Static documentation rebuilt by pkgdown

Use lazy = TRUE in the pd target for generating pkgdown documentation

8 files changed, 486 insertions, 24 deletions

diff --git a/docs/reference/index.html b/docs/reference/index.html
index b86df636..a8b326d7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -311,7 +311,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code> </p>
+          <p><code><a href="synthetic_data_for_UBA_2014.html">synthetic_data_for_UBA_2014</a></code> </p>
         </td>
         <td><p>Synthetic datasets for one parent compound with two metabolites</p></td>
       </tr><tr>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index dc052f2a..0767d2f8 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -408,15 +408,15 @@ Per default, parameters in the kinetic models are internally transformed in
 <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.6 
 #&gt; R version used for fitting:       3.6.1 
-#&gt; Date of fit:     Wed Sep 18 18:22:06 2019 
-#&gt; Date of summary: Wed Sep 18 18:22:06 2019 
+#&gt; Date of fit:     Thu Sep 19 09:50:54 2019 
+#&gt; Date of summary: Thu Sep 19 09:50:54 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted using 222 model solutions performed in 0.459 s
+#&gt; Fitted using 222 model solutions performed in 0.458 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
@@ -490,7 +490,7 @@ Per default, parameters in the kinetic models are internally transformed in
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
                            <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       1.494       0.000       1.496 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt;       1.479       0.002       1.482 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_m1     m1_sink 
 #&gt;    0.485524    0.514476    1.000000 
 #&gt; 
@@ -563,7 +563,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; Sum of squared residuals at call 126: 371.2134
 #&gt; Sum of squared residuals at call 135: 371.2134
 #&gt; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       1.056       0.000       1.057 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
+#&gt;       1.053       0.000       1.054 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_m1     m1_sink 
 #&gt;    0.485524    0.514476    1.000000 
 #&gt; 
@@ -599,8 +599,8 @@ Per default, parameters in the kinetic models are internally transformed in
 <span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
                       <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.6 
 #&gt; R version used for fitting:       3.6.1 
-#&gt; Date of fit:     Wed Sep 18 18:22:22 2019 
-#&gt; Date of summary: Wed Sep 18 18:22:22 2019 
+#&gt; Date of fit:     Thu Sep 19 09:51:10 2019 
+#&gt; Date of summary: Thu Sep 19 09:51:10 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -608,7 +608,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 421 model solutions performed in 1.15 s
+#&gt; Fitted using 421 model solutions performed in 1.138 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
@@ -718,8 +718,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt;   120       m1    25.15  28.78984 -3.640e+00
 #&gt;   120       m1    33.31  28.78984  4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.6 
 #&gt; R version used for fitting:       3.6.1 
-#&gt; Date of fit:     Wed Sep 18 18:22:24 2019 
-#&gt; Date of summary: Wed Sep 18 18:22:24 2019 
+#&gt; Date of fit:     Thu Sep 19 09:51:12 2019 
+#&gt; Date of summary: Thu Sep 19 09:51:12 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -727,7 +727,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 979 model solutions performed in 2.553 s
+#&gt; Fitted using 979 model solutions performed in 2.565 s
 #&gt; 
 #&gt; Error model: Variance unique to each observed variable 
 #&gt; 
@@ -850,8 +850,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt;   120       m1    25.15  28.80429 -3.654e+00
 #&gt;   120       m1    33.31  28.80429  4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.6 
 #&gt; R version used for fitting:       3.6.1 
-#&gt; Date of fit:     Wed Sep 18 18:22:34 2019 
-#&gt; Date of summary: Wed Sep 18 18:22:34 2019 
+#&gt; Date of fit:     Thu Sep 19 09:51:22 2019 
+#&gt; Date of summary: Thu Sep 19 09:51:22 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -859,7 +859,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 2289 model solutions performed in 9.369 s
+#&gt; Fitted using 2289 model solutions performed in 9.24 s
 #&gt; 
 #&gt; Error model: Two-component variance function 
 #&gt; 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index a5cdd04d..f592af1c 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -239,7 +239,7 @@ For the definition of model types and their parameters, the equations given
 <span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
   <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt;  /usr/lib/R/bin/R CMD SHLIB file310b6c1fede0.c 2&gt; file310b6c1fede0.c.err.txt 
+#&gt;  /usr/lib/R/bin/R CMD SHLIB file663b71dc323f.c 2&gt; file663b71dc323f.c.err.txt 
 #&gt; Program source:
 #&gt;   1: #include &lt;R.h&gt;
 #&gt;   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 97d3ca3a..5faff3c7 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -332,17 +332,17 @@
