Static documentation rebuilt by pkgdown

1 files changed, 35 insertions, 46 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index ed41e555..341c7e7d 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -30,7 +30,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
       </span>
     </div>
 
@@ -88,7 +88,7 @@
       <h1>Example evaluation of FOCUS Example Dataset D</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-07-04</h4>
+            <h4 class="date">2019-07-05</h4>
       
       
       <div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -156,20 +156,18 @@
 ##             "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="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>
+<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>
 <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="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>
+<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>
 <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="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:    0.9.49.5 
+<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 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu Jul  4 08:04:23 2019 
-## Date of summary: Thu Jul  4 08:04:24 2019 
+## Date of fit:     Fri Jul  5 15:52:50 2019 
+## Date of summary: Fri Jul  5 15:52:50 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,19 +175,16 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 0.982 s
+## Fitted with method Port using 153 model solutions performed in 0.63 s
 ## 
-## Error model: Constant variance 
-## 
-## Error model algorithm: d_3 
+## Weighting: none
 ## 
 ## Starting values for parameters to be optimised:
-##                    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
+##                  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
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##                        value lower upper
@@ -197,7 +192,6 @@
 ## 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
@@ -205,38 +199,31 @@
 ## 
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##                   Estimate Std. Error  Lower   Upper
-## 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
+## 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
 ## 
 ## Parameter correlation:
-##                     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
+##                   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
 ## 
 ## 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  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
+## 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
 ## 
-## FOCUS Chi2 error levels in percent:
+## Chi2 error levels in percent:
 ##          err.min n.optim df
 ## All data   6.398       4 15
 ## parent     6.827       3  6
@@ -273,6 +260,8 @@
 ##    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
@@ -287,8 +276,8 @@
 ##    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  36.44703  3.643e+00
-##    75       m1    33.85  36.44703 -2.597e+00
+##    75       m1    40.09  36.44704  3.643e+00
+##    75       m1    33.85  36.44704 -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