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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-11 19:49:25 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-11 19:49:25 +0100
commitc0c82d9523da8965f5fb7a5f8cf1410750885d30 (patch)
tree8db6015dfa8eb14df8318b9661b07424bb92620f
parente13189e6a34d87fabf650c777d0432057bcacbb9 (diff)
Update static docs
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/Rplot001.pngbin19395 -> 1011 bytes
-rw-r--r--docs/dev/reference/mccall81_245T-1.pngbin0 -> 65341 bytes
-rw-r--r--docs/dev/reference/mccall81_245T.html77
-rw-r--r--docs/dev/reference/saem.html50
-rw-r--r--docs/dev/reference/summary.saem.mmkin.html432
-rw-r--r--man/saem.Rd14
7 files changed, 306 insertions, 269 deletions
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 20533121..438c79b7 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2020-11-11T08:36Z
+last_built: 2020-11-11T18:47Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index bca41e2c..17a35806 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
diff --git a/docs/dev/reference/mccall81_245T-1.png b/docs/dev/reference/mccall81_245T-1.png
new file mode 100644
index 00000000..5daa5f18
--- /dev/null
+++ b/docs/dev/reference/mccall81_245T-1.png
Binary files differ
diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html
index fa352d0a..255c3568 100644
--- a/docs/dev/reference/mccall81_245T.html
+++ b/docs/dev/reference/mccall81_245T.html
@@ -74,7 +74,7 @@
</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>
@@ -122,7 +122,7 @@
</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>
@@ -151,12 +151,12 @@
extracts.</p>
</div>
- <pre class="usage"><span class='no'>mccall81_245T</span></pre>
+ <pre class="usage"><span class='va'>mccall81_245T</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
- <p>A dataframe containing the following variables.</p><dl'>
+ <p>A dataframe containing the following variables.</p><dl>
<dt><code>name</code></dt><dd><p>the name of the compound observed. Note that T245 is used as
an acronym for 2,4,5-T. T245 is a legitimate object name
in R, which is necessary for specifying models using
@@ -174,46 +174,71 @@
<a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</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'>"phenol"</span>),
- <span class='kw'>phenol</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'>"anisole"</span>),
- <span class='kw'>anisole</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>))</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'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</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'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t)
-#&gt; T245_0 1.038550e+02 2.184707514 47.537272 4.472189e-18
-#&gt; k_T245 4.337042e-02 0.001898397 22.845818 2.276912e-13
-#&gt; k_phenol 4.050581e-01 0.298699428 1.356073 9.756994e-02
-#&gt; k_anisole 6.678742e-03 0.000802144 8.326114 2.623179e-07
-#&gt; f_T245_to_phenol 6.227599e-01 0.398534167 1.562626 6.949418e-02
-#&gt; f_phenol_to_anisole 1.000000e+00 0.671844168 1.488440 7.867794e-02
-#&gt; sigma 2.514628e+00 0.490755943 5.123989 6.233164e-05
+ <pre class="examples"><div class='input'> <span class='va'>SFO_SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>,
+ phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span><span class='op'>)</span>,
+ anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <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'>fit.1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
+</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t)
+#&gt; T245_0 1.038550e+02 2.1847074888 47.537272 4.472189e-18
+#&gt; k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13
+#&gt; k_phenol 4.050581e-01 0.2986993400 1.356073 9.756988e-02
+#&gt; k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07
+#&gt; f_T245_to_phenol 6.227599e-01 0.3985340295 1.562627 6.949412e-02
+#&gt; f_phenol_to_anisole 1.000000e+00 0.6718439378 1.488441 7.867787e-02
+#&gt; sigma 2.514628e+00 0.4907558750 5.123989 6.233156e-05
#&gt; Lower Upper
-#&gt; T245_0 99.246061371 1.084640e+02
+#&gt; T245_0 99.246061370 1.084640e+02
#&gt; k_T245 0.039631621 4.746194e-02
#&gt; k_phenol 0.218013878 7.525762e-01
#&gt; k_anisole 0.005370739 8.305299e-03
-#&gt; f_T245_to_phenol 0.547559082 6.924813e-01
+#&gt; f_T245_to_phenol 0.547559083 6.924813e-01
#&gt; f_phenol_to_anisole 0.000000000 1.000000e+00
-#&gt; sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+#&gt; sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $ff
#&gt; T245_phenol T245_sink phenol_anisole phenol_sink
-#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 1.748047e-10
+#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; T245 15.982025 53.09114
