 19 14:59:41 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.028 s +#> Fitted using 131 model solutions performed in 0.033 s #> #> Error model: Constant variance #> diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html index d35e8713..d016796e 100644 --- a/docs/dev/reference/summary.nlme.mmkin.html +++ b/docs/dev/reference/summary.nlme.mmkin.html @@ -265,8 +265,8 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> </div><div class='output co'>#> nlme version used for fitting: 3.1.150.1 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Nov 7 13:28:06 2020 -#> Date of summary: Sat Nov 7 13:28:06 2020 +#> Date of fit: Thu Nov 19 14:59:43 2020 +#> Date of summary: Thu Nov 19 14:59:43 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -276,7 +276,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 0.588 s using 5 iterations +#> Fitted in 0.681 s using 5 iterations #> #> Variance model: Two-component variance function #> @@ -293,24 +293,20 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> 555.792 570.7908 -271.896 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> lower est. upper -#> parent_0 94.701336 97.763446 100.82556 -#> log_k_parent -5.007574 -4.461767 -3.91596 +#> lower est. upper +#> parent_0 94.701 97.763 100.826 +#> log_k_parent -5.008 -4.462 -3.916 #> #> Correlation: #> prnt_0 #> log_k_parent 0.024 #> -#> Backtransformed parameters with asymmetric confidence intervals: -#> lower est. upper -#> parent_0 94.701335804 97.76344625 100.82555670 -#> k_parent 0.006687109 0.01154195 0.01992142 #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k_parent Residual -#> StdDev: 16.65969 3.516961 5.709013 +#> StdDev: 2.898 0.6119 1 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate @@ -319,6 +315,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> const prop #> 1.55075176 0.05680853 #> +#> Backtransformed parameters with asymmetric confidence intervals: +#> lower est. upper +#> parent_0 94.701336 97.76345 100.82556 +#> k_parent 0.006687 0.01154 0.01992 +#> #> Estimated disappearance times: #> DT50 DT90 #> parent 60.05 199.5 diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 8a5d001a..b7804247 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -260,16 +260,15 @@ saemix authors for the parts inherited from saemix.</p> quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span> <span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:36 2020" +#> [1] "Thu Nov 19 14:59:46 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:48 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> -#> LL by is "-401.01 (df=14)"</div><div class='output co'>#> saemix version used for fitting: 3.1.9000 +#> [1] "Thu Nov 19 15:00:00 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Nov 11 19:48:49 2020 -#> Date of summary: Wed Nov 11 19:48:49 2020 +#> Date of fit: Thu Nov 19 15:00:01 2020 +#> Date of summary: Thu Nov 19 15:00:01 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -284,7 +283,7 @@ saemix authors for the parts inherited from saemix.