Update pkgdown docs

1 files changed, 124 insertions, 77 deletions

diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index 16df54af..d186d785 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ have been obtained by fitting the same model to a list of datasets." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -141,7 +141,7 @@ have been obtained by fitting the same model to a list of datasets." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Create an nlme model for an mmkin row object</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
     <div class="hidden name"><code>nlme.mmkin.Rd</code></div>
     </div>
 
@@ -152,28 +152,28 @@ have been obtained by fitting the same model to a list of datasets.</p>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mmkin</span>
-<span class='fu'>nlme</span>(
-  <span class='no'>model</span>,
-  <span class='kw'>data</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span>()),
-  <span class='no'>fixed</span>,
-  <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>fixed</span>,
-  <span class='no'>groups</span>,
-  <span class='no'>start</span>,
-  <span class='kw'>correlation</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>weights</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='no'>subset</span>,
-  <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"ML"</span>, <span class='st'>"REML"</span>),
-  <span class='kw'>na.action</span> <span class='kw'>=</span> <span class='no'>na.fail</span>,
-  <span class='no'>naPattern</span>,
-  <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(),
-  <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
-)
+<span class='fu'>nlme</span><span class='op'>(</span>
+  <span class='va'>model</span>,
+  data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>,
+  <span class='va'>fixed</span>,
+  random <span class='op'>=</span> <span class='va'>fixed</span>,
+  <span class='va'>groups</span>,
+  <span class='va'>start</span>,
+  correlation <span class='op'>=</span> <span class='cn'>NULL</span>,
+  weights <span class='op'>=</span> <span class='cn'>NULL</span>,
+  <span class='va'>subset</span>,
+  method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"ML"</span>, <span class='st'>"REML"</span><span class='op'>)</span>,
+  na.action <span class='op'>=</span> <span class='va'>na.fail</span>,
+  <span class='va'>naPattern</span>,
+  control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='op'>)</span>,
+  verbose <span class='op'>=</span> <span class='cn'>FALSE</span>
+<span class='op'>)</span>
 