#&gt; phenol 1.711229 5.68458
#&gt; anisole 103.784092 344.76329
-#&gt; </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
- <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
- <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
- <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Initial parameter(s) k_phenol_sink not used in the model</span></div><div class='output co'>#&gt; <span class='error'>Error in data.frame(value = c(state.ini.fixed, parms.fixed)): row names contain missing values</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+#&gt; </div><div class='input'> <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span>
+ <span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span>
+ <span class='co'># the sink in the model generation</span>
+ <span class='va'>SFO_SFO_SFO_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>,
+ phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
+ anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <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='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='va'>SFO_SFO_SFO_2</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>,
+ quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
+</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; T245_0 1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526
+#&gt; k_T245 4.337042e-02 0.0018343666 23.643268 3.573555e-14 0.039650977
+#&gt; k_phenol 4.050582e-01 0.1177237248 3.440752 1.679252e-03 0.218746585
+#&gt; k_anisole 6.678741e-03 0.0006829745 9.778903 1.872894e-08 0.005377083
+#&gt; f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12 0.547975628
+#&gt; sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655
+#&gt; Upper
+#&gt; T245_0 108.43904097
+#&gt; k_T245 0.04743877
+#&gt; k_phenol 0.75005577
+#&gt; k_anisole 0.00829550
+#&gt; f_T245_to_phenol 0.69212306
+#&gt; sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $ff
#&gt; T245_phenol T245_sink phenol_anisole phenol_sink
-#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 1.748047e-10
+#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; T245 15.982025 53.09114
#&gt; phenol 1.711229 5.68458
#&gt; anisole 103.784092 344.76329
-#&gt; </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): object 'fit.2' not found</span></div><div class='input'> # }
+#&gt; </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
+</div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -230,7 +255,7 @@
</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/saem.html b/docs/dev/reference/saem.html
index bc54e1e1..d0c3495a 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -141,7 +141,7 @@ Expectation Maximisation algorithm (SAEM)." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Fit nonlinear mixed models with SAEM</h1>
- <small class="dont-index">Source: <a href='https://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/saem.R'><code>R/saem.R</code></a></small>
<div class="hidden name"><code>saem.Rd</code></div>
</div>
@@ -161,6 +161,7 @@ Expectation Maximisation algorithm (SAEM).</p>
cores <span class='op'>=</span> <span class='fl'>1</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
suppressPlot <span class='op'>=</span> <span class='cn'>TRUE</span>,
+ quiet <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
@@ -185,19 +186,19 @@ Expectation Maximisation algorithm (SAEM).</p>
</tr>
<tr>
<th>...</th>
- <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixData.html'>saemix::saemixData</a>
-and <a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel</a>.</p></td>
+ <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel</a>.</p></td>
</tr>
<tr>
<th>cores</th>
<td><p>The number of cores to be used for multicore processing using
<code><a href='https://rdrr.io/r/parallel/mclapply.html'>parallel::mclapply()</a></code>. Using more than 1 core is experimental and may
-lead to uncontrolled forking, apparently depending on the BLAS version
+lead to excessive forking, apparently depending on the BLAS version
used.</p></td>
</tr>
<tr>
<th>verbose</th>
- <td><p>Should we print information about created objects?</p></td>
+ <td><p>Should we print information about created objects of
+type <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> and <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a>?</p></td>
</tr>
<tr>
<th>suppressPlot</th>
@@ -205,6 +206,11 @@ used.</p></td>
by the saemix function?</p></td>
</tr>
<tr>
+ <th>quiet</th>
+ <td><p>Should we suppress the messages saemix prints at the beginning
+and the end of the optimisation process?</p></td>
+ </tr>
+ <tr>
<th>x</th>
<td><p>An saem.mmkin object to print</p></td>
</tr>