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 13.272 s using 300, 100 iterations +#> Fitted in 15.23 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> @@ -354,178 +353,178 @@ saemix authors for the parts inherited from saemix.</p> #> m1 40.60 134.88 NA NA NA #> #> Data: -#> ds name time observed predicted residual standardized -#> ds 1 parent 0 89.8 9.869e+01 -8.894553 1.273163 -#> ds 1 parent 0 104.1 9.869e+01 5.405447 -0.773734 -#> ds 1 parent 1 88.7 9.413e+01 -5.426448 0.810727 -#> ds 1 parent 1 95.5 9.413e+01 1.373552 -0.205213 -#> ds 1 parent 3 81.8 8.576e+01 -3.961821 0.643463 -#> ds 1 parent 3 94.5 8.576e+01 8.738179 -1.419220 -#> ds 1 parent 7 71.5 7.168e+01 -0.184828 0.035175 -#> ds 1 parent 7 70.3 7.168e+01 -1.384828 0.263550 -#> ds 1 parent 14 54.2 5.351e+01 0.688235 -0.168298 -#> ds 1 parent 14 49.6 5.351e+01 -3.911765 0.956565 -#> ds 1 parent 28 31.5 3.209e+01 -0.590445 0.217395 -#> ds 1 parent 28 28.8 3.209e+01 -3.290445 1.211502 -#> ds 1 parent 60 12.1 1.272e+01 -0.618158 0.419377 -#> ds 1 parent 60 13.6 1.272e+01 0.881842 -0.598269 -#> ds 1 parent 90 6.2 6.085e+00 0.115212 -0.109861 -#> ds 1 parent 90 8.3 6.085e+00 2.215212 -2.112329 -#> ds 1 parent 120 2.2 3.009e+00 -0.809439 0.950563 -#> ds 1 parent 120 2.4 3.009e+00 -0.609439 0.715693 -#> ds 1 m1 1 0.3 1.129e+00 -0.828817 1.133869 -#> ds 1 m1 1 0.2 1.129e+00 -0.928817 1.270675 -#> ds 1 m1 3 2.2 3.141e+00 -0.940880 1.094093 -#> ds 1 m1 3 3.0 3.141e+00 -0.140880 0.163821 -#> ds 1 m1 7 6.5 6.326e+00 0.174162 -0.163662 -#> ds 1 m1 7 5.0 6.326e+00 -1.325838 1.245901 -#> ds 1 m1 14 10.2 9.883e+00 0.317417 -0.245642 -#> ds 1 m1 14 9.5 9.883e+00 -0.382583 0.296072 -#> ds 1 m1 28 12.2 1.251e+01 -0.309856 0.212138 -#> ds 1 m1 28 13.4 1.251e+01 0.890144 -0.609422 -#> ds 1 m1 60 11.8 1.086e+01 0.940009 -0.693807 -#> ds 1 m1 60 13.2 1.086e+01 2.340009 -1.727126 -#> ds 1 m1 90 6.6 7.823e+00 -1.222977 1.054158 -#> ds 1 m1 90 9.3 7.823e+00 1.477023 -1.273135 -#> ds 1 m1 120 3.5 5.315e+00 -1.815201 1.816354 -#> ds 1 m1 120 5.4 5.315e+00 0.084799 -0.084853 -#> ds 2 parent 0 118.0 1.031e+02 14.876736 -2.046284 -#> ds 2 parent 0 99.8 1.031e+02 -3.323264 0.457112 -#> ds 2 parent 1 90.2 9.757e+01 -7.371379 1.066126 -#> ds 2 parent 1 94.6 9.757e+01 -2.971379 0.429752 -#> ds 2 parent 3 96.1 8.788e+01 8.222746 -1.306721 -#> ds 2 parent 3 78.4 8.788e+01 -9.477254 1.506081 -#> ds 2 parent 7 77.9 7.293e+01 4.972272 -0.932149 -#> ds 2 parent 7 77.7 7.293e+01 4.772272 -0.894656 -#> ds 2 parent 14 56.0 5.602e+01 -0.016773 0.003947 -#> ds 2 parent 14 54.7 5.602e+01 -1.316773 0.309830 -#> ds 2 parent 28 36.6 3.855e+01 -1.945779 0.621680 -#> ds 2 parent 28 36.8 3.855e+01 -1.745779 0.557779 -#> ds 2 parent 60 22.1 2.101e+01 1.086693 -0.541771 -#> ds 2 parent 60 24.7 2.101e+01 3.686693 -1.838002 -#> ds 2 parent 90 12.4 1.246e+01 -0.058759 0.040319 -#> ds 2 parent 90 10.8 1.246e+01 -1.658759 1.138195 -#> ds 2 parent 120 6.8 7.406e+00 -0.606226 0.534861 -#> ds 2 parent 120 7.9 7.406e+00 0.493774 -0.435647 -#> ds 2 m1 1 1.3 1.438e+00 -0.138236 