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| -rw-r--r-- | docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png | bin | 20999 -> 22316 bytes | |||
| -rw-r--r-- | docs/articles/web_only/NAFTA_examples.html | 691 | ||||
| -rw-r--r-- | docs/articles/web_only/benchmarks.html | 22 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 12 |
5 files changed, 435 insertions, 509 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index c4c69b8f..3cda0261 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -131,94 +131,86 @@ <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></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"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.Z.2a, data = FALSE): Could not calculate -## correlation; no covariance matrix</code></pre> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 9.7015e+01 NA NA NA NA NA -## k_Z0_sink 7.2231e-10 NA NA NA NA NA -## k_Z0_Z1 2.2360e+00 NA NA NA NA NA -## k_Z1_sink 4.8212e-01 NA NA NA NA NA -## sigma 4.8041e+00 NA NA NA NA NA</code></pre> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 9.7015e+01 3.393176 2.8591e+01 6.4352e-21 91.66556 102.3642 +## k_Z0_sink 7.2231e-10 0.225254 3.2067e-09 5.0000e-01 0.00000 Inf +## k_Z0_Z1 2.2360e+00 0.159134 1.4051e+01 1.1369e-13 1.95303 2.5600 +## k_Z1_sink 4.8212e-01 0.065454 7.3658e+00 5.1186e-08 0.40341 0.5762 +## sigma 4.8041e+00 0.637618 7.5345e+00 3.4431e-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="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> -<a class="sourceLine" id="cb10-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb10-3" title="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> +<a class="sourceLine" id="cb9-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb9-3" title="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></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="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></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="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.Z.2a.ff, data = FALSE): Could not calculate -## correlation; no covariance matrix</code></pre> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 NA NA NA NA NA -## k_Z0 2.23601 NA NA NA NA NA -## k_Z1 0.48212 NA NA NA NA NA -## f_Z0_to_Z1 1.00000 NA NA NA NA NA -## sigma 4.80411 NA NA NA NA NA</code></pre> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></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 +## k_Z1 0.48212 0.063265 7.6207 2.8155e-08 0.40341 0.5762 +## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000 +## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</code></pre> <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="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb18-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb16-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></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="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div> +<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></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="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.Z.3, data = FALSE): Could not calculate -## correlation; no covariance matrix</code></pre> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 NA NA NA NA NA -## k_Z0 2.23601 NA NA NA NA NA -## k_Z1 0.48212 NA NA NA NA NA -## sigma 4.80411 NA NA NA NA NA</code></pre> +<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></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 +## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760 +## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</code></pre> <p>As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.</p> </div> <div id="metabolites-z2-and-z3" class="section level1"> <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="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1">Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb26-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb26-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb23-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb23-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></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="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></code></pre></div> +<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></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="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1">Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb31-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb31-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb31-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb31-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1">Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb28-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb28-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb28-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb28-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb33-2" title="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a> -<a class="sourceLine" id="cb33-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb30-2" title="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a> +<a