@@ -241,27 +247,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
state.ini <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>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:41 2020"
+#&gt; [1] "Wed Nov 11 19:47:58 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:43 2020"</div><div class='input'>
+#&gt; [1] "Wed Nov 11 19:48:00 2020"</div><div class='input'>
<span class='va'>f_mmkin_parent</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'>"FOMC"</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><span class='op'>)</span>
<span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:44 2020"
+#&gt; [1] "Wed Nov 11 19:48:01 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:45 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 19:48:03 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:46 2020"
+#&gt; [1] "Wed Nov 11 19:48:03 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:48 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 19:48:05 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:48 2020"
+#&gt; [1] "Wed Nov 11 19:48:06 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:51 2020"</div><div class='input'>
+#&gt; [1] "Wed Nov 11 19:48:08 2020"</div><div class='input'>
<span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
<span class='co'># functions from saemix</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>
@@ -307,10 +313,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
<span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:54 2020"
+#&gt; [1] "Wed Nov 11 19:48:11 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:59 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 19:48:16 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
#&gt; 1 467.7096 464.9757
#&gt; 2 469.5208 466.3963</div><div class='input'>
@@ -330,15 +336,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># solutions written for mkin this took around four minutes</span>
<span class='va'>f_saem_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:37:01 2020"
+#&gt; [1] "Wed Nov 11 19:48:18 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:37:06 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 19:48:23 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:37:06 2020"
+#&gt; [1] "Wed Nov 11 19:48:23 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:37:15 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Wed Nov 11 19:48:32 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by SAEM
#&gt; Structural model:
@@ -384,8 +390,8 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; LL by is "-407.78 (df=13)"</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
#&gt; mkin version used for pre-fitting: 0.9.50.4
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Wed Nov 11 09:37:16 2020
-#&gt; Date of summary: Wed Nov 11 09:37:16 2020
+#&gt; Date of fit: Wed Nov 11 19:48:33 2020
+#&gt; Date of summary: Wed Nov 11 19:48:33 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -400,7 +406,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 9.691 s using 300, 100 iterations
+#&gt; Fitted in 9.564 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
index e718806e..8a5d001a 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -156,7 +156,7 @@ endpoints such as formation fractions and DT50 values. Optionally
</div>
<pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for summary.saem.mmkin</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>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</span>, <span class='va'>...</span><span class='op'>)</span></pre>
@@ -256,18 +256,20 @@ saemix authors for the parts inherited from saemix.</p>
<span class='co'># \dontrun{</span>
<span class='co'># Evaluate using mmkin and saem</span>
-<span class='va'>f_mmkin_dfop_sfo</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='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_syn_dfop_sfo</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span>
+<span class='va'>f_mmkin_dfop_sfo</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='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_syn_dfop_sfo</span>,
+ quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span>
<span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 09:24:08 2020"
+#&gt; [1] "Wed Nov 11 19:48:36 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 09:24:21 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
+#&gt; [1] "Wed Nov 11 19:48:48 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;
+#&gt; LL by is "-401.01 (df=14)"</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
#&gt; mkin version used for pre-fitting: 0.9.50.4
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Nov 9 09:24:22 2020