 <span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
 
 <span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
+<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -257,38 +257,43 @@ parameters taken from the mmkin object are used</p></td>
 with additional elements</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p><code><a href='nlme.html'>nlme_function</a></code></p></div>
+    <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function</a></code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
- <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>))
-<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0195</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.011</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>)
-<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f</span><span class='kw'>[[</span><span class='fl'>1</span>]])</div><div class='output co'>#&gt; $distimes
-#&gt;            DT50     DT90
-#&gt; parent 11.96183 39.73634
-#&gt; </div><div class='input'><span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt;   Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent) 
+    <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
+ <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span><span class='op'>)</span>
+<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0195</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.00985</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.011</span></div><div class='input'><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
+<span class='va'>f_nlme_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+<span class='va'>f_nlme_dfop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;             df      AIC
+#&gt; f_nlme_sfo   5 625.0539
+#&gt; f_nlme_dfop  9 495.1270</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
+#&gt;   Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k1,      log_k2, g_ilr) 
 #&gt;   Data: "Not shown" 
-#&gt;   Log-likelihood: -307.5269
-#&gt;   Fixed: list(parent_0 ~ 1, log_k_parent ~ 1) 
-#&gt;     parent_0 log_k_parent 
-#&gt;    85.541149    -3.229596 
+#&gt;   Log-likelihood: -238.5635
+#&gt;   Fixed: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) 
+#&gt;    parent_0      log_k1      log_k2       g_ilr 
+#&gt; 94.17015133 -1.80015306 -4.14738870  0.02290935 
 #&gt; 
 #&gt; Random effects:
-#&gt;  Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
+#&gt;  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
 #&gt;  Level: ds
 #&gt;  Structure: Diagonal
-#&gt;         parent_0 log_k_parent Residual
-#&gt; StdDev:  1.30857     1.288591 6.304906
+#&gt;         parent_0    log_k1  log_k2     g_ilr Residual
+#&gt; StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364
 #&gt; 
 #&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#&gt; $distimes
-#&gt;            DT50     DT90
-#&gt; parent 17.51545 58.18505
+#&gt; Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $distimes
+#&gt;            DT50     DT90 DT50back  DT50_k1  DT50_k2
+#&gt; parent 10.79857 100.7937 30.34193 4.193938 43.85443
 #&gt; </div><div class='input'><span class='co'># \dontrun{</span>
-  <span class='no'>f_nlme_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))
-  <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
+  <span class='va'>f_nlme_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nlme_2</span>, random <span class='op'>=</span> <span class='va'>parent_0</span> <span class='op'>~</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
 #&gt;   Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent) 
 #&gt;   Data: "Not shown" 
 #&gt;   Log-likelihood: -404.3729
@@ -302,34 +307,37 @@ with additional elements</p>
 #&gt; StdDev: 0.002416792 21.63027
 #&gt; 
 #&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </div><div class='input'>  <span class='co'># Test on some real data</span>
-  <span class='no'>ds_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
-   <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)])
-  <span class='no'>m_sfo_sfo</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'>"A1"</span>),
-    <span class='kw'>A1</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'>"min"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='no'>m_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'>"A1"</span>),
-    <span class='kw'>A1</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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='no'>m_fomc_sfo</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'>"FOMC"</span>, <span class='st'>"A1"</span>),
-    <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='no'>m_dfop_sfo</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'>"DFOP"</span>, <span class='st'>"A1"</span>),
-    <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-
-  <span class='no'>f_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_sfo_sfo</span>,
-   <span class='st'>"SFO-SFO-ff"</span> <span class='kw'>=</span> <span class='no'>m_sfo_sfo_ff</span>,
-   <span class='st'>"FOMC-SFO"</span> <span class='kw'>=</span> <span class='no'>m_fomc_sfo</span>,
-   <span class='st'>"DFOP-SFO"</span> <span class='kw'>=</span> <span class='no'>m_dfop_sfo</span>),
-    <span class='no'>ds_2</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/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>]) <span class='co'># Separate fits for datasets 3 and 4</span></div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='no'>f_nlme_sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ])
+#&gt; Number of Groups: 5 </div><div class='input'>  <span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
+   <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
+  <span class='va'>m_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
+    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  <span class='va'>m_sfo_sfo_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
+    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  <span class='va'>m_fomc_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
+    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  <span class='va'>m_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
+    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+
+  <span class='va'>f_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
+   <span class='st'>"SFO-SFO-ff"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo_ff</span>,
+   <span class='st'>"FOMC-SFO"</span> <span class='op'>=</span> <span class='va'>m_fomc_sfo</span>,
+   <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
+    <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Separate fits for datasets 3 and 4</span>
+</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='va'>f_nlme_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
   <span class='co'># plot(f_nlme_sfo_sfo) # not feasible with pkgdown figures</span>
-  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_sfo_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>) <span class='co'># Global mixed model: Fits for datasets 3 and 4</span></div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span> <span class='co'># Global mixed model: Fits for datasets 3 and 4</span>
+</div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
   <span class='co'># With formation fractions</span>
-  <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO-ff"</span>, ])