class="sourceLine" id="cb30-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> <pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z. ## 5$bparms.ode, : Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div> +<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></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="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.Z.FOCUS, data = FALSE): Could not calculate -## correlation; no covariance matrix</code></pre> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 96.838607 NA NA NA NA NA -## k_Z0 2.215405 NA NA NA NA NA -## k_Z1 0.478300 NA NA NA NA NA -## k_Z2 0.451618 NA NA NA NA NA -## k_Z3 0.058693 NA NA NA NA NA -## f_Z2_to_Z3 0.471508 NA NA NA NA NA -## sigma 3.984431 NA NA NA NA NA</code></pre> -<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div> +<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 96.838607 1.994273 48.5584 4.0283e-42 92.826626 100.850589 +## k_Z0 2.215405 0.118459 18.7018 1.0415e-23 1.989465 2.467003 +## k_Z1 0.478300 0.028257 16.9267 6.2408e-22 0.424701 0.538662 +## k_Z2 0.451618 0.042138 10.7177 1.6308e-14 0.374328 0.544867 +## k_Z3 0.058693 0.015246 3.8498 1.7806e-04 0.034805 0.098978 +## f_Z2_to_Z3 0.471508 0.058352 8.0804 9.6648e-11 0.357735 0.588320 +## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</code></pre> +<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div> <pre><code>## $ff ## Z2_Z3 Z2_sink ## 0.47151 0.52849 @@ -239,77 +231,102 @@ <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="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1">Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb41-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb41-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb41-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" title="1">Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb37-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb37-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb37-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" title="1">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></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="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div> +<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></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="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.Z.mkin.1, data = FALSE): Could not calculate -## correlation; no covariance matrix</code></pre> -<pre><code>## NULL</code></pre> +<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> +<pre><code>## Z0_0 log_k_Z0_Z1 log_k_Z1_Z2 log_k_Z2_sink +## Z0_0 3.8375e+00 5.4918e-03 3.0584e-02 1.2969e-01 +## log_k_Z0_Z1 5.4918e-03 2.7613e-03 -1.8820e-04 2.6634e-04 +## log_k_Z1_Z2 3.0584e-02 -1.8820e-04 3.3807e-03 3.2177e-03 +## log_k_Z2_sink 1.2969e-01 2.6634e-04 3.2177e-03 3.4256e-02 +## log_k_Z2_Z3_free -2.4223e-02 -2.6169e-04 -1.1845e-03 -8.1134e-03 +## log_k_Z3_free_sink -6.5467e-02 -4.0815e-04 -3.2978e-03 -3.6010e-02 +## log_k_Z3_free_bound -6.0659e-02 -4.4768e-04 -3.0588e-03 -3.9074e-02 +## log_k_Z3_bound_free 5.2844e-01 4.5458e-03 7.9800e-03 4.6274e-02 +## sigma 2.0366e-10 -3.4658e-10 8.9910e-11 -2.5946e-10 +## log_k_Z2_Z3_free log_k_Z3_free_sink +## Z0_0 -2.4223e-02 -6.5467e-02 +## log_k_Z0_Z1 -2.6169e-04 -4.0815e-04 +## log_k_Z1_Z2 -1.1845e-03 -3.2978e-03 +## log_k_Z2_sink -8.1134e-03 -3.6010e-02 +## log_k_Z2_Z3_free 1.5500e-02 2.1583e-02 +## log_k_Z3_free_sink 2.1583e-02 7.5705e-02 +## log_k_Z3_free_bound 2.5836e-02 1.1964e-01 +## log_k_Z3_bound_free 5.2534e-02 2.9441e-01 +## sigma 1.3063e-10 3.4170e-10 +## log_k_Z3_free_bound log_k_Z3_bound_free sigma +## Z0_0 -6.0659e-02 5.2844e-01 2.0366e-10 +## log_k_Z0_Z1 -4.4768e-04 4.5458e-03 -3.4658e-10 +## log_k_Z1_Z2 -3.0588e-03 7.9800e-03 8.9910e-11 +## log_k_Z2_sink -3.9074e-02 4.6274e-02 -2.5946e-10 +## log_k_Z2_Z3_free 2.5836e-02 5.2534e-02 1.3063e-10 +## log_k_Z3_free_sink 1.1964e-01 2.9441e-01 3.4170e-10 +## log_k_Z3_free_bound 6.5902e-01 5.4737e+00 -6.7704e-10 +## log_k_Z3_bound_free 5.4737e+00 2.8722e+08 7.2421e-02 +## sigma -6.7704e-10 7.2421e-02 1.4170e-01</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="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" title="1">Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb49-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb49-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1">Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb44-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb44-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></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="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div> +<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></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="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb54-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb54-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb54-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" title="1">Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb49-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb49-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb49-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" title="1">m.Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb56-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a> -<a class="sourceLine" id="cb56-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1">m.Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb51-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a> +<a class="sourceLine" id="cb51-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></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> -<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div> +<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></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="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1">Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb59-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb59-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb59-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb54-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb54-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb54-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1">m.Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb61-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a> -<a class="sourceLine" id="cb61-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" title="1">m.Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb56-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a> +<a class="sourceLine" id="cb56-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> <pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. ## 4$bparms.ode[1:4], : Observations with value of zero were removed from the ## data</code></pre> -<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div> +<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></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="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb64-2" title="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> -<a class="sourceLine" id="cb64-3" title="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> -<a class="sourceLine" id="cb64-4" title="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> -<a class="sourceLine" id="cb64-5" title="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb59-2" title="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> +<a class="sourceLine" id="cb59-3" title="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> +<a class="sourceLine" id="cb59-4" title="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> +<a class="sourceLine" id="cb59-5" title="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></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> -<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></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="cb67"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb67-1" title="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(object): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></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="cb69"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb69-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> <pre><code>## $ff ## Z0_free_Z1 Z1_Z2 Z2_sink Z2_Z3_free Z3_free_sink ## 1.00000 1.00000 0.46344 0.53656 1.00000 diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png Binary files differindex 4304f6d2..8188c4cf 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index f6f7c60a..237b506e 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -111,19 +111,11 @@ <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="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">p5a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5a"</span>]])</a></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 - -## 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="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -133,25 +125,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 95.8401 NA NA NA -## k_parent_sink 0.0102 NA NA NA -## sigma 4.8230 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 95.8401 4.67e-21 92.245 99.4357 +## k_parent_sink 0.0102 3.92e-12 0.009 0.0117 +## sigma 4.8230 3.81e-06 3.214 6.4318 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA NA NA -## k__iore_parent_sink 1.54e-05 NA NA NA -## N_parent 2.57e+00 NA NA NA -## sigma 1.68e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 NA 9.91e+01 1.02e+02 +## k__iore_parent_sink 1.54e-05 NA 4.08e-06 5.84e-05 +## N_parent 2.57e+00 NA 2.25e+00 2.89e+00 +## sigma 1.68e+00 NA 1.12e+00 2.24e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.99e+01 NA NA NA -## k1 2.67e-02 NA NA NA -## k2 2.86e-12 NA NA NA -## g 6.47e-01 NA NA NA -## sigma 1.27e+00 NA NA NA +## 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 2.86e-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 ## ## ## DTx values: @@ -166,20 +158,12 @@ <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="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></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 - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></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="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -189,25 +173,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.497 NA NA NA -## k_parent_sink 