0.184118 -#> ds 2 m1 3 3.7 3.879e+00 -0.178617 0.196874 -#> ds 2 m1 3 4.7 3.879e+00 0.821383 -0.905344 -#> ds 2 m1 7 8.1 7.389e+00 0.710951 -0.627868 -#> ds 2 m1 7 7.9 7.389e+00 0.510951 -0.451240 -#> ds 2 m1 14 10.1 1.069e+01 -0.593533 0.441556 -#> ds 2 m1 14 10.3 1.069e+01 -0.393533 0.292767 -#> ds 2 m1 28 10.7 1.240e+01 -1.703647 1.171837 -#> ds 2 m1 28 12.2 1.240e+01 -0.203647 0.140077 -#> ds 2 m1 60 10.7 1.055e+01 0.147672 -0.110605 -#> ds 2 m1 60 12.5 1.055e+01 1.947672 -1.458786 -#> ds 2 m1 90 9.1 8.010e+00 1.090041 -0.929963 -#> ds 2 m1 90 7.4 8.010e+00 -0.609959 0.520383 -#> ds 2 m1 120 6.1 5.793e+00 0.306797 -0.297858 -#> ds 2 m1 120 4.5 5.793e+00 -1.293203 1.255523 -#> ds 3 parent 0 106.2 1.035e+02 2.712344 -0.371886 -#> ds 3 parent 0 106.9 1.035e+02 3.412344 -0.467862 -#> ds 3 parent 1 107.4 9.548e+01 11.924044 -1.758752 -#> ds 3 parent 1 96.1 9.548e+01 0.624044 -0.092044 -#> ds 3 parent 3 79.4 8.246e+01 -3.056105 0.514055 -#> ds 3 parent 3 82.6 8.246e+01 0.143895 -0.024204 -#> ds 3 parent 7 63.9 6.489e+01 -0.991141 0.205676 -#> ds 3 parent 7 62.4 6.489e+01 -2.491141 0.516947 -#> ds 3 parent 14 51.0 4.869e+01 2.306824 -0.610198 -#> ds 3 parent 14 47.1 4.869e+01 -1.593176 0.421425 -#> ds 3 parent 28 36.1 3.480e+01 1.304261 -0.451388 -#> ds 3 parent 28 36.6 3.480e+01 1.804261 -0.624431 -#> ds 3 parent 60 20.1 1.988e+01 0.221952 -0.114821 -#> ds 3 parent 60 19.8 1.988e+01 -0.078048 0.040376 -#> ds 3 parent 90 11.3 1.194e+01 -0.642458 0.451083 -#> ds 3 parent 90 10.7 1.194e+01 -1.242458 0.872355 -#> ds 3 parent 120 8.2 7.176e+00 1.023847 -0.915231 -#> ds 3 parent 120 7.3 7.176e+00 0.123847 -0.110709 -#> ds 3 m1 0 0.8 8.527e-13 0.800000 -1.214712 -#> ds 3 m1 1 1.8 1.856e+00 -0.055925 0.071921 -#> ds 3 m1 1 2.3 1.856e+00 0.444075 -0.571099 -#> ds 3 m1 3 4.2 4.780e+00 -0.580164 0.601168 -#> ds 3 m1 3 4.1 4.780e+00 -0.680164 0.704788 -#> ds 3 m1 7 6.8 8.410e+00 -1.609920 1.344090 -#> ds 3 m1 7 10.1 8.410e+00 1.690080 -1.411014 -#> ds 3 m1 14 11.4 1.098e+01 0.424444 -0.311572 -#> ds 3 m1 14 12.8 1.098e+01 1.824444 -1.339271 -#> ds 3 m1 28 11.5 1.142e+01 0.079336 -0.057043 -#> ds 3 m1 28 10.6 1.142e+01 -0.820664 0.590065 -#> ds 3 m1 60 7.5 9.110e+00 -1.610231 1.295778 -#> ds 3 m1 60 8.6 9.110e+00 -0.510231 0.410591 -#> ds 3 m1 90 7.3 6.799e+00 0.501085 -0.457825 -#> ds 3 m1 90 8.1 6.799e+00 1.301085 -1.188759 -#> ds 3 m1 120 5.3 4.868e+00 0.431505 -0.444518 -#> ds 3 m1 120 3.8 4.868e+00 -1.068495 1.100718 -#> ds 4 parent 0 104.7 9.926e+01 5.444622 -0.775351 -#> ds 4 parent 0 88.3 9.926e+01 -10.955378 1.560119 -#> ds 4 parent 1 94.2 9.618e+01 -1.978413 0.289883 -#> ds 4 parent 1 94.6 9.618e+01 -1.578413 0.231274 -#> ds 4 parent 3 78.1 9.037e+01 -12.268550 1.901399 -#> ds 4 parent 3 96.5 9.037e+01 6.131450 -0.950262 -#> ds 4 parent 7 76.2 7.999e+01 -3.794958 0.655739 -#> ds 4 parent 7 77.8 7.999e+01 -2.194958 0.379272 -#> ds 4 parent 14 70.8 6.518e+01 5.624996 -1.162874 -#> ds 4 parent 14 67.3 6.518e+01 2.124996 -0.439307 -#> ds 4 parent 28 43.1 4.462e+01 -1.517860 0.431312 -#> ds 