-#&gt; Date of summary: Mon Nov 9 09:24:22 2020
+#&gt; Date of fit: Wed Nov 11 19:48:49 2020
+#&gt; Date of summary: Wed Nov 11 19:48:49 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -282,7 +284,7 @@ saemix authors for the parts inherited from saemix.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 13.457 s using 300, 100 iterations
+#&gt; Fitted in 13.272 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Two-component variance function
#&gt;
@@ -298,232 +300,232 @@ saemix authors for the parts inherited from saemix.</p>
#&gt; Results:
#&gt;
#&gt; Likelihood computed by importance sampling
-#&gt; AIC BIC logLik
-#&gt; 828.8639 823.396 -400.432
+#&gt; AIC BIC logLik
+#&gt; 830 824.5 -401
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; est. lower upper
-#&gt; parent_0 101.35835807 97.8846505 104.8320657
-#&gt; log_k_m1 -4.06644838 -4.1861445 -3.9467523
-#&gt; f_parent_qlogis -0.94818070 -1.3124706 -0.5838908
-#&gt; log_k1 -2.92096208 -3.7684319 -2.0734922
-#&gt; log_k2 -3.54529352 -4.2532018 -2.8373852
-#&gt; g_qlogis -0.09254475 -0.9675848 0.7824953
+#&gt; est. lower upper
+#&gt; parent_0 101.4423 97.862 105.0224
+#&gt; log_k_m1 -4.0703 -4.191 -3.9495
+#&gt; f_parent_qlogis -0.9539 -1.313 -0.5949
+#&gt; log_k1 -2.9724 -3.811 -2.1342
+#&gt; log_k2 -3.4977 -4.206 -2.7895
+#&gt; g_qlogis -0.0449 -1.116 1.0262
#&gt;
#&gt; Correlation:
#&gt; prnt_0 lg_k_1 f_prn_ log_k1 log_k2
-#&gt; log_k_m1 -0.217
-#&gt; f_parent_qlogis -0.153 0.203
-#&gt; log_k1 0.066 -0.067 -0.035
-#&gt; log_k2 0.002 0.010 0.001 -0.041
-#&gt; g_qlogis -0.014 0.005 0.015 -0.163 -0.106
+#&gt; log_k_m1 -0.207
+#&gt; f_parent_qlogis -0.148 0.202
+#&gt; log_k1 0.040 -0.038 -0.022
+#&gt; log_k2 0.022 -0.015 -0.009 0.001
+#&gt; g_qlogis -0.012 0.005 0.011 -0.173 -0.130
#&gt;
#&gt; Random effects:
-#&gt; est. lower upper
-#&gt; SD.parent_0 2.70034095 -0.7003441 6.1010260
-#&gt; SD.log_k_m1 0.08269959 -0.0456860 0.2110852
-#&gt; SD.f_parent_qlogis 0.39452161 0.1376650 0.6513782
-#&gt; SD.log_k1 0.90605744 0.2946394 1.5174755
-#&gt; SD.log_k2 0.77604374 0.2646031 1.2874844
-#&gt; SD.g_qlogis 0.37531563 -0.6836568 1.4342881
+#&gt; est. lower upper
+#&gt; SD.parent_0 2.88564 -0.5163 6.2876
+#&gt; SD.log_k_m1 0.08502 -0.0427 0.2127
+#&gt; SD.f_parent_qlogis 0.38857 0.1350 0.6421
+#&gt; SD.log_k1 0.92338 0.3296 1.5172
+#&gt; SD.log_k2 0.78644 0.2817 1.2912
+#&gt; SD.g_qlogis 0.34614 -0.8727 1.5650
#&gt;
#&gt; Variance model:
-#&gt; est. lower upper
-#&gt; a.1 0.65736042 0.48750246 0.82721839
-#&gt; b.1 0.06424086 0.05011127 0.07837046
+#&gt; est. lower upper
+#&gt; a.1 0.65859 0.49250 0.82469
+#&gt; b.1 0.06411 0.05006 0.07817
#&gt;
#&gt; Backtransformed parameters with asymmetric confidence intervals:
-#&gt; est. lower upper
-#&gt; parent_0 101.35835807 97.88465048 104.83206565
-#&gt; k_m1 0.01713815 0.01520479 0.01931734
-#&gt; f_parent_to_m1 0.27925085 0.21207372 0.35803781
-#&gt; k1 0.05388182 0.02308824 0.12574588
-#&gt; k2 0.02886015 0.01421864 0.05857864
-#&gt; g 0.47688031 0.27536216 0.68621766
+#&gt; est. lower upper
+#&gt; parent_0 101.44231 97.86220 105.02241
+#&gt; k_m1 0.01707 0.01513 0.01926
+#&gt; f_parent_to_m1 0.27811 0.21201 0.35551
+#&gt; k1 0.05118 0.02213 0.11834
+#&gt; k2 0.03027 0.01491 0.06145
+#&gt; g 0.48878 0.24675 0.73618
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_m1 0.2793
-#&gt; parent_sink 0.7207
+#&gt; parent_m1 0.2781
+#&gt; parent_sink 0.7219
#&gt;
#&gt; Estimated disappearance times:
#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
-#&gt; parent 17.57 63.28 19.05 12.86 24.02
-#&gt; m1 40.44 134.35 NA NA NA
+#&gt; parent 17.53 61.64 18.55 13.54 22.9
+#&gt; m1 40.60 134.88 NA NA NA
#&gt;
#&gt; Data:
-#&gt; ds name time observed predicted residual standardized
-#&gt; ds 1 parent 0 89.8 9.848e+01 -8.68339 1.243323
-#&gt; ds 1 parent 0 104.1 9.848e+01 5.61661 -0.804209
-#&gt; ds 1 parent 1 88.7 9.403e+01 -5.32943 0.795687
-#&gt; ds 1 parent 1 95.5 9.403e+01 1.47057 -0.219557
-#&gt; ds 1 parent 3 81.8 8.584e+01 -4.04129 0.654791
-#&gt; ds 1 parent 3 94.5 8.584e+01 8.65871 -1.402929
-#&gt; ds 1 parent 7 71.5 7.196e+01 -0.46034 0.087182
-#&gt; ds 1 parent 7 70.3 7.196e+01 -1.66034 0.314448
-#&gt; ds 1 parent 14 54.2 5.384e+01 0.36125 -0.087766
-#&gt; ds 1 parent 14 49.6 5.384e+01 -4.23875 1.029821
-#&gt; ds 1 parent 28 31.5 3.220e+01 -0.69922 0.256514
-#&gt; ds 1 parent 28 28.8 3.220e+01 -3.39922 1.247025
-#&gt; ds 1 parent 60 12.1 1.264e+01 -0.53539 0.364441
-#&gt; ds 1 parent 60 13.6 1.264e+01 0.96461 -0.656614
-#&gt; ds 1 parent 90 6.2 6.081e+00 0.11929 -0.113824
-#&gt; ds 1 parent 90 8.3 6.081e+00 2.21929 -2.117659
-#&gt; ds 1 parent 120 2.2 3.055e+00 -0.85531 1.001955
-#&gt; ds 1 parent 120 2.4 3.055e+00 -0.65531 0.767664
