From 272aba066f0d7502e319b7e7f14009318cd44348 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 15 Oct 2020 12:27:40 +0200
Subject: Updating docs of current dev version

---
 docs/dev/reference/endpoints.html |  30 ++--
 docs/dev/reference/index.html     |   4 +-
 docs/dev/reference/saemix-1.png   | Bin 31551 -> 50490 bytes
 docs/dev/reference/saemix-2.png   | Bin 58815 -> 60503 bytes
 docs/dev/reference/saemix-3.png   | Bin 0 -> 16942 bytes
 docs/dev/reference/saemix-4.png   | Bin 0 -> 65995 bytes
 docs/dev/reference/saemix.html    | 323 ++++++++++++++++++++++++++++++++------
 7 files changed, 299 insertions(+), 58 deletions(-)
 create mode 100644 docs/dev/reference/saemix-3.png
 create mode 100644 docs/dev/reference/saemix-4.png

(limited to 'docs/dev/reference')

diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html
index 1858e243..5a20a34c 100644
--- a/docs/dev/reference/endpoints.html
+++ b/docs/dev/reference/endpoints.html
@@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." />
       </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>
 
@@ -126,7 +126,7 @@ advantage that the SFORB model can also be used for metabolites." />
       </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>
@@ -146,7 +146,7 @@ advantage that the SFORB model can also be used for metabolites." />
     <div class="page-header">
     <h1>Function to calculate endpoints for further use from kinetic models fitted
 with mkinfit</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/endpoints.R'><code>R/endpoints.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/endpoints.R'><code>R/endpoints.R</code></a></small>
     <div class="hidden name"><code>endpoints.Rd</code></div>
     </div>
 
@@ -158,7 +158,7 @@ are equivalent to the rate constants of the DFOP model, but with the
 advantage that the SFORB model can also be used for metabolites.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre>
+    <pre class="usage"><span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -179,20 +179,26 @@ of these SFORB models, equivalent to DFOP rate constants</p>
     <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
 
     <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $distimes
+  <span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $distimes
 #&gt;            DT50    DT90 DT50back
 #&gt; parent 1.785233 15.1479 4.559973
 #&gt; </div><div class='input'>  <span class='co'># \dontrun{</span>
-    <span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</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'>endpoints</span>(<span class='no'>fit_2</span>)</div><div class='output co'>#&gt; $distimes
+    <span class='va'>fit_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+    <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $distimes
 #&gt;            DT50     DT90 DT50back  DT50_k1  DT50_k2
 #&gt; parent 1.886925 21.25106 6.397207 1.508293 38.83438
-#&gt; </div><div class='input'>    <span class='no'>fit_3</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFORB"</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'>endpoints</span>(<span class='no'>fit_3</span>)</div><div class='output co'>#&gt; $ff
+#&gt; </div><div class='input'>    <span class='va'>fit_3</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFORB"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+    <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit_3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $ff
 #&gt; parent_free 
 #&gt;           1 
 #&gt; 
@@ -203,7 +209,7 @@ of these SFORB models, equivalent to DFOP rate constants</p>
 #&gt; $distimes
 #&gt;            DT50     DT90 DT50back DT50_parent_b1 DT50_parent_b2
 #&gt; parent 1.886925 21.25106 6.397208       1.508293       38.83438
-#&gt; </div><div class='input'>  # }
+#&gt; </div><div class='input'>  <span class='co'># }</span>
 
 </div></pre>
   </div>
@@ -221,7 +227,7 @@ of these SFORB models, equivalent to DFOP rate constants</p>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index a5cd6663..5d70a450 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -71,7 +71,7 @@
       </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>
 
@@ -678,7 +678,7 @@ kinetic models fitted with mkinfit</p></td>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/saemix-1.png b/docs/dev/reference/saemix-1.png
index 0d79300d..696fa7d9 100644
Binary files a/docs/dev/reference/saemix-1.png and b/docs/dev/reference/saemix-1.png differ
diff --git a/docs/dev/reference/saemix-2.png b/docs/dev/reference/saemix-2.png
index 04de70b5..6525a36c 100644
Binary files a/docs/dev/reference/saemix-2.png and b/docs/dev/reference/saemix-2.png differ
diff --git a/docs/dev/reference/saemix-3.png b/docs/dev/reference/saemix-3.png
new file mode 100644
index 00000000..13157f91
Binary files /dev/null and b/docs/dev/reference/saemix-3.png differ
diff --git a/docs/dev/reference/saemix-4.png b/docs/dev/reference/saemix-4.png
new file mode 100644
index 00000000..1e717cb2
Binary files /dev/null and b/docs/dev/reference/saemix-4.png differ
diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html
index da28bff1..5b160959 100644
--- a/docs/dev/reference/saemix.html
+++ b/docs/dev/reference/saemix.html
@@ -75,7 +75,7 @@ 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>
 
