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-rw-r--r--docs/dev/404.html2
-rw-r--r--docs/dev/articles/FOCUS_D.html8
-rw-r--r--docs/dev/articles/FOCUS_L.html40
-rw-r--r--docs/dev/articles/index.html2
-rw-r--r--docs/dev/articles/mkin.html2
-rw-r--r--docs/dev/articles/twa.html2
-rw-r--r--docs/dev/articles/web_only/FOCUS_Z.html2
-rw-r--r--docs/dev/articles/web_only/NAFTA_examples.html2
-rw-r--r--docs/dev/articles/web_only/benchmarks.html20
-rw-r--r--docs/dev/articles/web_only/compiled_models.html14
-rw-r--r--docs/dev/authors.html2
-rw-r--r--docs/dev/index.html4
-rw-r--r--docs/dev/news/index.html2
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/confint.mkinfit.html6
-rw-r--r--docs/dev/reference/index.html2
-rw-r--r--docs/dev/reference/mkinfit.html28
-rw-r--r--docs/dev/reference/mmkin.html6
-rw-r--r--docs/dev/reference/nlme-1.pngbin71631 -> 70555 bytes
-rw-r--r--docs/dev/reference/nlme.html20
-rw-r--r--docs/dev/reference/nlme.mmkin.html2
-rw-r--r--docs/dev/reference/parms.html2
-rw-r--r--docs/dev/reference/saemix.html14
-rw-r--r--docs/dev/reference/transform_odeparms.html4
24 files changed, 94 insertions, 94 deletions
diff --git a/docs/dev/404.html b/docs/dev/404.html
index 535f64b6..1434d6b8 100644
--- a/docs/dev/404.html
+++ b/docs/dev/404.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html
index 0b3ae03a..7d5dd732 100644
--- a/docs/dev/articles/FOCUS_D.html
+++ b/docs/dev/articles/FOCUS_D.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -181,8 +181,8 @@
<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.3
## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 06:02:21 2020
-## Date of summary: Wed May 27 06:02:21 2020
+## Date of fit: Wed May 27 07:51:36 2020
+## Date of summary: Wed May 27 07:51:37 2020
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -190,7 +190,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 421 model solutions performed in 0.177 s
+## Fitted using 421 model solutions performed in 0.173 s
##
## Error model: Constant variance
##
diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 91043d0f..d69815ab 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -127,15 +127,15 @@
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L1.SFO</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.3
## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 06:02:23 2020
-## Date of summary: Wed May 27 06:02:23 2020
+## Date of fit: Wed May 27 07:51:39 2020
+## Date of summary: Wed May 27 07:51:39 2020
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.03 s
+## Fitted using 133 model solutions performed in 0.031 s
##
## Error model: Constant variance
##
@@ -228,8 +228,8 @@
## doubtful</code></pre>
<pre><code>## mkin version used for fitting: 0.9.50.3
## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 06:02:24 2020
-## Date of summary: Wed May 27 06:02:24 2020
+## Date of fit: Wed May 27 07:51:39 2020
+## Date of summary: Wed May 27 07:51:39 2020
##
##
## Warning: Optimisation did not converge:
@@ -336,15 +336,15 @@
<div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.FOMC</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.3
## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 06:02:24 2020
-## Date of summary: Wed May 27 06:02:24 2020
+## Date of fit: Wed May 27 07:51:40 2020
+## Date of summary: Wed May 27 07:51:40 2020
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 239 model solutions performed in 0.047 s
+## Fitted using 239 model solutions performed in 0.048 s
##
## Error model: Constant variance
##
@@ -415,8 +415,8 @@
<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.DFOP</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.3
## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 06:02:24 2020
-## Date of summary: Wed May 27 06:02:24 2020
+## Date of fit: Wed May 27 07:51:40 2020
+## Date of summary: Wed May 27 07:51:40 2020
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -518,8 +518,8 @@
<div class="sourceCode" id="cb24"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L3</span><span class="kw">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span>]])</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.3
## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 06:02:25 2020
-## Date of summary: Wed May 27 06:02:25 2020
+## Date of fit: Wed May 27 07:51:41 2020
+## Date of summary: Wed May 27 07:51:41 2020
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -528,7 +528,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 373 model solutions performed in 0.08 s
+## Fitted using 373 model solutions performed in 0.079 s
##
## Error model: Constant variance
##
@@ -627,15 +627,15 @@
<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.3
## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 06:02:25 2020
-## Date of summary: Wed May 27 06:02:26 2020
+## Date of fit: Wed May 27 07:51:41 2020
+## Date of summary: Wed May 27 07:51:41 2020
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 142 model solutions performed in 0.029 s
+## Fitted using 142 model solutions performed in 0.028 s
##
## Error model: Constant variance
##
@@ -691,15 +691,15 @@
<div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.3
## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 06:02:25 2020
-## Date of summary: Wed May 27 06:02:26 2020
+## Date of fit: Wed May 27 07:51:41 2020
+## Date of summary: Wed May 27 07:51:41 2020
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 224 model solutions performed in 0.043 s