-#&gt; ds 1 m1 1 0.3 1.115e+00 -0.81540 1.118502
-#&gt; ds 1 m1 1 0.2 1.115e+00 -0.91540 1.255673
-#&gt; ds 1 m1 3 2.2 3.111e+00 -0.91095 1.062691
-#&gt; ds 1 m1 3 3.0 3.111e+00 -0.11095 0.129432
-#&gt; ds 1 m1 7 6.5 6.292e+00 0.20799 -0.195930
-#&gt; ds 1 m1 7 5.0 6.292e+00 -1.29201 1.217079
-#&gt; ds 1 m1 14 10.2 9.886e+00 0.31362 -0.242650
-#&gt; ds 1 m1 14 9.5 9.886e+00 -0.38638 0.298948
-#&gt; ds 1 m1 28 12.2 1.259e+01 -0.39388 0.268603
-#&gt; ds 1 m1 28 13.4 1.259e+01 0.80612 -0.549726
-#&gt; ds 1 m1 60 11.8 1.092e+01 0.87659 -0.644982
-#&gt; ds 1 m1 60 13.2 1.092e+01 2.27659 -1.675083
-#&gt; ds 1 m1 90 6.6 7.814e+00 -1.21445 1.047509
-#&gt; ds 1 m1 90 9.3 7.814e+00 1.48555 -1.281347
-#&gt; ds 1 m1 120 3.5 5.275e+00 -1.77526 1.781944
-#&gt; ds 1 m1 120 5.4 5.275e+00 0.12474 -0.125213
-#&gt; ds 2 parent 0 118.0 1.045e+02 13.54366 -1.838241
-#&gt; ds 2 parent 0 99.8 1.045e+02 -4.65634 0.631992
-#&gt; ds 2 parent 1 90.2 9.872e+01 -8.51733 1.216927
-#&gt; ds 2 parent 1 94.6 9.872e+01 -4.11733 0.588270
-#&gt; ds 2 parent 3 96.1 8.872e+01 7.38009 -1.160975
-#&gt; ds 2 parent 3 78.4 8.872e+01 -10.31991 1.623443
-#&gt; ds 2 parent 7 77.9 7.337e+01 4.52584 -0.842647
-#&gt; ds 2 parent 7 77.7 7.337e+01 4.32584 -0.805409
-#&gt; ds 2 parent 14 56.0 5.616e+01 -0.15795 0.037034
-#&gt; ds 2 parent 14 54.7 5.616e+01 -1.45795 0.341841
-#&gt; ds 2 parent 28 36.6 3.859e+01 -1.99435 0.635813
-#&gt; ds 2 parent 28 36.8 3.859e+01 -1.79435 0.572052
-#&gt; ds 2 parent 60 22.1 2.113e+01 0.97273 -0.482843
-#&gt; ds 2 parent 60 24.7 2.113e+01 3.57273 -1.773425
-#&gt; ds 2 parent 90 12.4 1.258e+01 -0.17909 0.122205
-#&gt; ds 2 parent 90 10.8 1.258e+01 -1.77909 1.214019
-#&gt; ds 2 parent 120 6.8 7.509e+00 -0.70864 0.621767
-#&gt; ds 2 parent 120 7.9 7.509e+00 0.39136 -0.343380
-#&gt; ds 2 m1 1 1.3 1.466e+00 -0.16566 0.220431
-#&gt; ds 2 m1 3 3.7 3.947e+00 -0.24719 0.271357
-#&gt; ds 2 m1 3 4.7 3.947e+00 0.75281 -0.826421
-#&gt; ds 2 m1 7 8.1 7.501e+00 0.59910 -0.525881
-#&gt; ds 2 m1 7 7.9 7.501e+00 0.39910 -0.350323
-#&gt; ds 2 m1 14 10.1 1.082e+01 -0.71564 0.529253
-#&gt; ds 2 m1 14 10.3 1.082e+01 -0.51564 0.381342
-#&gt; ds 2 m1 28 10.7 1.248e+01 -1.78322 1.221977
-#&gt; ds 2 m1 28 12.2 1.248e+01 -0.28322 0.194082
-#&gt; ds 2 m1 60 10.7 1.058e+01 0.12295 -0.091967
-#&gt; ds 2 m1 60 12.5 1.058e+01 1.92295 -1.438427
-#&gt; ds 2 m1 90 9.1 8.029e+00 1.07074 -0.912688
-#&gt; ds 2 m1 90 7.4 8.029e+00 -0.62926 0.536381
-#&gt; ds 2 m1 120 6.1 5.816e+00 0.28391 -0.275375
-#&gt; ds 2 m1 120 4.5 5.816e+00 -1.31609 1.276529
-#&gt; ds 3 parent 0 106.2 1.048e+02 1.43237 -0.193885
-#&gt; ds 3 parent 0 106.9 1.048e+02 2.13237 -0.288636
-#&gt; ds 3 parent 1 107.4 9.616e+01 11.23530 -1.643774
-#&gt; ds 3 parent 1 96.1 9.616e+01 -0.06470 0.009466
-#&gt; ds 3 parent 3 79.4 8.238e+01 -2.97800 0.500554
-#&gt; ds 3 parent 3 82.6 8.238e+01 0.22200 -0.037315
-#&gt; ds 3 parent 7 63.9 6.427e+01 -0.36601 0.076477
-#&gt; ds 3 parent 7 62.4 6.427e+01 -1.86601 0.389900
-#&gt; ds 3 parent 14 51.0 4.825e+01 2.74941 -0.731807
-#&gt; ds 3 parent 14 47.1 4.825e+01 -1.15059 0.306250
-#&gt; ds 3 parent 28 36.1 3.501e+01 1.09474 -0.376700
-#&gt; ds 3 parent 28 36.6 3.501e+01 1.59474 -0.548750
-#&gt; ds 3 parent 60 20.1 2.050e+01 -0.40214 0.203675
-#&gt; ds 3 parent 60 19.8 2.050e+01 -0.70214 0.355617
-#&gt; ds 3 parent 90 11.3 1.257e+01 -1.27210 0.868328
-#&gt; ds 3 parent 90 10.7 1.257e+01 -1.87210 1.277883
-#&gt; ds 3 parent 120 8.2 7.710e+00 0.48984 -0.424960
-#&gt; ds 3 parent 120 7.3 7.710e+00 -0.41016 0.355837
-#&gt; ds 3 m1 0 0.8 -1.421e-13 0.80000 -1.216988
-#&gt; ds 3 m1 1 1.8 1.928e+00 -0.12842 0.164382
-#&gt; ds 3 m1 1 2.3 1.928e+00 0.37158 -0.475623
-#&gt; ds 3 m1 3 4.2 4.925e+00 -0.72511 0.744654
-#&gt; ds 3 m1 3 4.1 4.925e+00 -0.82511 0.847349
-#&gt; ds 3 m1 7 6.8 8.542e+00 -1.74215 1.444429
-#&gt; ds 3 m1 7 10.1 8.542e+00 1.55785 -1.291627
-#&gt; ds 3 m1 14 11.4 1.096e+01 0.44492 -0.326877
-#&gt; ds 3 m1 14 12.8 1.096e+01 1.84492 -1.355438
-#&gt; ds 3 m1 28 11.5 1.122e+01 0.27920 -0.202587
-#&gt; ds 3 m1 28 10.6 1.122e+01 -0.62080 0.450442
-#&gt; ds 3 m1 60 7.5 8.912e+00 -1.41171 1.147867
-#&gt; ds 3 m1 60 8.6 8.912e+00 -0.31171 0.253453
-#&gt; ds 3 m1 90 7.3 6.683e+00 0.61657 -0.567369
-#&gt; ds 3 m1 90 8.1 6.683e+00 1.41657 -1.303536
-#&gt; ds 3 m1 120 5.3 4.825e+00 0.47527 -0.491339
-#&gt; ds 3 m1 120 3.8 4.825e+00 -1.02473 1.059361
-#&gt; ds 4 parent 0 104.7 9.956e+01 5.14415 -0.729366
-#&gt; ds 4 parent 0 88.3 9.956e+01 -11.25585 1.595915
-#&gt; ds 4 parent 1 94.2 9.639e+01 -2.19462 0.320391
-#&gt; ds 4 parent 1 94.6 9.639e+01 -1.79462 0.261995
-#&gt; ds 4 parent 3 78.1 9.044e+01 -12.34368 1.908558
-#&gt; ds 4 parent 3 96.5 9.044e+01 6.05632 -0.936418
-#&gt; ds 4 parent 7 76.2 7.988e+01 -3.67799 0.635364