4 parent 28 45.1 4.462e+01 0.482140 -0.137004 -#> ds 4 parent 60 21.3 2.130e+01 0.003305 -0.001633 -#> ds 4 parent 60 23.5 2.130e+01 2.203305 -1.088598 -#> ds 4 parent 90 11.8 1.180e+01 -0.002834 0.002002 -#> ds 4 parent 90 12.1 1.180e+01 0.297166 -0.209966 -#> ds 4 parent 120 7.0 6.868e+00 0.132251 -0.120348 -#> ds 4 parent 120 6.2 6.868e+00 -0.667749 0.607650 -#> ds 4 m1 0 1.6 0.000e+00 1.600000 -2.429424 -#> ds 4 m1 1 0.9 6.826e-01 0.217363 -0.309476 -#> ds 4 m1 3 3.7 1.935e+00 1.765082 -2.255277 -#> ds 4 m1 3 2.0 1.935e+00 0.065082 -0.083157 -#> ds 4 m1 7 3.6 4.035e+00 -0.434805 0.474018 -#> ds 4 m1 7 3.8 4.035e+00 -0.234805 0.255981 -#> ds 4 m1 14 7.1 6.652e+00 0.448187 -0.413053 -#> ds 4 m1 14 6.6 6.652e+00 -0.051813 0.047751 -#> ds 4 m1 28 9.5 9.156e+00 0.343805 -0.276011 -#> ds 4 m1 28 9.3 9.156e+00 0.143805 -0.115448 -#> ds 4 m1 60 8.3 8.848e+00 -0.547762 0.446843 -#> ds 4 m1 60 9.0 8.848e+00 0.152238 -0.124190 -#> ds 4 m1 90 6.6 6.674e+00 -0.073979 0.068090 -#> ds 4 m1 90 7.7 6.674e+00 1.026021 -0.944353 -#> ds 4 m1 120 3.7 4.668e+00 -0.967537 1.010122 -#> ds 4 m1 120 3.5 4.668e+00 -1.167537 1.218925 -#> ds 5 parent 0 110.4 1.022e+02 8.170986 -1.132847 -#> ds 5 parent 0 112.1 1.022e+02 9.870986 -1.368539 -#> ds 5 parent 1 93.5 9.513e+01 -1.630764 0.241319 -#> ds 5 parent 1 91.0 9.513e+01 -4.130764 0.611268 -#> ds 5 parent 3 71.0 8.296e+01 -11.964279 2.001495 -#> ds 5 parent 3 89.7 8.296e+01 6.735721 -1.126813 -#> ds 5 parent 7 60.4 6.495e+01 -4.547441 0.942951 -#> ds 5 parent 7 59.1 6.495e+01 -5.847441 1.212518 -#> ds 5 parent 14 56.5 4.626e+01 10.241319 -2.825682 -#> ds 5 parent 14 47.0 4.626e+01 0.741319 -0.204537 -#> ds 5 parent 28 30.2 3.026e+01 -0.058478 0.022504 -#> ds 5 parent 28 23.9 3.026e+01 -6.358478 2.446932 -#> ds 5 parent 60 17.0 1.792e+01 -0.919046 0.508481 -#> ds 5 parent 60 18.7 1.792e+01 0.780954 -0.432079 -#> ds 5 parent 90 11.3 1.187e+01 -0.573917 0.404206 -#> ds 5 parent 90 11.9 1.187e+01 0.026083 -0.018370 -#> ds 5 parent 120 9.0 7.898e+00 1.102089 -0.946039 -#> ds 5 parent 120 8.1 7.898e+00 0.202089 -0.173474 -#> ds 5 m1 0 0.7 -1.421e-14 0.700000 -1.062873 -#> ds 5 m1 1 3.0 3.144e+00 -0.143526 0.166865 -#> ds 5 m1 1 2.6 3.144e+00 -0.543526 0.631910 -#> ds 5 m1 3 5.1 8.390e+00 -3.290265 2.749870 -#> ds 5 m1 3 7.5 8.390e+00 -0.890265 0.744048 -#> ds 5 m1 7 16.5 1.566e+01 0.841368 -0.506082 -#> ds 5 m1 7 19.0 1.566e+01 3.341368 -2.009830 -#> ds 5 m1 14 22.9 2.188e+01 1.017753 -0.493689 -#> ds 5 m1 14 23.2 2.188e+01 1.317753 -0.639212 -#> ds 5 m1 28 22.2 2.386e+01 -1.655914 0.756794 -#> ds 5 m1 28 24.4 2.386e+01 0.544086 -0.248661 -#> ds 5 m1 60 15.5 1.859e+01 -3.091124 1.670405 -#> ds 5 m1 60 19.8 1.859e+01 1.208876 -0.653262 -#> ds 5 m1 90 14.9 1.372e+01 1.176815 -0.764948 -#> ds 5 m1 90 14.2 1.372e+01 0.476815 -0.309937 -#> ds 5 m1 120 10.9 9.961e+00 0.938796 -0.723690 -#> ds 5 m1 120 10.4 9.961e+00 0.438796 -0.338255</div><div class='input'><span class='co'># }</span> +#> ds name time observed predicted residual std standardized +#> ds 1 parent 