                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
                 <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
 #&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.003       0.000       0.004 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
+#&gt;       0.004       0.000       0.004 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
     <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
                 <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
 #&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.001       0.000       0.002 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
+#&gt;       0.002       0.000       0.002 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
     <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
                 <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
 #&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.021       0.000       0.022 </div><div class='input'>
+#&gt;       0.022       0.000       0.021 </div><div class='input'>
   <span class='co'># \dontrun{</span>
     <span class='co'># Predict from a fitted model</span>
     <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 81ebde7c..0f384062 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -199,8 +199,8 @@
 <span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
 
 <span class='no'>time_default</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.013       0.039       5.128 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;      18.942       0.000      18.951 </div><div class='input'>
+#&gt;       0.016       0.029       4.960 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt;        User      System verstrichen 
+#&gt;      19.084       0.004      19.099 </div><div class='input'>
 <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
 #&gt;   parent_M1 parent_sink       M1_M2     M1_sink 
 #&gt;   0.7340481   0.2659519   0.7505684   0.2494316 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index c5d58911..73410181 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -215,15 +215,15 @@
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.6 
 #&gt; R version used for fitting:       3.6.1 
-#&gt; Date of fit:     Wed Sep 18 18:23:52 2019 
-#&gt; Date of summary: Wed Sep 18 18:23:52 2019 
+#&gt; Date of fit:     Thu Sep 19 09:52:40 2019 
+#&gt; Date of summary: Thu Sep 19 09:52:40 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent_sink * parent
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted using 131 model solutions performed in 0.268 s
+#&gt; Fitted using 131 model solutions performed in 0.27 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png
new file mode 100644
index 00000000..9d8c0931
--- /dev/null
+++ b/docs/reference/synthetic_data_for_UBA_2014-1.png
diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html
new file mode 100644
index 00000000..2c4480d9
--- /dev/null
+++ b/docs/reference/synthetic_data_for_UBA_2014.html
@@ -0,0 +1,462 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title>
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
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+<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" />
+
+<meta property="og:description" content="The 12 datasets were generated using four different models and three different
+ variance components. The four models are either the SFO or the DFOP model with either
+ two sequential or two parallel metabolites.
+Variance component 'a' is based on a normal distribution with standard deviation of 3,
+ Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7.
+ Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the
+ minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07
+ for the increase of the standard deviation with y. Note that this is a simplified version
+ of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the
+ measured values approximates lognormal distribution for high values, whereas we are using
+ normally distributed error components all along.
+Initial concentrations for metabolites and all values where adding the variance component resulted
+ in a value below the assumed limit of detection of 0.1 were set to NA.
+As an example, the first dataset has the title SFO_lin_a and is based on the SFO model
+ with two sequential metabolites (linear pathway), with added variance component 'a'.
+Compare also the code in the example section to see the degradation models." />
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+    <div class="page-header">
+    <h1>Synthetic datasets for one parent compound with two metabolites</h1>
+    
+    <div class="hidden name"><code>synthetic_data_for_UBA_2014.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    
+    <p>The 12 datasets were generated using four different models and three different
+ variance components. The four models are either the SFO or the DFOP model with either
+ two sequential or two parallel metabolites.</p>
+<p>Variance component 'a' is based on a normal distribution with standard deviation of 3,
+ Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7.
+ Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the
+ minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07
+ for the increase of the standard deviation with y. Note that this is a simplified version
+ of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the
+ measured values approximates lognormal distribution for high values, whereas we are using
+ normally distributed error components all along.</p>
+<p>Initial concentrations for metabolites and all values where adding the variance component resulted
+ in a value below the assumed limit of detection of 0.1 were set to <code>NA</code>.</p>
+<p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model
+ with two sequential metabolites (linear pathway), with added variance component 'a'.</p>
+<p>Compare also the code in the example section to see the degradation models.</p>
+    
+    </div>
+
+    <pre class="usage"><span class='no'>synthetic_data_for_UBA_2014</span></pre>
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>,
+  each containing, among others, the following components</p><dl class='dl-horizontal'>
+    <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd>
+    <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
+  
+</dl>
+
+    
+    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+    <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
+  zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p>
+<p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
+  measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='co'># The data have been generated using the following kinetic models</span>
+<span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
+                           <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
+                           <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+
+<span class='no'>m_synth_SFO_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
+                                         <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
+                           <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
+                           <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='no'>m_synth_DFOP_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
+                            <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
+                            <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
+                                          <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
+                            <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
+                            <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='co'># The model predictions without intentional error were generated as follows</span>
+<span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
+
+<span class='no'>d_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_SFO_lin</span>,
+                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.8</span>,
+                                 <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>, <span class='kw'>f_M1_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
+                                 <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
+                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>),
+                               <span class='no'>sampling_times</span>)
+
+<span class='no'>d_synth_DFOP_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_DFOP_lin</span>,
+                                <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
+                                  <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>,
+                                  <span class='kw'>f_M1_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
+                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>),
+                                 <span class='no'>sampling_times</span>)
+
+<span class='no'>d_synth_SFO_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_SFO_par</span>,
+                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.2</span>,
+                                 <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.8</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>,
+                                 <span class='kw'>f_parent_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
+                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>),
+                                 <span class='no'>sampling_times</span>)
+
+<span class='no'>d_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_DFOP_par</span>,
+                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
+                                 <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.6</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.04</span>,
+                                 <span class='kw'>f_parent_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.4</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>),
+                                 <span class='no'>sampling_times</span>)