-#&gt; ds 4 parent 7 77.8 7.988e+01 -2.07799 0.358968
-#&gt; ds 4 parent 14 70.8 6.492e+01 5.88059 -1.218059
-#&gt; ds 4 parent 14 67.3 6.492e+01 2.38059 -0.493097
-#&gt; ds 4 parent 28 43.1 4.442e+01 -1.32411 0.377111
-#&gt; ds 4 parent 28 45.1 4.442e+01 0.67589 -0.192494
-#&gt; ds 4 parent 60 21.3 2.136e+01 -0.06143 0.030267
-#&gt; ds 4 parent 60 23.5 2.136e+01 2.13857 -1.053671
-#&gt; ds 4 parent 90 11.8 1.187e+01 -0.06548 0.046122
-#&gt; ds 4 parent 90 12.1 1.187e+01 0.23452 -0.165204
-#&gt; ds 4 parent 120 7.0 6.864e+00 0.13645 -0.124240
-#&gt; ds 4 parent 120 6.2 6.864e+00 -0.66355 0.604171
-#&gt; ds 4 m1 0 1.6 8.811e-13 1.60000 -2.433977
-#&gt; ds 4 m1 1 0.9 6.943e-01 0.20568 -0.293006
-#&gt; ds 4 m1 3 3.7 1.964e+00 1.73568 -2.215152
-#&gt; ds 4 m1 3 2.0 1.964e+00 0.03568 -0.045539
-#&gt; ds 4 m1 7 3.6 4.082e+00 -0.48184 0.523977
-#&gt; ds 4 m1 7 3.8 4.082e+00 -0.28184 0.306486
-#&gt; ds 4 m1 14 7.1 6.694e+00 0.40571 -0.373099
-#&gt; ds 4 m1 14 6.6 6.694e+00 -0.09429 0.086710
-#&gt; ds 4 m1 28 9.5 9.147e+00 0.35343 -0.283895
-#&gt; ds 4 m1 28 9.3 9.147e+00 0.15343 -0.123245
-#&gt; ds 4 m1 60 8.3 8.788e+00 -0.48803 0.399399
-#&gt; ds 4 m1 60 9.0 8.788e+00 0.21197 -0.173474
-#&gt; ds 4 m1 90 6.6 6.644e+00 -0.04431 0.040866
-#&gt; ds 4 m1 90 7.7 6.644e+00 1.05569 -0.973711
-#&gt; ds 4 m1 120 3.7 4.667e+00 -0.96735 1.010605
-#&gt; ds 4 m1 120 3.5 4.667e+00 -1.16735 1.219548
-#&gt; ds 5 parent 0 110.4 1.020e+02 8.37855 -1.161863
-#&gt; ds 5 parent 0 112.1 1.020e+02 10.07855 -1.397604
-#&gt; ds 5 parent 1 93.5 9.494e+01 -1.43722 0.212725
-#&gt; ds 5 parent 1 91.0 9.494e+01 -3.93722 0.582755
-#&gt; ds 5 parent 3 71.0 8.280e+01 -11.80256 1.974773
-#&gt; ds 5 parent 3 89.7 8.280e+01 6.89744 -1.154061
-#&gt; ds 5 parent 7 60.4 6.485e+01 -4.45291 0.923157
-#&gt; ds 5 parent 7 59.1 6.485e+01 -5.75291 1.192667
-#&gt; ds 5 parent 14 56.5 4.626e+01 10.24038 -2.821727
-#&gt; ds 5 parent 14 47.0 4.626e+01 0.74038 -0.204011
-#&gt; ds 5 parent 28 30.2 3.034e+01 -0.13506 0.051824
-#&gt; ds 5 parent 28 23.9 3.034e+01 -6.43506 2.469220
-#&gt; ds 5 parent 60 17.0 1.795e+01 -0.95206 0.525822
-#&gt; ds 5 parent 60 18.7 1.795e+01 0.74794 -0.413085
-#&gt; ds 5 parent 90 11.3 1.186e+01 -0.56163 0.395692
-#&gt; ds 5 parent 90 11.9 1.186e+01 0.03837 -0.027033
-#&gt; ds 5 parent 120 9.0 7.866e+00 1.13427 -0.975579
-#&gt; ds 5 parent 120 8.1 7.866e+00 0.23427 -0.201493
-#&gt; ds 5 m1 0 0.7 -4.263e-14 0.70000 -1.064865
-#&gt; ds 5 m1 1 3.0 3.169e+00 -0.16908 0.196384
-#&gt; ds 5 m1 1 2.6 3.169e+00 -0.56908 0.660990
-#&gt; ds 5 m1 3 5.1 8.455e+00 -3.35479 2.794486
-#&gt; ds 5 m1 3 7.5 8.455e+00 -0.95479 0.795325
-#&gt; ds 5 m1 7 16.5 1.577e+01 0.73235 -0.438460
-#&gt; ds 5 m1 7 19.0 1.577e+01 3.23235 -1.935208
-#&gt; ds 5 m1 14 22.9 2.202e+01 0.88393 -0.426673
-#&gt; ds 5 m1 14 23.2 2.202e+01 1.18393 -0.571482
-#&gt; ds 5 m1 28 22.2 2.399e+01 -1.79091 0.814583
-#&gt; ds 5 m1 28 24.4 2.399e+01 0.40909 -0.186073
-#&gt; ds 5 m1 60 15.5 1.872e+01 -3.21988 1.731175
-#&gt; ds 5 m1 60 19.8 1.872e+01 1.08012 -0.580725
-#&gt; ds 5 m1 90 14.9 1.383e+01 1.06749 -0.690500
-#&gt; ds 5 m1 90 14.2 1.383e+01 0.36749 -0.237710
-#&gt; ds 5 m1 120 10.9 1.004e+01 0.85568 -0.656897
-#&gt; ds 5 m1 120 10.4 1.004e+01 0.35568 -0.273054</div><div class='input'><span class='co'># }</span>
+#&gt; ds name time observed predicted residual standardized
+#&gt; ds 1 parent 0 89.8 9.869e+01 -8.894553 1.273163
+#&gt; ds 1 parent 0 104.1 9.869e+01 5.405447 -0.773734
+#&gt; ds 1 parent 1 88.7 9.413e+01 -5.426448 0.810727
+#&gt; ds 1 parent 1 95.5 9.413e+01 1.373552 -0.205213
+#&gt; ds 1 parent 3 81.8 8.576e+01 -3.961821 0.643463
+#&gt; ds 1 parent 3 94.5 8.576e+01 8.738179 -1.419220
+#&gt; ds 1 parent 7 71.5 7.168e+01 -0.184828 0.035175
+#&gt; ds 1 parent 7 70.3 7.168e+01 -1.384828 0.263550
+#&gt; ds 1 parent 14 54.2 5.351e+01 0.688235 -0.168298
+#&gt; ds 1 parent 14 49.6 5.351e+01 -3.911765 0.956565
+#&gt; ds 1 parent 28 31.5 3.209e+01 -0.590445 0.217395
+#&gt; ds 1 parent 28 28.8 3.209e+01 -3.290445 1.211502
+#&gt; ds 1 parent 60 12.1 1.272e+01 -0.618158 0.419377
+#&gt; ds 1 parent 60 13.6 1.272e+01 0.881842 -0.598269
+#&gt; ds 1 parent 90 6.2 6.085e+00 0.115212 -0.109861
+#&gt; ds 1 parent 90 8.3 6.085e+00 2.215212 -2.112329
+#&gt; ds 1 parent 120 2.2 3.009e+00 -0.809439 0.950563
+#&gt; ds 1 parent 120 2.4 3.009e+00 -0.609439 0.715693
+#&gt; ds 1 m1 1 0.3 1.129e+00 -0.828817 1.133869
+#&gt; ds 1 m1 1 0.2 1.129e+00 -0.928817 1.270675
+#&gt; ds 1 m1 3 2.2 3.141e+00 -0.940880 1.094093
+#&gt; ds 1 m1 3 3.0 3.141e+00 -0.140880 0.163821
+#&gt; ds 1 m1 7 6.5 6.326e+00 0.174162 -0.163662
+#&gt; ds 1 m1 7 5.0 6.326e+00 -1.325838 1.245901
+#&gt; ds 1 m1 14 10.2 9.883e+00 0.317417 -0.245642
