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@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-07-05</h4>
+ <h4 class="date">2019-07-09</h4>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -156,18 +156,20 @@
## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre>
<p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">fit &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
+## value of zero were removed from the data</code></pre>
<p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</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"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div>
<p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p>
<p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p>
-<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</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="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div>
<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
-<div class="sourceCode" id="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/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
-<pre><code>## mkin version used for fitting: 0.9.48.1
+<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/summary">summary</a></span>(fit)</a></code></pre></div>
+<pre><code>## mkin version used for fitting: 0.9.49.6
## R version used for fitting: 3.6.0
-## Date of fit: Fri Jul 5 15:52:50 2019
-## Date of summary: Fri Jul 5 15:52:50 2019
+## Date of fit: Tue Jul 9 09:00:18 2019
+## Date of summary: Tue Jul 9 09:00:18 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -175,16 +177,19 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.63 s
+## Fitted using 389 model solutions performed in 1.003 s
##
-## Weighting: none
+## Error model: Constant variance
+##
+## Error model algorithm: OLS
##
## Starting values for parameters to be optimised:
-## value type
-## parent_0 100.7500 state
-## k_parent_sink 0.1000 deparm
-## k_parent_m1 0.1001 deparm
-## k_m1_sink 0.1002 deparm
+## value type
+## parent_0 100.750000 state
+## k_parent_sink 0.100000 deparm
+## k_parent_m1 0.100100 deparm
+## k_m1_sink 0.100200 deparm
+## sigma 3.125504 error
##
## Starting values for the transformed parameters actually optimised:
## value lower upper
@@ -192,6 +197,7 @@
## log_k_parent_sink -2.302585 -Inf Inf
## log_k_parent_m1 -2.301586 -Inf Inf
## log_k_m1_sink -2.300587 -Inf Inf
+## sigma 3.125504 0 Inf
##
## Fixed parameter values:
## value type
@@ -199,31 +205,38 @@
##
## Optimised, transformed parameters with symmetric confidence intervals:
## Estimate Std. Error Lower Upper
-## parent_0 99.600 1.61400 96.330 102.900
-## log_k_parent_sink -3.038 0.07826 -3.197 -2.879
-## log_k_parent_m1 -2.980 0.04124 -3.064 -2.897
-## log_k_m1_sink -5.248 0.13610 -5.523 -4.972
+## parent_0 99.600 1.57000 96.400 102.800
+## log_k_parent_sink -3.038 0.07626 -3.193 -2.883
+## log_k_parent_m1 -2.980 0.04033 -3.062 -2.898
+## log_k_m1_sink -5.248 0.13320 -5.518 -4.977
+## sigma 3.126 0.35850 2.396 3.855
##
## Parameter correlation:
-## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
-## parent_0 1.00000 0.6075 -0.06625 -0.1701
-## log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
-## log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
-## log_k_m1_sink -0.17006 -0.6253 0.47164 1.0000
-##
-## Residual standard error: 3.211 on 36 degrees of freedom
+## parent_0 log_k_parent_sink log_k_parent_m1
+## parent_0 1.000e+00 6.067e-01 -6.372e-02
+## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02
+## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00
+## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01
+## sigma 1.164e-09 -8.908e-10 1.652e-08
+## log_k_m1_sink sigma
+## parent_0 -1.688e-01 1.164e-09
+## log_k_parent_sink -6.252e-01 -8.908e-10
+## log_k_parent_m1 4.731e-01 1.652e-08
+## log_k_m1_sink 1.000e+00 -1.340e-10
+## sigma -1.340e-10 1.000e+00
##
## Backtransformed parameters:
## Confidence intervals for internally transformed parameters are asymmetric.
## t-test (unrealistically) based on the assumption of normal distribution
## for estimators of untransformed parameters.
## Estimate t value Pr(&gt;t) Lower Upper
-## parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
-## k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02
-## k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02
-## k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03
+## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
+## k_parent_sink 0.047920 13.110 6.126e-15 0.041030 5.596e-02
+## k_parent_m1 0.050780 24.800 3.269e-23 0.046780 5.512e-02
+## k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03
+## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
##
-## Chi2 error levels in percent:
+## FOCUS Chi2 error levels in percent:
## err.min n.optim df
## All data 6.398 4 15
## parent 6.827 3 6
@@ -260,8 +273,6 @@
## 50 parent 0.63 0.71624 -8.624e-02
## 75 parent 0.05 0.06074 -1.074e-02
## 75 parent 0.06 0.06074 -7.382e-04
-## 0 m1 0.00 0.00000 0.000e+00
-## 0 m1 0.00 0.00000 0.000e+00
## 1 m1 4.84 4.80296 3.704e-02
## 1 m1 5.64 4.80296 8.370e-01
## 3 m1 12.91 13.02400 -1.140e-01
@@ -276,8 +287,8 @@
## 35 m1 37.95 43.31312 -5.363e+00
## 50 m1 41.19 41.21831 -2.831e-02
## 50 m1 40.01 41.21831 -1.208e+00
-## 75 m1 40.09 36.44704 3.643e+00
-## 75 m1 33.85 36.44704 -2.597e+00
+## 75 m1 40.09 36.44703 3.643e+00
+## 75 m1 33.85 36.44703 -2.597e+00
## 100 m1 31.04 31.98163 -9.416e-01
## 100 m1 33.13 31.98163 1.148e+00
## 120 m1 25.15 28.78984 -3.640e+00

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