@@ -123,7 +123,7 @@ 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>
@@ -142,7 +142,7 @@ a list of datasets." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Create saemix models from mmkin row objects</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small>
     <div class="hidden name"><code>saemix.Rd</code></div>
     </div>
 
@@ -153,9 +153,9 @@ list of mkinfit objects that have been obtained by fitting the same model to
 a list of datasets.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>saemix_model</span>(<span class='no'>object</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span>())
+    <pre class="usage"><span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
 
-<span class='fu'>saemix_data</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>saemix_data</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">
@@ -187,14 +187,17 @@ mmkin. Starting variances of the random effects (argument omega.init) are the
 variances of the deviations of the parameters from these mean values.</p>
 
     <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='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>)
-<span class='no'>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>))</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'># \dontrun{</span>
-<span class='no'>f_mmkin</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'>sfo_sfo</span>), <span class='no'>ds</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/library.html'>library</a></span>(<span class='no'>saemix</span>)</div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
-#&gt; <span class='message'>  please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='no'>m_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#&gt; 
+    <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='op'>)</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
+<span class='va'>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><span class='op'>)</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'># \dontrun{</span>
+<span class='va'>f_mmkin</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'>sfo_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
+#&gt; <span class='message'>  please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='va'>m_saemix</span> <span class='op'>&lt;-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 
 #&gt; 
 #&gt; The following SaemixModel object was successfully created:
 #&gt; 
@@ -234,8 +237,8 @@ variances of the deviations of the parameters from these mean values.</p>
 #&gt;     res &lt;- unlist(res_list)
 #&gt;     return(res)
 #&gt; }
-#&gt; &lt;bytecode: 0x55555bbf17c0&gt;
-#&gt; &lt;environment: 0x55555bbec4e0&gt;
+#&gt; &lt;bytecode: 0x55555c1e7720&gt;
+#&gt; &lt;environment: 0x55555c1eff38&gt;
 #&gt;   Nb of parameters: 4 
 #&gt;       parameter names:  parent_0 log_k_parent log_k_A1 f_parent_ilr_1 
 #&gt;       distribution:
@@ -250,11 +253,12 @@ variances of the deviations of the parameters from these mean values.</p>
 #&gt; log_k_parent          0            1        0              0
 #&gt; log_k_A1              0            0        1              0
 #&gt; f_parent_ilr_1        0            0        0              1
-#&gt;   Error model: constant , initial values: a.1=1 
+#&gt;   Error model: constant , initial values: a.1=4.97259024646577 
 #&gt;     No covariate in the model.
 #&gt;     Initial values
 #&gt;              parent_0 log_k_parent  log_k_A1 f_parent_ilr_1
-#&gt; Pop.CondInit 86.53449    -3.207005 -3.060308      -1.920449</div><div class='input'><span class='no'>d_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#&gt; 
+#&gt; Pop.CondInit 86.53449    -3.207005 -3.060308      -1.920449</div><div class='input'><span class='va'>d_saemix</span> <span class='op'>&lt;-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 
 #&gt; 
 #&gt; The following SaemixData object was successfully created:
 #&gt; 
@@ -262,14 +266,15 @@ variances of the deviations of the parameters from these mean values.</p>
 #&gt;     longitudinal data for use with the SAEM algorithm
 #&gt; Dataset ds_saemix 
 #&gt;     Structured data: value ~ time + name | ds 
-#&gt;     X variable for graphs: time () </div><div class='input'><span class='no'>saemix_options</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>,