+#&gt; ds 1 m1 14 9.5 9.883e+00 -0.382583 0.296072
+#&gt; ds 1 m1 28 12.2 1.251e+01 -0.309856 0.212138
+#&gt; ds 1 m1 28 13.4 1.251e+01 0.890144 -0.609422
+#&gt; ds 1 m1 60 11.8 1.086e+01 0.940009 -0.693807
+#&gt; ds 1 m1 60 13.2 1.086e+01 2.340009 -1.727126
+#&gt; ds 1 m1 90 6.6 7.823e+00 -1.222977 1.054158
+#&gt; ds 1 m1 90 9.3 7.823e+00 1.477023 -1.273135
+#&gt; ds 1 m1 120 3.5 5.315e+00 -1.815201 1.816354
+#&gt; ds 1 m1 120 5.4 5.315e+00 0.084799 -0.084853
+#&gt; ds 2 parent 0 118.0 1.031e+02 14.876736 -2.046284
+#&gt; ds 2 parent 0 99.8 1.031e+02 -3.323264 0.457112
+#&gt; ds 2 parent 1 90.2 9.757e+01 -7.371379 1.066126
+#&gt; ds 2 parent 1 94.6 9.757e+01 -2.971379 0.429752
+#&gt; ds 2 parent 3 96.1 8.788e+01 8.222746 -1.306721
+#&gt; ds 2 parent 3 78.4 8.788e+01 -9.477254 1.506081
+#&gt; ds 2 parent 7 77.9 7.293e+01 4.972272 -0.932149
+#&gt; ds 2 parent 7 77.7 7.293e+01 4.772272 -0.894656
+#&gt; ds 2 parent 14 56.0 5.602e+01 -0.016773 0.003947
+#&gt; ds 2 parent 14 54.7 5.602e+01 -1.316773 0.309830
+#&gt; ds 2 parent 28 36.6 3.855e+01 -1.945779 0.621680
+#&gt; ds 2 parent 28 36.8 3.855e+01 -1.745779 0.557779
+#&gt; ds 2 parent 60 22.1 2.101e+01 1.086693 -0.541771
+#&gt; ds 2 parent 60 24.7 2.101e+01 3.686693 -1.838002
+#&gt; ds 2 parent 90 12.4 1.246e+01 -0.058759 0.040319
+#&gt; ds 2 parent 90 10.8 1.246e+01 -1.658759 1.138195
+#&gt; ds 2 parent 120 6.8 7.406e+00 -0.606226 0.534861
+#&gt; ds 2 parent 120 7.9 7.406e+00 0.493774 -0.435647
+#&gt; ds 2 m1 1 1.3 1.438e+00 -0.138236 0.184118
+#&gt; ds 2 m1 3 3.7 3.879e+00 -0.178617 0.196874
+#&gt; ds 2 m1 3 4.7 3.879e+00 0.821383 -0.905344
+#&gt; ds 2 m1 7 8.1 7.389e+00 0.710951 -0.627868
+#&gt; ds 2 m1 7 7.9 7.389e+00 0.510951 -0.451240
+#&gt; ds 2 m1 14 10.1 1.069e+01 -0.593533 0.441556
+#&gt; ds 2 m1 14 10.3 1.069e+01 -0.393533 0.292767
+#&gt; ds 2 m1 28 10.7 1.240e+01 -1.703647 1.171837
+#&gt; ds 2 m1 28 12.2 1.240e+01 -0.203647 0.140077
+#&gt; ds 2 m1 60 10.7 1.055e+01 0.147672 -0.110605
+#&gt; ds 2 m1 60 12.5 1.055e+01 1.947672 -1.458786
+#&gt; ds 2 m1 90 9.1 8.010e+00 1.090041 -0.929963
+#&gt; ds 2 m1 90 7.4 8.010e+00 -0.609959 0.520383
+#&gt; ds 2 m1 120 6.1 5.793e+00 0.306797 -0.297858
+#&gt; ds 2 m1 120 4.5 5.793e+00 -1.293203 1.255523
+#&gt; ds 3 parent 0 106.2 1.035e+02 2.712344 -0.371886
+#&gt; ds 3 parent 0 106.9 1.035e+02 3.412344 -0.467862
+#&gt; ds 3 parent 1 107.4 9.548e+01 11.924044 -1.758752
+#&gt; ds 3 parent 1 96.1 9.548e+01 0.624044 -0.092044
+#&gt; ds 3 parent 3 79.4 8.246e+01 -3.056105 0.514055
+#&gt; ds 3 parent 3 82.6 8.246e+01 0.143895 -0.024204
+#&gt; ds 3 parent 7 63.9 6.489e+01 -0.991141 0.205676
+#&gt; ds 3 parent 7 62.4 6.489e+01 -2.491141 0.516947
+#&gt; ds 3 parent 14 51.0 4.869e+01 2.306824 -0.610198
+#&gt; ds 3 parent 14 47.1 4.869e+01 -1.593176 0.421425
+#&gt; ds 3 parent 28 36.1 3.480e+01 1.304261 -0.451388
+#&gt; ds 3 parent 28 36.6 3.480e+01 1.804261 -0.624431
+#&gt; ds 3 parent 60 20.1 1.988e+01 0.221952 -0.114821
+#&gt; ds 3 parent 60 19.8 1.988e+01 -0.078048 0.040376
+#&gt; ds 3 parent 90 11.3 1.194e+01 -0.642458 0.451083
+#&gt; ds 3 parent 90 10.7 1.194e+01 -1.242458 0.872355
+#&gt; ds 3 parent 120 8.2 7.176e+00 1.023847 -0.915231
+#&gt; ds 3 parent 120 7.3 7.176e+00 0.123847 -0.110709
+#&gt; ds 3 m1 0 0.8 8.527e-13 0.800000 -1.214712
+#&gt; ds 3 m1 1 1.8 1.856e+00 -0.055925 0.071921
+#&gt; ds 3 m1 1 2.3 1.856e+00 0.444075 -0.571099
+#&gt; ds 3 m1 3 4.2 4.780e+00 -0.580164 0.601168
+#&gt; ds 3 m1 3 4.1 4.780e+00 -0.680164 0.704788
+#&gt; ds 3 m1 7 6.8 8.410e+00 -1.609920 1.344090
+#&gt; ds 3 m1 7 10.1 8.410e+00 1.690080 -1.411014
+#&gt; ds 3 m1 14 11.4 1.098e+01 0.424444 -0.311572
+#&gt; ds 3 m1 14 12.8 1.098e+01 1.824444 -1.339271
+#&gt; ds 3 m1 28 11.5 1.142e+01 0.079336 -0.057043
+#&gt; ds 3 m1 28 10.6 1.142e+01 -0.820664 0.590065
+#&gt; ds 3 m1 60 7.5 9.110e+00 -1.610231 1.295778
+#&gt; ds 3 m1 60 8.6 9.110e+00 -0.510231 0.410591
+#&gt; ds 3 m1 90 7.3 6.799e+00 0.501085 -0.457825
+#&gt; ds 3 m1 90 8.1 6.799e+00 1.301085 -1.188759
+#&gt; ds 3 m1 120 5.3 4.868e+00 0.431505 -0.444518
+#&gt; ds 3 m1 120 3.8 4.868e+00 -1.068495 1.100718
+#&gt; ds 4 parent 0 104.7 9.926e+01 5.444622 -0.775351
+#&gt; ds 4 parent 0 88.3 9.926e+01 -10.955378 1.560119
+#&gt; ds 4 parent 1 94.2 9.618e+01 -1.978413 0.289883
+#&gt; ds 4 parent 1 94.6 9.618e+01 -1.578413 0.231274
+#&gt; ds 4 parent 3 78.1 9.037e+01 -12.268550 1.901399
+#&gt; ds 4 parent 3 96.5 9.037e+01 6.131450 -0.950262
+#&gt; ds 4 parent 7 76.2 7.999e+01 -3.794958 0.655739
+#&gt; ds 4 parent 7 77.8 7.999e+01 -2.194958 0.379272
+#&gt; ds 4 parent 14 70.8 6.518e+01 5.624996 -1.162874
+#&gt; ds 4 parent 14 67.3 6.518e+01 2.124996 -0.439307
+#&gt; ds 4 parent 28 43.1 4.462e+01 -1.517860 0.431312