0.008 NA NA NA -## sigma 2.295 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 96.497 2.32e-24 94.85271 98.14155 +## k_parent_sink 0.008 3.42e-14 0.00737 0.00869 +## sigma 2.295 1.22e-05 1.47976 3.11036 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 NA NA NA -## k__iore_parent_sink 1.53e-04 NA NA NA -## N_parent 1.94e+00 NA NA NA -## sigma 7.49e-01 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01 +## k__iore_parent_sink 1.53e-04 6.50e-03 7.21e-05 3.26e-04 +## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00 +## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.84e+01 NA NA NA -## k1 1.55e-02 NA NA NA -## k2 1.16e-11 NA NA NA -## g 6.89e-01 NA NA NA -## sigma 6.48e-01 NA NA NA +## 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 1.16e-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 ## ## ## DTx values: @@ -222,20 +206,12 @@ <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="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></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 - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></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="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> +<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> +<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -245,25 +221,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7759 NA NA NA -## k_parent_sink 0.0179 NA NA NA -## sigma 3.0696 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 94.7759 7.29e-24 92.3478 97.2039 +## k_parent_sink 0.0179 8.02e-16 0.0166 0.0194 +## sigma 3.0696 3.81e-06 2.0456 4.0936 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 97.12446 NA NA NA -## k__iore_parent_sink 0.00252 NA NA NA -## N_parent 1.49587 NA NA NA -## sigma 1.59698 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.12446 2.63e-26 95.62461 98.62431 +## k__iore_parent_sink 0.00252 1.95e-03 0.00134 0.00472 +## N_parent 1.49587 4.07e-13 1.33896 1.65279 +## sigma 1.59698 5.05e-06 1.06169 2.13227 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.66e+01 NA NA NA -## k1 2.55e-02 NA NA NA -## k2 4.90e-11 NA NA NA -## g 8.61e-01 NA NA NA -## sigma 1.46e+00 NA NA NA +## 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 4.90e-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 ## ## ## DTx values: @@ -278,20 +254,12 @@ <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="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></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 - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></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="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -301,25 +269,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.41796 NA NA NA -## k_parent_sink 0.00735 NA NA NA -## sigma 7.94557 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 96.41796 4.80e-53 93.32245 99.51347 +## k_parent_sink 0.00735 7.64e-21 0.00641 0.00843 +## sigma 7.94557 1.83e-15 6.46713 9.42401 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.92e+01 NA NA NA -## k__iore_parent_sink 1.60e-05 NA NA NA -## N_parent 2.45e+00 NA NA NA -## sigma 7.42e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.92e+01 NA 9.55e+01 1.03e+02 +## k__iore_parent_sink 1.60e-05 NA 1.45e-07 1.77e-03 +## N_parent 2.45e+00 NA 1.35e+00 3.54e+00 +## sigma 7.42e+00 NA 6.04e+00 8.80e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 NA NA NA -## k1 1.81e-02 NA NA NA -## k2 1.97e-10 NA NA NA -## g 6.06e-01 NA NA NA -## sigma 7.40e+00 NA NA NA +## 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 1.97e-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 ## ## ## DTx values: @@ -339,20 +307,17 @@ <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="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> +<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></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 - -## 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="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -369,11 +334,11 @@ ## sigma 7.44786 NA NA NA ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.77e+01 NA NA NA -## k__iore_parent_sink 6.14e-05 NA NA NA -## N_parent 2.27e+00 NA NA NA -## sigma 3.52e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02 +## k__iore_parent_sink 6.14e-05 3.20e-02 2.12e-05 1.78e-04 +## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00 +## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00 ## ## $DFOP ## Estimate Pr(>t) Lower Upper @@ -401,20 +366,12 @@ <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="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></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 - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></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="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -424,25 +381,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.1933 NA NA NA -## k_parent_sink 0.0409 NA NA NA -## sigma 7.2429 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 88.1933 3.06e-12 79.9447 96.4419 +## k_parent_sink 0.0409 2.07e-07 0.0324 0.0516 +## sigma 7.2429 3.92e-05 4.4768 10.0090 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 NA NA NA -## k__iore_parent_sink 1.93e-05 NA NA