0 89.8 9.869e+01 8.894553 6.3618 1.398124 +#> ds 1 parent 0 104.1 9.869e+01 -5.405447 6.3618 -0.849676 +#> ds 1 parent 1 88.7 9.413e+01 5.426448 6.0706 0.893897 +#> ds 1 parent 1 95.5 9.413e+01 -1.373552 6.0706 -0.226265 +#> ds 1 parent 3 81.8 8.576e+01 3.961821 5.5377 0.715422 +#> ds 1 parent 3 94.5 8.576e+01 -8.738179 5.5377 -1.577932 +#> ds 1 parent 7 71.5 7.168e+01 0.184828 4.6429 0.039809 +#> ds 1 parent 7 70.3 7.168e+01 1.384828 4.6429 0.298270 +#> ds 1 parent 14 54.2 5.351e+01 -0.688235 3.4934 -0.197008 +#> ds 1 parent 14 49.6 5.351e+01 3.911765 3.4934 1.119747 +#> ds 1 parent 28 31.5 3.209e+01 0.590445 2.1603 0.273322 +#> ds 1 parent 28 28.8 3.209e+01 3.290445 2.1603 1.523177 +#> ds 1 parent 60 12.1 1.272e+01 0.618158 1.0481 0.589761 +#> ds 1 parent 60 13.6 1.272e+01 -0.881842 1.0481 -0.841332 +#> ds 1 parent 90 6.2 6.085e+00 -0.115212 0.7655 -0.150512 +#> ds 1 parent 90 8.3 6.085e+00 -2.215212 0.7655 -2.893953 +#> ds 1 parent 120 2.2 3.009e+00 0.809439 0.6863 1.179470 +#> ds 1 parent 120 2.4 3.009e+00 0.609439 0.6863 0.888041 +#> ds 1 m1 1 0.3 1.129e+00 0.828817 0.6626 1.250938 +#> ds 1 m1 1 0.2 1.129e+00 0.928817 0.6626 1.401869 +#> ds 1 m1 3 2.2 3.141e+00 0.940880 0.6887 1.366187 +#> ds 1 m1 3 3.0 3.141e+00 0.140880 0.6887 0.204562 +#> ds 1 m1 7 6.5 6.326e+00 -0.174162 0.7735 -0.225175 +#> ds 1 m1 7 5.0 6.326e+00 1.325838 0.7735 1.714181 +#> ds 1 m1 14 10.2 9.883e+00 -0.317417 0.9139 -0.347326 +#> ds 1 m1 14 9.5 9.883e+00 0.382583 0.9139 0.418631 +#> ds 1 m1 28 12.2 1.251e+01 0.309856 1.0378 0.298572 +#> ds 1 m1 28 13.4 1.251e+01 -0.890144 1.0378 -0.857726 +#> ds 1 m1 60 11.8 1.086e+01 -0.940009 0.9584 -0.980812 +#> ds 1 m1 60 13.2 1.086e+01 -2.340009 0.9584 -2.441581 +#> ds 1 m1 90 6.6 7.823e+00 1.222977 0.8278 1.477332 +#> ds 1 m1 90 9.3 7.823e+00 -1.477023 0.8278 -1.784214 +#> ds 1 m1 120 3.5 5.315e+00 1.815201 0.7415 2.447906 +#> ds 1 m1 120 5.4 5.315e+00 -0.084799 0.7415 -0.114356 +#> ds 2 parent 0 118.0 1.031e+02 -14.876736 6.6443 -2.239038 +#> ds 2 parent 0 99.8 1.031e+02 3.323264 6.6443 0.500171 +#> ds 2 parent 1 90.2 9.757e+01 7.371379 6.2902 1.171891 +#> ds 2 parent 1 94.6 9.757e+01 2.971379 6.2902 0.472386 +#> ds 2 parent 3 96.1 8.788e+01 -8.222746 5.6724 -1.449599 +#> ds 2 parent 3 78.4 8.788e+01 9.477254 5.6724 1.670758 +#> ds 2 parent 7 77.9 7.293e+01 -4.972272 4.7218 -1.053054 +#> ds 2 parent 7 77.7 7.293e+01 -4.772272 4.7218 -1.010697 +#> ds 2 parent 14 56.0 5.602e+01 0.016773 3.6513 0.004594 +#> ds 2 parent 14 54.7 5.602e+01 1.316773 3.6513 0.360633 +#> ds 2 parent 28 36.6 3.855e+01 1.945779 2.5575 0.760803 +#> ds 2 parent 28 36.8 3.855e+01 1.745779 2.5575 0.682603 +#> ds 2 parent 60 22.1 2.101e+01 -1.086693 1.4996 -0.724663 +#> ds 2 parent 60 24.7 2.101e+01 -3.686693 1.4996 -2.458475 +#> ds 2 parent 90 12.4 1.246e+01 0.058759 1.0353 0.056757 +#> ds 2 parent 90 10.8 1.246e+01 1.658759 1.0353 1.602256 +#> ds 2 parent 120 6.8 7.406e+00 0.606226 0.8119 0.746659 +#> ds 2 parent 120 7.9 7.406e+00 -0.493774 0.8119 -0.608157 +#> ds 2 m1 1 1.3 1.438e+00 