+#&gt; ds 4 parent 28 45.1 4.462e+01 0.482140 -0.137004
+#&gt; ds 4 parent 60 21.3 2.130e+01 0.003305 -0.001633
+#&gt; ds 4 parent 60 23.5 2.130e+01 2.203305 -1.088598
+#&gt; ds 4 parent 90 11.8 1.180e+01 -0.002834 0.002002
+#&gt; ds 4 parent 90 12.1 1.180e+01 0.297166 -0.209966
+#&gt; ds 4 parent 120 7.0 6.868e+00 0.132251 -0.120348
+#&gt; ds 4 parent 120 6.2 6.868e+00 -0.667749 0.607650
+#&gt; ds 4 m1 0 1.6 0.000e+00 1.600000 -2.429424
+#&gt; ds 4 m1 1 0.9 6.826e-01 0.217363 -0.309476
+#&gt; ds 4 m1 3 3.7 1.935e+00 1.765082 -2.255277
+#&gt; ds 4 m1 3 2.0 1.935e+00 0.065082 -0.083157
+#&gt; ds 4 m1 7 3.6 4.035e+00 -0.434805 0.474018
+#&gt; ds 4 m1 7 3.8 4.035e+00 -0.234805 0.255981
+#&gt; ds 4 m1 14 7.1 6.652e+00 0.448187 -0.413053
+#&gt; ds 4 m1 14 6.6 6.652e+00 -0.051813 0.047751
+#&gt; ds 4 m1 28 9.5 9.156e+00 0.343805 -0.276011
+#&gt; ds 4 m1 28 9.3 9.156e+00 0.143805 -0.115448
+#&gt; ds 4 m1 60 8.3 8.848e+00 -0.547762 0.446843
+#&gt; ds 4 m1 60 9.0 8.848e+00 0.152238 -0.124190
+#&gt; ds 4 m1 90 6.6 6.674e+00 -0.073979 0.068090
+#&gt; ds 4 m1 90 7.7 6.674e+00 1.026021 -0.944353
+#&gt; ds 4 m1 120 3.7 4.668e+00 -0.967537 1.010122
+#&gt; ds 4 m1 120 3.5 4.668e+00 -1.167537 1.218925
+#&gt; ds 5 parent 0 110.4 1.022e+02 8.170986 -1.132847
+#&gt; ds 5 parent 0 112.1 1.022e+02 9.870986 -1.368539
+#&gt; ds 5 parent 1 93.5 9.513e+01 -1.630764 0.241319
+#&gt; ds 5 parent 1 91.0 9.513e+01 -4.130764 0.611268
+#&gt; ds 5 parent 3 71.0 8.296e+01 -11.964279 2.001495
+#&gt; ds 5 parent 3 89.7 8.296e+01 6.735721 -1.126813
+#&gt; ds 5 parent 7 60.4 6.495e+01 -4.547441 0.942951
+#&gt; ds 5 parent 7 59.1 6.495e+01 -5.847441 1.212518
+#&gt; ds 5 parent 14 56.5 4.626e+01 10.241319 -2.825682
+#&gt; ds 5 parent 14 47.0 4.626e+01 0.741319 -0.204537
+#&gt; ds 5 parent 28 30.2 3.026e+01 -0.058478 0.022504
+#&gt; ds 5 parent 28 23.9 3.026e+01 -6.358478 2.446932
+#&gt; ds 5 parent 60 17.0 1.792e+01 -0.919046 0.508481
+#&gt; ds 5 parent 60 18.7 1.792e+01 0.780954 -0.432079
+#&gt; ds 5 parent 90 11.3 1.187e+01 -0.573917 0.404206
+#&gt; ds 5 parent 90 11.9 1.187e+01 0.026083 -0.018370
+#&gt; ds 5 parent 120 9.0 7.898e+00 1.102089 -0.946039
+#&gt; ds 5 parent 120 8.1 7.898e+00 0.202089 -0.173474
+#&gt; ds 5 m1 0 0.7 -1.421e-14 0.700000 -1.062873
+#&gt; ds 5 m1 1 3.0 3.144e+00 -0.143526 0.166865
+#&gt; ds 5 m1 1 2.6 3.144e+00 -0.543526 0.631910
+#&gt; ds 5 m1 3 5.1 8.390e+00 -3.290265 2.749870
+#&gt; ds 5 m1 3 7.5 8.390e+00 -0.890265 0.744048
+#&gt; ds 5 m1 7 16.5 1.566e+01 0.841368 -0.506082
+#&gt; ds 5 m1 7 19.0 1.566e+01 3.341368 -2.009830
+#&gt; ds 5 m1 14 22.9 2.188e+01 1.017753 -0.493689
+#&gt; ds 5 m1 14 23.2 2.188e+01 1.317753 -0.639212
+#&gt; ds 5 m1 28 22.2 2.386e+01 -1.655914 0.756794
+#&gt; ds 5 m1 28 24.4 2.386e+01 0.544086 -0.248661
+#&gt; ds 5 m1 60 15.5 1.859e+01 -3.091124 1.670405
+#&gt; ds 5 m1 60 19.8 1.859e+01 1.208876 -0.653262
+#&gt; ds 5 m1 90 14.9 1.372e+01 1.176815 -0.764948
+#&gt; ds 5 m1 90 14.2 1.372e+01 0.476815 -0.309937
+#&gt; ds 5 m1 120 10.9 9.961e+00 0.938796 -0.723690
+#&gt; ds 5 m1 120 10.4 9.961e+00 0.438796 -0.338255</div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
diff --git a/man/saem.Rd b/man/saem.Rd
index c37fbcfe..3cd9f7f8 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/saemix.R
+% Please edit documentation in R/saem.R
\name{saem}
\alias{saem}
\alias{saem.mmkin}
@@ -17,6 +17,7 @@ saem(object, control, ...)
cores = 1,
verbose = FALSE,
suppressPlot = TRUE,
+ quiet = FALSE,
...
)
@@ -32,19 +33,22 @@ saemix_data(object, verbose = FALSE, ...)
\item{control}{Passed to \link[saemix:saemix]{saemix::saemix}}
-\item{\dots}{Further parameters passed to \link[saemix:saemixData]{saemix::saemixData}
-and \link[saemix:saemixModel]{saemix::saemixModel}.}
+\item{\dots}{Further parameters passed to \link[saemix:saemixModel]{saemix::saemixModel}.}
\item{cores}{The number of cores to be used for multicore processing using
\code{\link[parallel:mclapply]{parallel::mclapply()}}. Using more than 1 core is experimental and may
-lead to uncontrolled forking, apparently depending on the BLAS version
+lead to excessive forking, apparently depending on the BLAS version
used.}
-\item{verbose}{Should we print information about created objects?}
+\item{verbose}{Should we print information about created objects of
+type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?}
\item{suppressPlot}{Should we suppress any plotting that is done
by the saemix function?}
+\item{quiet}{Should we suppress the messages saemix prints at the beginning
+and the end of the optimisation process?}
+
\item{x}{An saem.mmkin object to print}
\item{digits}{Number of digits to use for printing}

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