+
+<span class='co'># Construct names for datasets with errors</span>
+<span class='no'>d_synth_names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"d_synth_"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO_lin"</span>, <span class='st'>"SFO_par"</span>,
+                                     <span class='st'>"DFOP_lin"</span>, <span class='st'>"DFOP_par"</span>))
+
+<span class='co'># Original function used or adding errors. The add_err function now published</span>
+<span class='co'># with this package is a slightly generalised version where the names of</span>
+<span class='co'># secondary compartments that should have an initial value of zero (M1 and M2</span>
+<span class='co'># in this case) are not hardcoded any more.</span>
+<span class='co'># add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)</span>
+<span class='co'># {</span>
+<span class='co'>#   set.seed(seed)</span>
+<span class='co'>#   d_long = mkin_wide_to_long(d, time = "time")</span>
+<span class='co'>#   d_rep = data.frame(lapply(d_long, rep, each = 2))</span>
+<span class='co'>#   d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span>
+<span class='co'>#</span>
+<span class='co'>#   d_rep[d_rep$time == 0 &amp; match(d_rep$name, c("M1", "M2"), "value"] &lt;- 0</span>
+<span class='co'>#   d_NA &lt;- transform(d_rep, value = ifelse(value &lt; LOD, NA, value))</span>
+<span class='co'>#   d_NA$value &lt;- round(d_NA$value, 1)</span>
+<span class='co'>#   return(d_NA)</span>
+<span class='co'># }</span>
+
+<span class='co'># The following is the simplified version of the two-component model of Rocke</span>
+<span class='co'># and Lorenzato (1995)</span>
+<span class='no'>sdfunc_twocomp</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>value</span>, <span class='no'>sd_low</span>, <span class='no'>rsd_high</span>) {
+  <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span>(<span class='no'>sd_low</span>^<span class='fl'>2</span> + <span class='no'>value</span>^<span class='fl'>2</span> * <span class='no'>rsd_high</span>^<span class='fl'>2</span>)
+}
+
+<span class='co'># Add the errors.</span>
+<span class='kw'>for</span> (<span class='no'>d_synth_name</span> <span class='kw'>in</span> <span class='no'>d_synth_names</span>)
+{
+  <span class='no'>d_synth</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/get.html'>get</a></span>(<span class='no'>d_synth_name</span>)
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_a"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>3</span>))
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_b"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>7</span>))
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_c"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>,
+                           <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fu'>sdfunc_twocomp</span>(<span class='no'>value</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>)))
+
+}
+
+<span class='no'>d_synth_err_names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(
+  <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='no'>d_synth_names</span>, <span class='kw'>each</span> <span class='kw'>=</span> <span class='fl'>3</span>), <span class='no'>letters</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"_"</span>)
+)
+
+<span class='co'># This is just one example of an evaluation using the kinetic model used for</span>
+<span class='co'># the generation of the data</span>
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>,
+               <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.6 
+#&gt; R version used for fitting:       3.6.1 
+#&gt; Date of fit:     Thu Sep 19 12:43:02 2019 
+#&gt; Date of summary: Thu Sep 19 12:43:02 2019 
+#&gt; 
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
+#&gt; d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2
+#&gt; 
+#&gt; Model predictions using solution type deSolve 
+#&gt; 
+#&gt; Fitted using 847 model solutions performed in 2.51 s
+#&gt; 
+#&gt; Error model: Constant variance 
+#&gt; 
+#&gt; Error model algorithm: OLS 
+#&gt; 
+#&gt; Starting values for parameters to be optimised:
+#&gt;                     value   type
+#&gt; parent_0       101.350000  state
+#&gt; k_parent         0.100000 deparm
+#&gt; k_M1             0.100100 deparm
+#&gt; k_M2             0.100200 deparm
+#&gt; f_parent_to_M1   0.500000 deparm
+#&gt; f_M1_to_M2       0.500000 deparm
+#&gt; sigma            2.273126  error
+#&gt; 
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt;                     value lower upper
+#&gt; parent_0       101.350000  -Inf   Inf
+#&gt; log_k_parent    -2.302585  -Inf   Inf
+#&gt; log_k_M1        -2.301586  -Inf   Inf
+#&gt; log_k_M2        -2.300587  -Inf   Inf
+#&gt; f_parent_ilr_1   0.000000  -Inf   Inf
+#&gt; f_M1_ilr_1       0.000000  -Inf   Inf
+#&gt; sigma            2.273126     0   Inf
+#&gt; 
+#&gt; Fixed parameter values:
+#&gt;      value  type
+#&gt; M1_0     0 state
+#&gt; M2_0     0 state
+#&gt; 
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt;                Estimate Std. Error   Lower    Upper