-  <span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.graphs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>displayProgress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>nbiter.saemix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>200</span>, <span class='fl'>80</span>))
-<span class='no'>f_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span>(<span class='no'>m_saemix</span>, <span class='no'>d_saemix</span>, <span class='no'>saemix_options</span>)</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed May 27 07:45:07 2020"
+#&gt;     X variable for graphs: time () </div><div class='input'><span class='va'>saemix_options</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>seed <span class='op'>=</span> <span class='fl'>123456</span>,
+  save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span>, displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  nbiter.saemix <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='fl'>200</span>, <span class='fl'>80</span><span class='op'>)</span><span class='op'>)</span>
+<span class='va'>f_saemix</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix</span>, <span class='va'>d_saemix</span>, <span class='va'>saemix_options</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Thu Oct 15 11:55:14 2020"
 #&gt; ..
 #&gt;     Minimisation finished
-#&gt; [1] "Wed May 27 07:51:24 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
+#&gt; [1] "Thu Oct 15 11:57:07 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
 #&gt; -----------------------------------
 #&gt; ----          Data             ----
 #&gt; -----------------------------------
@@ -333,8 +338,8 @@ variances of the deviations of the parameters from these mean values.</p>
 #&gt;     res &lt;- unlist(res_list)
 #&gt;     return(res)
 #&gt; }
-#&gt; &lt;bytecode: 0x55555bbf17c0&gt;
-#&gt; &lt;environment: 0x55555bbec4e0&gt;
+#&gt; &lt;bytecode: 0x55555c1e7720&gt;
+#&gt; &lt;environment: 0x55555c1eff38&gt;
 #&gt;   Nb of parameters: 4 
 #&gt;       parameter names:  parent_0 log_k_parent log_k_A1 f_parent_ilr_1 
 #&gt;       distribution:
@@ -349,7 +354,7 @@ variances of the deviations of the parameters from these mean values.</p>
 #&gt; log_k_parent          0            1        0              0
 #&gt; log_k_A1              0            0        1              0
 #&gt; f_parent_ilr_1        0            0        0              1
-#&gt;   Error model: constant , initial values: a.1=1 
+#&gt;   Error model: constant , initial values: a.1=4.97259024646577 
 #&gt;     No covariate in the model.
 #&gt;     Initial values
 #&gt;              parent_0 log_k_parent  log_k_A1 f_parent_ilr_1
@@ -375,20 +380,20 @@ variances of the deviations of the parameters from these mean values.</p>
 #&gt; ----------------------------------------------------
 #&gt; -----------------  Fixed effects  ------------------
 #&gt; ----------------------------------------------------
-#&gt;      Parameter      Estimate SE   CV(%)
-#&gt; [1,] parent_0       86.14    1.61  1.9 
-#&gt; [2,] log_k_parent   -3.21    0.59 18.5 
-#&gt; [3,] log_k_A1       -4.66    0.30  6.4 
-#&gt; [4,] f_parent_ilr_1 -0.33    0.30 91.7 
-#&gt; [5,] a.1             4.68    0.27  5.8 
+#&gt;   Parameter      Estimate SE   CV(%)
+#&gt;   parent_0       86.09    1.57  1.8 
+#&gt;   log_k_parent   -3.21    0.59 18.5 
+#&gt;   log_k_A1       -4.69    0.31  6.6 
+#&gt;   f_parent_ilr_1 -0.34    0.30 89.2 
+#&gt; a a.1             4.69    0.27  5.8 
 #&gt; ----------------------------------------------------
 #&gt; -----------  Variance of random effects  -----------
 #&gt; ----------------------------------------------------
 #&gt;                Parameter             Estimate SE   CV(%)
-#&gt; parent_0       omega2.parent_0       7.71     8.14 106  
-#&gt; log_k_parent   omega2.log_k_parent   1.76     1.12  63  
-#&gt; log_k_A1       omega2.log_k_A1       0.26     0.26 101  
-#&gt; f_parent_ilr_1 omega2.f_parent_ilr_1 0.39     0.28  71  
+#&gt; parent_0       omega2.parent_0       7.07     7.72 109  
+#&gt; log_k_parent   omega2.log_k_parent   1.75     1.11  63  
+#&gt; log_k_A1       omega2.log_k_A1       0.28     0.28  99  
+#&gt; f_parent_ilr_1 omega2.f_parent_ilr_1 0.39     0.27  71  
 #&gt; ----------------------------------------------------
 #&gt; ------  Correlation matrix of random effects  ------