0.138236 0.6650 0.207869 +#> ds 2 m1 3 3.7 3.879e+00 0.178617 0.7040 0.253726 +#> ds 2 m1 3 4.7 3.879e+00 -0.821383 0.7040 -1.166780 +#> ds 2 m1 7 8.1 7.389e+00 -0.710951 0.8113 -0.876337 +#> ds 2 m1 7 7.9 7.389e+00 -0.510951 0.8113 -0.629812 +#> ds 2 m1 14 10.1 1.069e+01 0.593533 0.9507 0.624328 +#> ds 2 m1 14 10.3 1.069e+01 0.393533 0.9507 0.413951 +#> ds 2 m1 28 10.7 1.240e+01 1.703647 1.0325 1.649956 +#> ds 2 m1 28 12.2 1.240e+01 0.203647 1.0325 0.197229 +#> ds 2 m1 60 10.7 1.055e+01 -0.147672 0.9442 -0.156405 +#> ds 2 m1 60 12.5 1.055e+01 -1.947672 0.9442 -2.062848 +#> ds 2 m1 90 9.1 8.010e+00 -1.090041 0.8351 -1.305210 +#> ds 2 m1 90 7.4 8.010e+00 0.609959 0.8351 0.730362 +#> ds 2 m1 120 6.1 5.793e+00 -0.306797 0.7561 -0.405759 +#> ds 2 m1 120 4.5 5.793e+00 1.293203 0.7561 1.710347 +#> ds 3 parent 0 106.2 1.035e+02 -2.712344 6.6675 -0.406801 +#> ds 3 parent 0 106.9 1.035e+02 -3.412344 6.6675 -0.511788 +#> ds 3 parent 1 107.4 9.548e+01 -11.924044 6.1566 -1.936801 +#> ds 3 parent 1 96.1 9.548e+01 -0.624044 6.1566 -0.101362 +#> ds 3 parent 3 79.4 8.246e+01 3.056105 5.3274 0.573662 +#> ds 3 parent 3 82.6 8.246e+01 -0.143895 5.3274 -0.027010 +#> ds 3 parent 7 63.9 6.489e+01 0.991141 4.2122 0.235304 +#> ds 3 parent 7 62.4 6.489e+01 2.491141 4.2122 0.591416 +#> ds 3 parent 14 51.0 4.869e+01 -2.306824 3.1906 -0.723013 +#> ds 3 parent 14 47.1 4.869e+01 1.593176 3.1906 0.499338 +#> ds 3 parent 28 36.1 3.480e+01 -1.304261 2.3260 -0.560722 +#> ds 3 parent 28 36.6 3.480e+01 -1.804261 2.3260 -0.775679 +#> ds 3 parent 60 20.1 1.988e+01 -0.221952 1.4346 -0.154719 +#> ds 3 parent 60 19.8 1.988e+01 0.078048 1.4346 0.054406 +#> ds 3 parent 90 11.3 1.194e+01 0.642458 1.0099 0.636132 +#> ds 3 parent 90 10.7 1.194e+01 1.242458 1.0099 1.230224 +#> ds 3 parent 120 8.2 7.176e+00 -1.023847 0.8034 -1.274423 +#> ds 3 parent 120 7.3 7.176e+00 -0.123847 0.8034 -0.154158 +#> ds 3 m1 0 0.8 8.527e-13 -0.800000 0.6586 -1.214712 +#> ds 3 m1 1 1.8 1.856e+00 0.055925 0.6693 0.083562 +#> ds 3 m1 1 2.3 1.856e+00 -0.444075 0.6693 -0.663537 +#> ds 3 m1 3 4.2 4.780e+00 0.580164 0.7264 0.798676 +#> ds 3 m1 3 4.1 4.780e+00 0.680164 0.7264 0.936340 +#> ds 3 m1 7 6.8 8.410e+00 1.609920 0.8512 1.891455 +#> ds 3 m1 7 10.1 8.410e+00 -1.690080 0.8512 -1.985633 +#> ds 3 m1 14 11.4 1.098e+01 -0.424444 0.9638 -0.440389 +#> ds 3 m1 14 12.8 1.098e+01 -1.824444 0.9638 -1.892979 +#> ds 3 m1 28 11.5 1.142e+01 -0.079336 0.9848 -0.080558 +#> ds 3 m1 28 10.6 1.142e+01 0.820664 0.9848 0.833311 +#> ds 3 m1 60 7.5 9.110e+00 1.610231 0.8803 1.829222 +#> ds 3 m1 60 8.6 9.110e+00 0.510231 0.8803 0.579622 +#> ds 3 m1 90 7.3 6.799e+00 -0.501085 0.7898 -0.634463 +#> ds 3 m1 90 8.1 6.799e+00 -1.301085 0.7898 -1.647404 +#> ds 3 m1 120 5.3 4.868e+00 -0.431505 0.7288 -0.592064 +#> ds 3 m1 120 3.8 4.868e+00 1.068495 0.7288 1.466073 +#> ds 4 parent 0 104.7 9.926e+01 -5.444622 6.3975 -0.851049 +#> ds 4 parent 0 88.3 9.926e+01 10.955378 6.3975 1.712436 +#> ds 4 parent 1 94.2 9.618e+01 1.978413 6.2013 0.319030 +#> ds 4 parent 1 94.6 9.618e+01 1.578413 