NA -## N_parent 2.91e+00 NA NA NA -## sigma 2.35e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02 +## k__iore_parent_sink 1.93e-05 1.13e-01 3.49e-06 1.06e-04 +## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00 +## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 NA NA NA -## k1 1.38e-01 NA NA NA -## k2 6.02e-13 NA NA NA -## g 6.52e-01 NA NA NA -## sigma 7.88e-01 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.85e+01 2.54e-20 97.390 99.672 +## k1 1.38e-01 3.52e-05 0.131 0.146 +## k2 6.02e-13 5.00e-01 0.000 Inf +## g 6.52e-01 8.13e-06 0.642 0.661 +## sigma 7.88e-01 6.13e-02 0.481 1.095 ## ## ## DTx values: @@ -458,20 +415,17 @@ <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -481,25 +435,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 NA NA NA -## k_parent_sink 0.0389 NA NA NA -## sigma 1.5957 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 2.15e-19 93.178 96.2464 +## k_parent_sink 0.0389 4.47e-14 0.037 0.0408 +## sigma 1.5957 1.28e-04 0.932 2.2595 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 93.863 NA NA NA -## k__iore_parent_sink 0.127 NA NA NA -## N_parent 0.711 NA NA NA -## sigma 1.288 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 93.863 2.32e-18 92.4565 95.269 +## k__iore_parent_sink 0.127 1.85e-02 0.0504 0.321 +## N_parent 0.711 1.88e-05 0.4843 0.937 +## sigma 1.288 1.76e-04 0.7456 1.830 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 NA NA NA -## k1 0.0389 NA NA NA -## k2 0.0389 NA NA NA -## g 0.7742 NA NA NA -## sigma 1.5957 NA NA NA +## 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 NaN NA NA +## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## ## DTx values: @@ -515,20 +469,12 @@ <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="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></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 - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></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="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -538,25 +484,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 NA NA NA -## k_parent_sink 0.0495 NA NA NA -## sigma 8.0152 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 6.42e-11 91.9259 111.5371 +## k_parent_sink 0.0495 1.70e-07 0.0404 0.0607 +## sigma 8.0152 1.28e-04 4.6813 11.3491 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.86 NA NA NA -## k__iore_parent_sink 2.96 NA NA NA -## N_parent 0.00 NA NA NA -## sigma 4.90 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 96.86 3.32e-12 90.848 102.863 +## k__iore_parent_sink 2.96 7.91e-02 0.687 12.761 +## N_parent 0.00 5.00e-01 -0.372 0.372 +## sigma 4.90 1.77e-04 2.837 6.968 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 NA NA NA -## k1 0.0495 NA NA NA -## k2 0.0495 NA NA NA -## g 0.6634 NA NA NA -## sigma 8.0152 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 1.41e-09 91.6534 111.8097 +## k1 0.0495 6.42e-04 0.0301 0.0814 +## k2 0.0495 1.66e-02 0.0200 0.1225 +## g 0.6634 5.00e-01 0.0000 1.0000 +## sigma 8.0152 2.50e-04 4.5886 11.4418 ## ## ## DTx values: @@ -576,20 +522,12 @@ <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="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></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 - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></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="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -599,25 +537,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.15820 NA NA NA -## k_parent_sink 0.00321 NA NA NA -## sigma 6.43473 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 96.15820 4.83e-13 90.24934 1.02e+02 +## k_parent_sink 0.00321 4.71e-05 0.00222 4.64e-03 +## sigma 6.43473 1.28e-04 3.75822 9.11e+00 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 NA NA NA -## k__iore_parent_sink 3.11e-17 NA NA NA -## N_parent 8.36e+00 NA NA NA -## sigma 3.82e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.05e+02 NA 9.90e+01 1.10e+02 +## k__iore_parent_sink 3.11e-17 NA 1.35e-20 7.18e-14 +## N_parent 8.36e+00 NA 6.62e+00 1.01e+01 +## sigma 3.82e+00 NA 2.21e+00 5.44e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 NA NA NA -## k1 4.41e-02 NA NA NA -## k2 7.25e-13 NA NA NA -## g 3.22e-01 NA NA NA -## sigma 3.22e+00 NA NA NA +## 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 +## g 3.22e-01 1.45e-03 0.2814 0.3650 +## sigma 3.22e+00 3.52e-04 1.8410 4.5906 ## ## ## DTx values: @@ -638,20 +576,14 @@ <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="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></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 - -## 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="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb69"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb69-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -661,10 +593,10 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 NA NA NA -## k_parent_sink 0.124 NA NA NA -## sigma 7.048 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 8.75e-12 92.461 108.581 +## k_parent_sink 0.124 3.61e-08 0.104 0.148 +## sigma 7.048 1.28e-04 4.116 9.980 ## ## $IORE ## Estimate Pr(>t) Lower Upper @@ -674,12 +606,12 @@ ## sigma 3.965 NA NA NA ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 