 #&gt; ----------------------------------------------------
@@ -406,15 +411,245 @@ variances of the deviations of the parameters from these mean values.</p>
 #&gt; ---------------  Statistical criteria  -------------
 #&gt; ----------------------------------------------------
 #&gt; Likelihood computed by linearisation
-#&gt;       -2LL= 1064.364 
-#&gt;       AIC = 1082.364 
-#&gt;       BIC = 1078.848 
+#&gt;       -2LL= 1064.35 
+#&gt;       AIC = 1082.35 
+#&gt;       BIC = 1078.835 
 #&gt; 
 #&gt; Likelihood computed by importance sampling
-#&gt;       -2LL= 1063.462 
-#&gt;       AIC = 1081.462 
-#&gt;       BIC = 1077.947 
-#&gt; ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span>(<span class='no'>f_saemix</span>, <span class='kw'>plot.type</span> <span class='kw'>=</span> <span class='st'>"convergence"</span>)</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'># }
+#&gt;       -2LL= 1063.475 
+#&gt;       AIC = 1081.475 
+#&gt;       BIC = 1077.96 
+#&gt; ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saemix</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+<span class='co'># Synthetic data with two-component error</span>
+<span class='va'>sampling_times</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='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='op'>)</span>
+<span class='va'>dt50_sfo_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>800</span>, <span class='fl'>900</span>, <span class='fl'>1000</span>, <span class='fl'>1111.11</span>, <span class='fl'>1250</span><span class='op'>)</span>
+<span class='va'>k_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in</span>
+
+<span class='va'>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='op'>)</span><span class='op'>)</span>
+
+<span class='va'>pred_sfo</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><span class='op'>)</span>,
+    <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span>
+<span class='op'>}</span>
+
+<span class='va'>ds_sfo_mean</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'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456L</span><span class='op'>)</span>
+<span class='va'>ds_sfo_syn</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'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>,
+     n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>
+ <span class='op'>}</span><span class='op'>)</span>
+<span class='va'>f_mmkin_syn</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>m_saemix_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 
+#&gt; 
+#&gt; The following SaemixModel object was successfully created:
+#&gt; 
+#&gt; Nonlinear mixed-effects model
+#&gt;   Model function:  Mixed model generated from mmkin object  Model type:  structural
+#&gt; function (psi, id, xidep) 
+#&gt; {
+#&gt;     uid &lt;- unique(id)
+#&gt;     res_list &lt;- parallel::mclapply(uid, function(i) {
+#&gt;         transparms_optim &lt;- psi[i, ]
+#&gt;         names(transparms_optim) &lt;- names(degparms_optim)
+#&gt;         odeini_optim &lt;- transparms_optim[odeini_optim_parm_names]
+#&gt;         names(odeini_optim) &lt;- gsub("_0$", "", odeini_optim_parm_names)
+#&gt;         odeini &lt;- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
+#&gt;         ode_transparms_optim_names &lt;- setdiff(names(transparms_optim), 
+#&gt;             odeini_optim_parm_names)
+#&gt;         odeparms_optim &lt;- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], 
+#&gt;             mkin_model, transform_rates = object[[1]]$transform_rates, 
+#&gt;             transform_fractions = object[[1]]$transform_fractions)
+#&gt;         odeparms &lt;- c(odeparms_optim, odeparms_fixed)
+#&gt;         xidep_i &lt;- subset(xidep, id == i)
+#&gt;         if (analytical) {
+#&gt;             out_values &lt;- mkin_model$deg_func(xidep_i, odeini, 
+#&gt;                 odeparms)
+#&gt;         }
+#&gt;         else {
+#&gt;             i_time &lt;- xidep_i$time
+#&gt;             i_name &lt;- xidep_i$name
+#&gt;             out_wide &lt;- mkinpredict(mkin_model, odeparms = odeparms, 
+#&gt;                 odeini = odeini, solution_type = object[[1]]$solution_type, 
+#&gt;                 outtimes = sort(unique(i_time)))
+#&gt;             out_index &lt;- cbind(as.character(i_time), as.character(i_name))
+#&gt;             out_values &lt;- out_wide[out_index]