-  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_sfo_sfo_ff</span>, <span class='fl'>3</span>:<span class='fl'>4</span>) <span class='co'># chi2 different due to different df attribution</span></div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='va'>f_nlme_sfo_sfo_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO-ff"</span>, <span class='op'>]</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_ff</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span> <span class='co'># chi2 different due to different df attribution</span>
+</div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
   <span class='co'># For more parameters, we need to increase pnlsMaxIter and the tolerance</span>
   <span class='co'># to get convergence</span>
-  <span class='no'>f_nlme_fomc_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ],
-    <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; 
+  <span class='va'>f_nlme_fomc_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>,
+    control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>100</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 
 #&gt; **Iteration 1
 #&gt; LME step: Loglik: -394.1603, nlminb iterations: 3
 #&gt; reStruct  parameters:
@@ -380,8 +388,9 @@ with additional elements</p>
 #&gt;  iterations: 100 
 #&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
 #&gt;        fixed     reStruct 
-#&gt; 1.027451e-06 2.275704e-05 </div><div class='input'>  <span class='no'>f_nlme_dfop_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ],
-    <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>120</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>5e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; 
+#&gt; 1.027451e-06 2.275704e-05 </div><div class='input'>  <span class='va'>f_nlme_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>,
+    control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 
 #&gt; **Iteration 1
 #&gt; LME step: Loglik: -404.9582, nlminb iterations: 1
 #&gt; reStruct  parameters:
@@ -406,15 +415,22 @@ with additional elements</p>
 #&gt;  iterations: 120 
 #&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
 #&gt;        fixed     reStruct 
-#&gt; 4.789774e-07 2.200661e-05 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test   L.Ratio p-value
+#&gt; 4.789774e-07 2.200661e-05 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span>
+</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span>
+</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span>
+</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span>
+</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_fomc_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test   L.Ratio p-value
 #&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                         
 #&gt; f_nlme_fomc_sfo     2 11  818.5149  853.0087 -398.2575 1 vs 2  21.33975  &lt;.0001
-#&gt; f_nlme_sfo_sfo      3  9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716  &lt;.0001</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test  L.Ratio p-value
+#&gt; f_nlme_sfo_sfo      3  9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716  &lt;.0001</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> <span class='co'># if we ignore FOMC</span>
+</div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test  L.Ratio p-value
 #&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                        
 #&gt; f_nlme_sfo_sfo      2  9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274  &lt;.0001</div><div class='input'>
-  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#&gt; $ff
+  <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_A1     A1_sink 
 #&gt;   0.5912432   0.4087568   1.0000000 
 #&gt; 
@@ -422,7 +438,8 @@ with additional elements</p>
 #&gt;            DT50     DT90
 #&gt; parent 19.13518  63.5657
 #&gt; A1     66.02155 219.3189
-#&gt; </div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_dfop_sfo</span>)</div><div class='output co'>#&gt; $ff
+#&gt; </div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $ff
 #&gt;   parent_A1 parent_sink 
 #&gt;   0.2768574   0.7231426 
 #&gt; 
@@ -430,7 +447,37 @@ with additional elements</p>
 #&gt;             DT50     DT90 DT50back  DT50_k1  DT50_k2
 #&gt; parent  11.07091 104.6320 31.49738 4.462384 46.20825
 #&gt; A1     162.30536 539.1667       NA       NA       NA
-#&gt; </div><div class='input'># }
+#&gt; </div><div class='input'>
+  <span class='kw'>if</span> <span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span>
+    <span class='co'># Attempts to fit metabolite kinetics with the tc error model</span>
+    <span class='co'>#f_2_tc &lt;- mmkin(list("SFO-SFO" = m_sfo_sfo,</span>
+    <span class='co'>#  "SFO-SFO-ff" = m_sfo_sfo_ff,</span>
+    <span class='co'>#  "FOMC-SFO" = m_fomc_sfo,</span>
+    <span class='co'>#  "DFOP-SFO" = m_dfop_sfo),</span>
+    <span class='co'>#   ds_2, quiet = TRUE,</span>
+    <span class='co'>#   error_model = "tc")</span>
+    <span class='co'>#f_nlme_sfo_sfo_tc &lt;- nlme(f_2_tc["SFO-SFO", ], control = list(maxIter = 100))</span>
+    <span class='co'>#f_nlme_dfop_sfo_tc &lt;- nlme(f_2_tc["DFOP-SFO", ])</span>
+    <span class='co'>#f_nlme_dfop_sfo_tc &lt;- update(f_nlme_dfop_sfo, weights = varConstProp(),</span>
+    <span class='co'>#  control = list(sigma = 1, msMaxIter = 100, pnlsMaxIter = 15))</span>
+    <span class='co'># Fitting metabolite kinetics with nlme.mmkin and the two-component</span>
+    <span class='co'># error model currently does not work, at least not with these data.</span>
+
+    <span class='va'>f_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
+    <span class='va'>f_nlme_sfo_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_tc</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+    <span class='va'>f_nlme_dfop_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_tc</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+    <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_sfo_tc</span>, <span class='va'>f_nlme_dfop</span>, <span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
+    <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
+  <span class='op'>}</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in if (findFunction("varConstProp")) {    f_tc &lt;- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, error_model = "tc")    f_nlme_sfo_tc &lt;- nlme(f_tc["SFO", ])    f_nlme_dfop_tc &lt;- nlme(f_tc["DFOP", ])    AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc)    print(f_nlme_dfop_tc)}: argument is not interpretable as logical</span></div><div class='input'>  <span class='va'>f_2_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
+   <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
+    <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
+  <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+  <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span>
+  <span class='co'># parent and A1 are too similar in this case, so that the model is</span>
+  <span class='co'># overparameterised</span>
+  <span class='co'>#f_nlme_dfop_sfo_obs &lt;- nlme(f_2_obs["DFOP-SFO", ], control = list(maxIter = 100))</span>
+<span class='co'># }</span>
 </div></pre>
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@@ -447,7 +494,7 @@ with additional elements</p>
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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