NA NA NA -## k1 0.124 NA NA NA -## k2 0.124 NA NA NA -## g 0.877 NA NA NA -## sigma 7.048 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 2.74e-10 92.2366 108.805 +## k1 0.124 5.74e-06 0.0958 0.161 +## k2 0.124 6.61e-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 ## ## ## DTx values: @@ -694,20 +626,20 @@ <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="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></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 - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb67"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb67-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -717,25 +649,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NA NA NA -## k_parent_sink 0.0589 NA NA NA -## sigma 3.4323 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.6840 0.00039 85.9388 109.4292 +## k_parent_sink 0.0589 0.00261 0.0431 0.0805 +## sigma 3.4323 0.04356 -1.2377 8.1023 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.523 NA NA NA -## k__iore_parent_sink 0.333 NA NA NA -## N_parent 0.568 NA NA NA -## sigma 1.953 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 95.523 0.0055 74.539157 116.51 +## k__iore_parent_sink 0.333 0.1433 0.000717 154.57 +## N_parent 0.568 0.0677 -0.989464 2.13 +## sigma 1.953 0.0975 -5.893100 9.80 ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NA NA NA -## k1 0.0589 NA NA NA -## k2 0.0589 NA NA NA -## g 0.6902 NA NA NA -## sigma 3.4323 NA NA NA +## parent_0 97.6840 NaN NaN NaN +## k1 0.0589 NaN NA NA +## k2 0.0589 NaN NA NA +## g 0.6902 NaN NA NA +## sigma 3.4323 NaN NaN NaN ## ## ## DTx values: @@ -750,20 +682,16 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb80"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb80-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -773,25 +701,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 NA NA NA -## k_parent_sink 0.00258 NA NA NA -## sigma 3.41172 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 5.99e-17 89.61936 95.85065 +## k_parent_sink 0.00258 2.42e-09 0.00223 0.00299 +## sigma 3.41172 7.07e-05 2.05455 4.76888 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 91.6016 NA NA NA -## k__iore_parent_sink 0.0396 NA NA NA -## N_parent 0.3541 NA NA NA -## sigma 3.0811 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 91.6016 6.34e-16 88.53086 94.672 +## k__iore_parent_sink 0.0396 2.36e-01 0.00207 0.759 +## N_parent 0.3541 1.46e-01 -0.35153 1.060 +## sigma 3.0811 9.64e-05 1.84296 4.319 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 NA NA NA -## k1 0.00258 NA NA NA -## k2 0.00258 NA NA NA -## g 0.00442 NA NA NA -## sigma 3.41172 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01 +## k1 0.00258 4.28e-01 1.70e-08 3.92e+02 +## k2 0.00258 3.69e-08 2.20e-03 3.03e-03 +## g 0.00442 5.00e-01 NA NA +## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00 ## ## ## DTx values: @@ -807,20 +735,16 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb95"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb95-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -830,25 +754,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 99.47124 NA NA NA -## k_parent_sink 0.00279 NA NA NA -## sigma 1.55616 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 99.47124 2.06e-30 98.42254 1.01e+02 +## k_parent_sink 0.00279 3.75e-15 0.00256 3.04e-03 +## sigma 1.55616 3.81e-06 1.03704 2.08e+00 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 NA NA NA -## k__iore_parent_sink 9.44e-08 NA NA NA -## N_parent 3.31e+00 NA NA NA -## sigma 1.20e+00 NA NA NA +## parent_0 1.00e+02 NA NaN NaN +## k__iore_parent_sink 9.44e-08 NA NaN NaN +## N_parent 3.31e+00 NA NaN NaN +## sigma 1.20e+00 NA 0.796 1.6 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 NA NA NA -## k1 9.53e-03 NA NA NA -## k2 7.29e-12 NA NA NA -## g 3.98e-01 NA NA NA -## sigma 1.17e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 +## k1 9.53e-03 1.20e-01 0.00638 0.0143 +## k2 7.29e-12 5.00e-01 0.00000 Inf +## g 3.98e-01 2.19e-01 0.30481 0.4998 +## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## ## ## DTx values: @@ -864,20 +788,17 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb98"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb98-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- +## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -887,25 +808,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 NA NA NA -## k_parent_sink 0.00952 NA NA NA -## sigma 4.18778 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.96751 2.00e-15 94.32049 101.615 +## k_parent_sink 0.00952 4.93e-09 0.00824 0.011 +## sigma 4.18778 1.28e-04 2.44588 5.930 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.874 NA NA NA -## k__iore_parent_sink 0.629 NA NA NA -## N_parent 0.000 NA NA NA -## sigma 3.105 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 95.874 2.94e-15 92.937 98.811 +## k__iore_parent_sink 0.629 2.11e-01 0.044 8.982 +## N_parent 0.000 5.00e-01 -0.642 0.642 +## sigma 3.105 1.78e-04 1.795 4.416 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96752 NA NA NA -## k1 0.00952 NA NA NA -## k2 0.00952 NA NA NA -## g 0.17247 NA NA NA -## sigma 4.18778 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.96752 2.85e-13 94.21914 101.7159 +## k1 0.00952 