+#&gt;         }
+#&gt;         return(out_values)
+#&gt;     }, mc.cores = cores)
+#&gt;     res &lt;- unlist(res_list)
+#&gt;     return(res)
+#&gt; }
+#&gt; &lt;bytecode: 0x55555c1e7720&gt;
+#&gt; &lt;environment: 0x55555be5b848&gt;
+#&gt;   Nb of parameters: 2 
+#&gt;       parameter names:  parent_0 log_k_parent 
+#&gt;       distribution:
+#&gt;      Parameter    Distribution Estimated
+#&gt; [1,] parent_0     normal       Estimated
+#&gt; [2,] log_k_parent normal       Estimated
+#&gt;   Variance-covariance matrix:
+#&gt;              parent_0 log_k_parent
+#&gt; parent_0            1            0
+#&gt; log_k_parent        0            1
+#&gt;   Error model: combined , initial values: a.1=2.4206146215511 b.1=0.03831266409084 
+#&gt;     No covariate in the model.
+#&gt;     Initial values
+#&gt;              parent_0 log_k_parent
+#&gt; Pop.CondInit 100.2498     -9.33922</div><div class='input'><span class='va'>d_saemix_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 
+#&gt; 
+#&gt; The following SaemixData object was successfully created:
+#&gt; 
+#&gt; Object of class SaemixData
+#&gt;     longitudinal data for use with the SAEM algorithm
+#&gt; Dataset ds_saemix 
+#&gt;     Structured data: value ~ time + name | ds 
+#&gt;     X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_tc</span>, <span class='va'>d_saemix_tc</span>, <span class='va'>saemix_options</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Thu Oct 15 11:57:25 2020"
+#&gt; ..
+#&gt;     Minimisation finished
+#&gt; [1] "Thu Oct 15 11:58:16 2020"
+#&gt; Error in solve.default(Fth) : 
+#&gt;   Lapack routine dgesv: system is exactly singular: U[2,2] = 0
+#&gt; Error computing the Fisher Information Matrix: singular system.
+#&gt; Error in solve.default(FO) : 
+#&gt;   Lapack routine dgesv: system is exactly singular: U[2,2] = 0
+#&gt; Error computing the Fisher Information Matrix: singular system.</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
+#&gt; -----------------------------------
+#&gt; ----          Data             ----
+#&gt; -----------------------------------
+#&gt; Object of class SaemixData
+#&gt;     longitudinal data for use with the SAEM algorithm
+#&gt; Dataset ds_saemix 
+#&gt;     Structured data: value ~ time + name | ds 
+#&gt;     X variable for graphs: time () 
+#&gt; Dataset characteristics:
+#&gt;     number of subjects:     5 
+#&gt;     number of observations: 90 
+#&gt;     average/min/max nb obs: 18.00  /  18  /  18 
+#&gt; First 10 lines of data:
+#&gt;    ds time   name value mdv cens occ ytype
+#&gt; 1   1    0 parent 105.9   0    0   1     1
+#&gt; 2   1    0 parent  98.0   0    0   1     1
+#&gt; 3   1    1 parent  97.4   0    0   1     1
+#&gt; 4   1    1 parent 100.5   0    0   1     1
+#&gt; 5   1    3 parent 115.6   0    0   1     1
+#&gt; 6   1    3 parent 105.6   0    0   1     1
+#&gt; 7   1    7 parent 108.6   0    0   1     1
+#&gt; 8   1    7 parent 117.0   0    0   1     1
+#&gt; 9   1   14 parent 107.0   0    0   1     1
+#&gt; 10  1   14 parent  95.8   0    0   1     1
+#&gt; -----------------------------------
+#&gt; ----          Model            ----
+#&gt; -----------------------------------
+#&gt; Nonlinear mixed-effects model
+#&gt;   Model function:  Mixed model generated from mmkin object  Model type:  structural
+#&gt; function (psi, id, xidep) 
+#&gt; {
+#&gt;     uid &lt;- unique(id)
+#&gt;     res_list &lt;- parallel::mclapply(uid, function(i) {
+#&gt;         transparms_optim &lt;- psi[i, ]
+#&gt;         names(transparms_optim) &lt;- names(degparms_optim)
+#&gt;         odeini_optim &lt;- transparms_optim[odeini_optim_parm_names]
+#&gt;         names(odeini_optim) &lt;- gsub("_0$", "", odeini_optim_parm_names)
+#&gt;         odeini &lt;- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
+#&gt;         ode_transparms_optim_names &lt;- setdiff(names(transparms_optim), 
+#&gt;             odeini_optim_parm_names)
+#&gt;         odeparms_optim &lt;- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], 
+#&gt;             mkin_model, transform_rates = object[[1]]$transform_rates, 
+#&gt;             transform_fractions = object[[1]]$transform_fractions)
+#&gt;         odeparms &lt;- c(odeparms_optim, odeparms_fixed)
+#&gt;         xidep_i &lt;- subset(xidep, id == i)
+#&gt;         if (analytical) {