+## Fitted using 224 model solutions performed in 0.044 s
##
## Error model: Constant variance
##
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index 3d5dd360..472e9396 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/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-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html
index 2dd6dcb8..4cc06a43 100644
--- a/docs/dev/articles/mkin.html
+++ b/docs/dev/articles/mkin.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/articles/twa.html b/docs/dev/articles/twa.html
index d4754a1f..29be6c95 100644
--- a/docs/dev/articles/twa.html
+++ b/docs/dev/articles/twa.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html
index 7fca4e49..270232d7 100644
--- a/docs/dev/articles/web_only/FOCUS_Z.html
+++ b/docs/dev/articles/web_only/FOCUS_Z.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index 29f4cd8b..12499452 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index b46b873c..9e53f113 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -216,8 +216,8 @@
</tr>
<tr class="odd">
<td align="left">0.9.50.3</td>
-<td align="right">1.752</td>
-<td align="right">3.728</td>
+<td align="right">1.746</td>
+<td align="right">3.716</td>
</tr>
</tbody>
</table>
@@ -272,9 +272,9 @@
</tr>
<tr class="odd">
<td align="left">0.9.50.3</td>
-<td align="right">1.389</td>
-<td align="right">6.579</td>
-<td align="right">2.740</td>
+<td align="right">1.385</td>
+<td align="right">6.562</td>
+<td align="right">2.736</td>
</tr>
</tbody>
</table>
@@ -351,11 +351,11 @@
<tr class="odd">
<td align="left">0.9.50.3</td>
<td align="right">0.760</td>
-<td align="right">1.252</td>
-<td align="right">1.457</td>
-<td align="right">4.201</td>
+<td align="right">1.226</td>
+<td align="right">1.455</td>
+<td align="right">4.198</td>
<td align="right">2.007</td>
-<td align="right">2.979</td>
+<td align="right">2.976</td>
</tr>
</tbody>
</table>
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html
index 7b5dc8ca..997e90ea 100644
--- a/docs/dev/articles/web_only/compiled_models.html
+++ b/docs/dev/articles/web_only/compiled_models.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -153,10 +153,10 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)
}</pre></body></html></div>
<pre><code>## test replications relative elapsed
-## 4 analytical 1 1.000 0.202
-## 3 deSolve, compiled 1 1.703 0.344
-## 2 Eigenvalue based 1 1.990 0.402
-## 1 deSolve, not compiled 1 40.173 8.115</code></pre>
+## 4 analytical 1 1.000 0.201
+## 3 deSolve, compiled 1 1.711 0.344
+## 2 Eigenvalue based 1 1.960 0.394
+## 1 deSolve, not compiled 1 39.881 8.016</code></pre>
<p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p>
</div>
<div id="model-without-analytical-solution" class="section level2">
@@ -182,8 +182,8 @@
}</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications relative elapsed
-## 2 deSolve, compiled 1 1.000 0.469
-## 1 deSolve, not compiled 1 30.384 14.250</code></pre>
+## 2 deSolve, compiled 1 1.000 0.467
+## 1 deSolve, not compiled 1 30.244 14.124</code></pre>
<p>Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.50.3 on</p>
<pre><code>## R version 4.0.0 (2020-04-24)
diff --git a/docs/dev/authors.html b/docs/dev/authors.html
index 167a8d06..6473cdce 100644
--- a/docs/dev/authors.html
+++ b/docs/dev/authors.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/index.html b/docs/dev/index.html
index 4a71b99b..37cd7d50 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -38,7 +38,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -127,7 +127,7 @@
<div id="documentation" class="section level2">
<h2 class="hasAnchor">
<a href="#documentation" class="anchor"></a>Documentation</h2>
-<p>The HTML documentation is available at <a href="https://pkgdown.jrwb.de/mkin">jrwb.de</a>, at <a href="http://jranke.github.io/mkin">github</a> and at <a href="http://kinfit.r-forge.r-project.org/mkin_static/index.html">R-Forge</a>.</p>
+<p>The HTML documentation of the latest version released to CRAN is available at <a href="https://pkgdown.jrwb.de/mkin">jrwb.de</a> and <a href="http://jranke.github.io/mkin">github</a>. Documentation of the development version is found in the <a href="https://pkgdown.jrwb.de/mkin/dev">‘dev’ subdirectory</a>.</p>
</div>
<div id="features" class="section level2">
<h2 class="hasAnchor">
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 36f7025a..7e39aa46 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/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-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 0dbb110e..31ffe2ad 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
NAFTA_examples: web_only/NAFTA_examples.html
benchmarks: web_only/benchmarks.html
compiled_models: web_only/compiled_models.html
-last_built: 2020-05-27T03:53Z
+last_built: 2020-05-27T05:43Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html
index a03ecea8..074bed3e 100644
--- a/docs/dev/reference/confint.mkinfit.html
+++ b/docs/dev/reference/confint.mkinfit.html
@@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -281,12 +281,12 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>f_d_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</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/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; user system elapsed
-#&gt; 3.707 1.077 3.444 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
+#&gt; 3.610 1.071 3.378 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