+#&gt; parent_0       102.1000    1.57000 98.8600 105.3000
+#&gt; log_k_parent    -0.3020    0.03885 -0.3812  -0.2229
+#&gt; log_k_M1        -1.2070    0.07123 -1.3520  -1.0620
+#&gt; log_k_M2        -3.9010    0.06571 -4.0350  -3.7670
+#&gt; f_parent_ilr_1   0.8492    0.16640  0.5103   1.1880
+#&gt; f_M1_ilr_1       0.6780    0.17600  0.3196   1.0360
+#&gt; sigma            2.2730    0.25740  1.7490   2.7970
+#&gt; 
+#&gt; Parameter correlation:
+#&gt;                  parent_0 log_k_parent   log_k_M1   log_k_M2 f_parent_ilr_1
+#&gt; parent_0        1.000e+00    3.933e-01 -1.605e-01  2.819e-02     -4.624e-01
+#&gt; log_k_parent    3.933e-01    1.000e+00 -4.082e-01  7.166e-02     -5.682e-01
+#&gt; log_k_M1       -1.605e-01   -4.082e-01  1.000e+00 -3.929e-01      7.478e-01
+#&gt; log_k_M2        2.819e-02    7.166e-02 -3.929e-01  1.000e+00     -2.658e-01
+#&gt; f_parent_ilr_1 -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01      1.000e+00
+#&gt; f_M1_ilr_1      1.614e-01    4.102e-01 -8.109e-01  5.419e-01     -8.605e-01
+#&gt; sigma          -3.704e-09   -1.104e-08  5.922e-08 -3.673e-08      5.867e-08
+#&gt;                f_M1_ilr_1      sigma
+#&gt; parent_0        1.614e-01 -3.704e-09
+#&gt; log_k_parent    4.102e-01 -1.104e-08
+#&gt; log_k_M1       -8.109e-01  5.922e-08
+#&gt; log_k_M2        5.419e-01 -3.673e-08
+#&gt; f_parent_ilr_1 -8.605e-01  5.867e-08
+#&gt; f_M1_ilr_1      1.000e+00 -8.075e-08
+#&gt; sigma          -8.075e-08  1.000e+00
+#&gt; 
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt;                 Estimate t value    Pr(&gt;t)    Lower     Upper
+#&gt; parent_0       102.10000  65.000 7.281e-36 98.86000 105.30000
+#&gt; k_parent         0.73930  25.740 2.948e-23  0.68310   0.80020
+#&gt; k_M1             0.29920  14.040 1.577e-15  0.25880   0.34590
+#&gt; k_M2             0.02023  15.220 1.653e-16  0.01769   0.02312
+#&gt; f_parent_to_M1   0.76870  18.370 7.295e-19  0.67300   0.84290
+#&gt; f_M1_to_M2       0.72290  14.500 6.418e-16  0.61110   0.81240
+#&gt; sigma            2.27300   8.832 2.161e-10  1.74900   2.79700
+#&gt; 
+#&gt; FOCUS Chi2 error levels in percent:
+#&gt;          err.min n.optim df
+#&gt; All data   8.454       6 17
+#&gt; parent     8.660       2  6
+#&gt; M1        10.583       2  5
+#&gt; M2         3.586       2  6
+#&gt; 
+#&gt; Resulting formation fractions:
+#&gt;                 ff
+#&gt; parent_M1   0.7687
+#&gt; parent_sink 0.2313
+#&gt; M1_M2       0.7229
+#&gt; M1_sink     0.2771
+#&gt; 
+#&gt; Estimated disappearance times:
+#&gt;           DT50    DT90
+#&gt; parent  0.9376   3.114
+#&gt; M1      2.3170   7.697
+#&gt; M2     34.2689 113.839
+#&gt; 
+#&gt; Data:
+#&gt;  time variable observed  predicted residual
+#&gt;     0   parent    101.5  1.021e+02 -0.56248
+#&gt;     0   parent    101.2  1.021e+02 -0.86248
+#&gt;     1   parent     53.9  4.873e+01  5.17118
+#&gt;     1   parent     47.5  4.873e+01 -1.22882
+#&gt;     3   parent     10.4  1.111e+01 -0.70773
+#&gt;     3   parent      7.6  1.111e+01 -3.50773
+#&gt;     7   parent      1.1  5.772e-01  0.52283
+#&gt;     7   parent      0.3  5.772e-01 -0.27717
+#&gt;    14   parent      3.5  3.264e-03  3.49674
+#&gt;    28   parent      3.2  1.045e-07  3.20000
+#&gt;    90   parent      0.6 -1.875e-11  0.60000
+#&gt;   120   parent      3.5 -2.805e-11  3.50000
+#&gt;     1       M1     36.4  3.479e+01  1.61088
+#&gt;     1       M1     37.4  3.479e+01  2.61088
+#&gt;     3       M1     34.3  3.937e+01 -5.07027
+#&gt;     3       M1     39.8  3.937e+01  0.42973
+#&gt;     7       M1     15.1  1.549e+01 -0.38715
+#&gt;     7       M1     17.8  1.549e+01  2.31285
+#&gt;    14       M1      5.8  1.995e+00  3.80469
+#&gt;    14       M1      1.2  1.995e+00 -0.79531
+#&gt;    60       M1      0.5  2.111e-06  0.50000
+#&gt;    90       M1      3.2  2.913e-10  3.20000
+#&gt;   120       M1      1.5  3.625e-11  1.50000
+#&gt;   120       M1      0.6  3.625e-11  0.60000
+#&gt;     1       M2      4.8  4.455e+00  0.34517
+#&gt;     3       M2     20.9  2.153e+01 -0.62527
+#&gt;     3       M2     19.3  2.153e+01 -2.22527
+#&gt;     7       M2     42.0  4.192e+01  0.07941
+#&gt;     7       M2     43.1  4.192e+01  1.17941
+#&gt;    14       M2     49.4  4.557e+01  3.83353
+#&gt;    14       M2     44.3  4.557e+01 -1.26647
+#&gt;    28       M2     34.6  3.547e+01 -0.87275
+#&gt;    28       M2     33.0  3.547e+01 -2.47275
+#&gt;    60       M2     18.8  1.858e+01  0.21837
+#&gt;    60       M2     17.6  1.858e+01 -0.98163
+#&gt;    90       M2     10.6  1.013e+01  0.47130
+#&gt;    90       M2     10.8  1.013e+01  0.67130
+#&gt;   120       M2      9.8  5.521e+00  4.27893
+#&gt;   120       M2      3.3  5.521e+00 -2.22107</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      
+      <li><a href="#format">Format</a></li>
+
+      <li><a href="#source">Source</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
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+
+  </body>
+</html>
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