6.2013 0.254527 +#> ds 4 parent 3 78.1 9.037e+01 12.268550 5.8311 2.103985 +#> ds 4 parent 3 96.5 9.037e+01 -6.131450 5.8311 -1.051508 +#> ds 4 parent 7 76.2 7.999e+01 3.794958 5.1708 0.733918 +#> ds 4 parent 7 77.8 7.999e+01 2.194958 5.1708 0.424489 +#> ds 4 parent 14 70.8 6.518e+01 -5.624996 4.2301 -1.329742 +#> ds 4 parent 14 67.3 6.518e+01 -2.124996 4.2301 -0.502346 +#> ds 4 parent 28 43.1 4.462e+01 1.517860 2.9354 0.517085 +#> ds 4 parent 28 45.1 4.462e+01 -0.482140 2.9354 -0.164249 +#> ds 4 parent 60 21.3 2.130e+01 -0.003305 1.5159 -0.002180 +#> ds 4 parent 60 23.5 2.130e+01 -2.203305 1.5159 -1.453435 +#> ds 4 parent 90 11.8 1.180e+01 0.002834 1.0032 0.002825 +#> ds 4 parent 90 12.1 1.180e+01 -0.297166 1.0032 -0.296226 +#> ds 4 parent 120 7.0 6.868e+00 -0.132251 0.7922 -0.166937 +#> ds 4 parent 120 6.2 6.868e+00 0.667749 0.7922 0.842879 +#> ds 4 m1 0 1.6 0.000e+00 -1.600000 0.6586 -2.429424 +#> ds 4 m1 1 0.9 6.826e-01 -0.217363 0.6600 -0.329315 +#> ds 4 m1 3 3.7 1.935e+00 -1.765082 0.6702 -2.633768 +#> ds 4 m1 3 2.0 1.935e+00 -0.065082 0.6702 -0.097112 +#> ds 4 m1 7 3.6 4.035e+00 0.434805 0.7076 0.614501 +#> ds 4 m1 7 3.8 4.035e+00 0.234805 0.7076 0.331845 +#> ds 4 m1 14 7.1 6.652e+00 -0.448187 0.7846 -0.571220 +#> ds 4 m1 14 6.6 6.652e+00 0.051813 0.7846 0.066036 +#> ds 4 m1 28 9.5 9.156e+00 -0.343805 0.8822 -0.389696 +#> ds 4 m1 28 9.3 9.156e+00 -0.143805 0.8822 -0.163000 +#> ds 4 m1 60 8.3 8.848e+00 0.547762 0.8692 0.630185 +#> ds 4 m1 60 9.0 8.848e+00 -0.152238 0.8692 -0.175146 +#> ds 4 m1 90 6.6 6.674e+00 0.073979 0.7854 0.094194 +#> ds 4 m1 90 7.7 6.674e+00 -1.026021 0.7854 -1.306390 +#> ds 4 m1 120 3.7 4.668e+00 0.967537 0.7234 1.337503 +#> ds 4 m1 120 3.5 4.668e+00 1.167537 0.7234 1.613979 +#> ds 5 parent 0 110.4 1.022e+02 -8.170986 6.5872 -1.240433 +#> ds 5 parent 0 112.1 1.022e+02 -9.870986 6.5872 -1.498509 +#> ds 5 parent 1 93.5 9.513e+01 1.630764 6.1346 0.265832 +#> ds 5 parent 1 91.0 9.513e+01 4.130764 6.1346 0.673359 +#> ds 5 parent 3 71.0 8.296e+01 11.964279 5.3597 2.232268 +#> ds 5 parent 3 89.7 8.296e+01 -6.735721 5.3597 -1.256735 +#> ds 5 parent 7 60.4 6.495e+01 4.547441 4.2157 1.078684 +#> ds 5 parent 7 59.1 6.495e+01 5.847441 4.2157 1.387053 +#> ds 5 parent 14 56.5 4.626e+01 -10.241319 3.0380 -3.371047 +#> ds 5 parent 14 47.0 4.626e+01 -0.741319 3.0380 -0.244014 +#> ds 5 parent 28 30.2 3.026e+01 0.058478 2.0487 0.028544 +#> ds 5 parent 28 23.9 3.026e+01 6.358478 2.0487 3.103661 +#> ds 5 parent 60 17.0 1.792e+01 0.919046 1.3242 0.694024 +#> ds 5 parent 60 18.7 1.792e+01 -0.780954 1.3242 -0.589742 +#> ds 5 parent 90 11.3 1.187e+01 0.573917 1.0066 0.570144 +#> ds 5 parent 90 11.9 1.187e+01 -0.026083 1.0066 -0.025912 +#> ds 5 parent 120 9.0 7.898e+00 -1.102089 0.8307 -1.326622 +#> ds 5 parent 120 8.1 7.898e+00 -0.202089 0.8307 -0.243261 +#> ds 5 m1 0 0.7 -1.421e-14 -0.700000 0.6586 -1.062873 +#> ds 5 m1 1 3.0 3.144e+00 0.143526 0.6887 0.208390 +#> ds 5 m1 1 2.6 3.144e+00 0.543526 0.6887 0.789161 +#> ds 5 m1 3 5.1 8.390e+00 3.290265 0.8504 3.869277 +#> ds 5 m1 