6.80e-02 0.00277 0.0327 +## k2 0.00952 3.82e-06 0.00902 0.0100 +## g 0.17247 NaN NA NA +## sigma 4.18778 2.50e-04 2.39747 5.9781 ## ## ## DTx values: @@ -916,20 +837,16 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb108"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb108-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -939,25 +856,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA NA NA -## k_parent_sink 4.86e-03 NA NA NA -## sigma 2.76e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02 +## k_parent_sink 4.86e-03 2.48e-10 0.00435 5.42e-03 +## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 99.83 NA NA NA -## k__iore_parent_sink 0.38 NA NA NA -## N_parent 0.00 NA NA NA -## sigma 2.21 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 99.83 1.81e-16 97.51349 102.14 +## k__iore_parent_sink 0.38 3.22e-01 0.00352 41.05 +## N_parent 0.00 5.00e-01 -1.07695 1.08 +## sigma 2.21 2.57e-04 1.23245 3.19 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA NA NA -## k1 4.86e-03 NA NA NA -## k2 4.86e-03 NA NA NA -## g 1.50e-01 NA NA NA -## sigma 2.76e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 NA 9.82e+01 1.04e+02 +## k1 4.86e-03 NA 6.75e-04 3.49e-02 +## k2 4.86e-03 NA 3.37e-03 6.99e-03 +## g 1.50e-01 NA NA NA +## sigma 2.76e+00 NA 1.58e+00 3.94e+00 ## ## ## DTx values: @@ -973,22 +890,14 @@ <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="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></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 - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></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="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb123-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -998,25 +907,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 71.953 NA NA NA -## k_parent_sink 0.159 NA NA NA -## sigma 11.302 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 71.953 2.33e-13 60.509 83.40 +## k_parent_sink 0.159 4.86e-05 0.102 0.25 +## sigma 11.302 1.25e-08 8.308 14.30 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 8.74e+01 NA NA NA -## k__iore_parent_sink 4.55e-04 NA NA NA -## N_parent 2.70e+00 NA NA NA -## sigma 8.29e+00 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972 +## k__iore_parent_sink 4.55e-04 2.16e-01 3.48e-05 0.00595 +## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046 +## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 88.5333 NA NA NA -## k1 18.5561 NA NA NA -## k2 0.0776 NA NA NA -## g 0.4733 NA NA NA -## sigma 7.1902 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 88.5333 7.40e-18 79.9836 97.083 +## k1 18.5561 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 ## ## ## DTx values: diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 2e83cea9..a250f005 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -198,67 +198,67 @@ ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.866 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.982 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 16.533 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 17.777 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.247 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.545 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 11.124 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 16.684 ## t5 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.887 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.868 ## t6 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 1.317 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.66 ## t7 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.177 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.496 ## t8 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.991 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.919 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.175 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 11.683 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.776 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.344 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.658</code></pre> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.752</code></pre> <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> </div> </div> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index ad7716c1..54d3148f 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -163,14 +163,14 @@ ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 1.325 1.000 1.325 0 -## 1 deSolve, not compiled 3 11.175 8.434 11.170 0 -## 2 Eigenvalue based 3 1.799 1.358 1.798 0 +## 3 deSolve, compiled 3 3.067 1.000 3.065 0 +## 1 deSolve, not compiled 3 28.135 9.173 28.122 0 +## 2 Eigenvalue based 3 4.306 1.404 4.303 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 ## 2 0 0</code></pre> -<p>We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> +<p>We see that using the compiled model is by a factor of around 9 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> @@ -214,8 +214,8 @@ ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 2.322 1.000 2.320 0 -## 1 deSolve, not compiled 3 25.232 10.866 25.208 0 +## 2 deSolve, compiled 3 4.827 1.000 4.825 0 +## 1 deSolve, not compiled 3 52.646 10.907 52.622 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> |