+#&gt;             out_values &lt;- mkin_model$deg_func(xidep_i, odeini, 
+#&gt;                 odeparms)
+#&gt;         }
+#&gt;         else {
+#&gt;             i_time &lt;- xidep_i$time
+#&gt;             i_name &lt;- xidep_i$name
+#&gt;             out_wide &lt;- mkinpredict(mkin_model, odeparms = odeparms, 
+#&gt;                 odeini = odeini, solution_type = object[[1]]$solution_type, 
+#&gt;                 outtimes = sort(unique(i_time)))
+#&gt;             out_index &lt;- cbind(as.character(i_time), as.character(i_name))
+#&gt;             out_values &lt;- out_wide[out_index]
+#&gt;         }
+#&gt;         return(out_values)
+#&gt;     }, mc.cores = cores)
+#&gt;     res &lt;- unlist(res_list)
+#&gt;     return(res)
+#&gt; }
+#&gt; &lt;bytecode: 0x55555c1e7720&gt;
+#&gt; &lt;environment: 0x55555be5b848&gt;
+#&gt;   Nb of parameters: 2 
+#&gt;       parameter names:  parent_0 log_k_parent 
+#&gt;       distribution:
+#&gt;      Parameter    Distribution Estimated
+#&gt; [1,] parent_0     normal       Estimated
+#&gt; [2,] log_k_parent normal       Estimated
+#&gt;   Variance-covariance matrix:
+#&gt;              parent_0 log_k_parent
+#&gt; parent_0            1            0
+#&gt; log_k_parent        0            1
+#&gt;   Error model: combined , initial values: a.1=2.4206146215511 b.1=0.03831266409084 
+#&gt;     No covariate in the model.
+#&gt;     Initial values
+#&gt;              parent_0 log_k_parent
+#&gt; Pop.CondInit 100.2498     -9.33922
+#&gt; -----------------------------------
+#&gt; ----    Key algorithm options  ----
+#&gt; -----------------------------------
+#&gt;     Estimation of individual parameters (MAP)
+#&gt;     Estimation of standard errors and linearised log-likelihood
+#&gt;     Estimation of log-likelihood by importance sampling
+#&gt;     Number of iterations:  K1=200, K2=80 
+#&gt;     Number of chains:  10 
+#&gt;     Seed:  123456 
+#&gt;     Number of MCMC iterations for IS:  5000 
+#&gt;     Simulations:
+#&gt;         nb of simulated datasets used for npde:  1000 
+#&gt;         nb of simulated datasets used for VPC:  100 
+#&gt;     Input/output
+#&gt;         save the results to a file:  FALSE 
+#&gt;         save the graphs to files:  FALSE 
+#&gt; ----------------------------------------------------
+#&gt; ----                  Results                   ----
+#&gt; ----------------------------------------------------
+#&gt; -----------------  Fixed effects  ------------------
+#&gt; ----------------------------------------------------
+#&gt;   Parameter    Estimate SE   CV(%)
+#&gt;   parent_0      97.44   &lt;NA&gt; &lt;NA&gt; 
+#&gt;   log_k_parent -56.97   &lt;NA&gt; &lt;NA&gt; 
+#&gt; a a.1           -7.12   &lt;NA&gt; &lt;NA&gt; 
+#&gt; b b.1            0.15   &lt;NA&gt; &lt;NA&gt; 
+#&gt; ----------------------------------------------------
+#&gt; -----------  Variance of random effects  -----------
+#&gt; ----------------------------------------------------
+#&gt;              Parameter           Estimate SE CV(%)
+#&gt; parent_0     omega2.parent_0       2.8    NA NA   
+#&gt; log_k_parent omega2.log_k_parent 750.3    NA NA   
+#&gt; ----------------------------------------------------
+#&gt; ------  Correlation matrix of random effects  ------
+#&gt; ----------------------------------------------------
+#&gt;                     omega2.parent_0 omega2.log_k_parent
+#&gt; omega2.parent_0     1               0                  
+#&gt; omega2.log_k_parent 0               1                  
+#&gt; ----------------------------------------------------
+#&gt; ---------------  Statistical criteria  -------------
+#&gt; ----------------------------------------------------
+#&gt; Likelihood computed by linearisation
+#&gt;       -2LL= 623.7744 
+#&gt;       AIC = 635.7744 
+#&gt;       BIC = 633.431 
+#&gt; 
+#&gt; Likelihood computed by importance sampling
+#&gt;       -2LL= 621.1909 
+#&gt;       AIC = 633.1909 
+#&gt;       BIC = 630.8475 
+#&gt; ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saemix_tc</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Plotting convergence plots</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -431,7 +666,7 @@ variances of the deviations of the parameters from these mean values.</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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