3 7.5 8.390e+00 0.890265 0.8504 1.046932 +#> ds 5 m1 7 16.5 1.566e+01 -0.841368 1.2007 -0.700751 +#> ds 5 m1 7 19.0 1.566e+01 -3.341368 1.2007 -2.782928 +#> ds 5 m1 14 22.9 2.188e+01 -1.017753 1.5498 -0.656687 +#> ds 5 m1 14 23.2 2.188e+01 -1.317753 1.5498 -0.850257 +#> ds 5 m1 28 22.2 2.386e+01 1.655914 1.6652 0.994399 +#> ds 5 m1 28 24.4 2.386e+01 -0.544086 1.6652 -0.326731 +#> ds 5 m1 60 15.5 1.859e+01 3.091124 1.3618 2.269915 +#> ds 5 m1 60 19.8 1.859e+01 -1.208876 1.3618 -0.887718 +#> ds 5 m1 90 14.9 1.372e+01 -1.176815 1.0990 -1.070784 +#> ds 5 m1 90 14.2 1.372e+01 -0.476815 1.0990 -0.433854 +#> ds 5 m1 120 10.9 9.961e+00 -0.938796 0.9174 -1.023332 +#> ds 5 m1 120 10.4 9.961e+00 -0.438796 0.9174 -0.478308</div><div class='input'><span class='co'># }</span> </div></pre> </div> diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index 6b849d3f..0845d478 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -252,7 +252,7 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</ <span class='co'># \dontrun{</span> <span class='co'># Compare to the version without transforming rate parameters</span> <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='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.003 0 0.002</span></div><div class='input'><span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.002 0 0.003</span></div><div class='input'><span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> </div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span> diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index 02fca7f9..31b0abb1 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -10,6 +10,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/CAKE_export.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/D24_2014.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/DFOP.solution.html</loc> </url> <url> @@ -70,6 +73,12 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/experimental_data_for_UBA.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html</loc> + </url> + <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/focus_soil_moisture.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/get_deg_func.html</loc> </url> <url> @@ -103,6 +112,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/mkinds.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/mkindsg.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html</loc> </url> <url> @@ -127,9 +139,6 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/mkinresplot.html</loc> </url> <url> - <loc>https://pkgdown.jrwb.de/mkin/reference/mkinsub.html</loc> - </url> - <url> <loc>https://pkgdown.jrwb.de/mkin/reference/mmkin.html</loc> </url> <url> @@ -160,12 +169,6 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html</loc> </url> <url> - <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinds.html</loc> - </url> - <url> - <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinmod.html</loc> - </url> - <url> <loc>https://pkgdown.jrwb.de/mkin/reference/print.mmkin.html</loc> </url> <url> |
