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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> |