<span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span>
<span class='co'># minor interest), we get a nice performance improvement from about 50</span>
<span class='co'># seconds to about 12 seconds if we use at least four cores</span>
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile_no_parent_0</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.011 0.026 0.207</span></div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.005 0.04 0.206</span></div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003640 1.027703e+02
#&gt; k_parent 0.090911032 1.071578e-01
#&gt; k_m1 0.003892605 6.702778e-03
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 906bc2f8..f1ab22e6 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-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index 49e896fc..e1e75767 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -80,7 +80,7 @@ likelihood function." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -424,15 +424,15 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.3
#&gt; R version used for fitting: 4.0.0
-#&gt; Date of fit: Wed May 27 05:54:13 2020
-#&gt; Date of summary: Wed May 27 05:54:13 2020
+#&gt; Date of fit: Wed May 27 07:43:45 2020
+#&gt; Date of summary: Wed May 27 07:43:45 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 222 model solutions performed in 0.043 s
+#&gt; Fitted using 222 model solutions performed in 0.044 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -509,7 +509,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.414 0.000 0.418 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1 sigma
+#&gt; 0.405 0.001 0.407 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1 sigma
#&gt; 99.598481046 0.098697740 0.005260651 0.514475962 3.125503875 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_m1 parent_sink
#&gt; 0.514476 0.485524
@@ -599,7 +599,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt; Sum of squared residuals at call 165: 371.2134
#&gt; Sum of squared residuals at call 167: 371.2134
#&gt; Negative log-likelihood at call 177: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.371 0.001 0.370 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1 sigma
+#&gt; 0.361 0.000 0.361 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1 sigma
#&gt; 99.598480300 0.098697739 0.005260651 0.514475968 3.125503874 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_m1 parent_sink
#&gt; 0.514476 0.485524
@@ -633,8 +633,8 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.3
#&gt; R version used for fitting: 4.0.0
-#&gt; Date of fit: Wed May 27 05:54:19 2020
-#&gt; Date of summary: Wed May 27 05:54:19 2020
+#&gt; Date of fit: Wed May 27 07:43:50 2020
+#&gt; Date of summary: Wed May 27 07:43:50 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -642,7 +642,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 421 model solutions performed in 0.126 s
+#&gt; Fitted using 421 model solutions performed in 0.125 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -755,8 +755,8 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt; 120 m1 25.15 28.78984 -3.640e+00
#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.3
#&gt; R version used for fitting: 4.0.0
-#&gt; Date of fit: Wed May 27 05:54:19 2020
-#&gt; Date of summary: Wed May 27 05:54:19 2020
+#&gt; Date of fit: Wed May 27 07:43:51 2020
+#&gt; Date of summary: Wed May 27 07:43:51 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -764,7 +764,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 978 model solutions performed in 0.33 s
+#&gt; Fitted using 978 model solutions performed in 0.413 s
#&gt;
#&gt; Error model: Variance unique to each observed variable
#&gt;
@@ -892,8 +892,8 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt; 120 m1 25.15 28.80429 -3.654e+00
#&gt; 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.3
#&gt; R version used for fitting: 4.0.0
-#&gt; Date of fit: Wed May 27 05:54:20 2020
-#&gt; Date of summary: Wed May 27 05:54:20 2020
+#&gt; Date of fit: Wed May 27 07:43:52 2020
+#&gt; Date of summary: Wed May 27 07:43:52 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html
index 1b5c1592..3daf16e1 100644
--- a/docs/dev/reference/mmkin.html
+++ b/docs/dev/reference/mmkin.html
@@ -75,7 +75,7 @@ datasets specified in its first two arguments." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -220,8 +220,8 @@ plotting.</p></div>
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
#&gt; <span class='warning'>false convergence (8)</span></div><div class='input'>
<span class='no'>time_default</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 4.516 0.456 1.976 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 5.957 0.001 5.961 </div><div class='input'>
+#&gt; 4.499 0.456 1.983 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 5.771 0.003 5.777 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340479 0.2659521 0.7505687 0.2494313
diff --git a/docs/dev/reference/nlme-1.png b/docs/dev/reference/nlme-1.png
index bc04dea8..68ccb43f 100644
--- a/docs/dev/reference/nlme-1.png
+++ b/docs/dev/reference/nlme-1.png
Binary files differ
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index 8c64fb47..28a9f0a5 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -225,28 +225,28 @@ nlme for the case of a single grouping variable ds.</p>
#&gt; Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#&gt; Data: grouped_data
#&gt; AIC BIC logLik
-#&gt; 252.7798 262.1358 -121.3899
+#&gt; 298.2781 307.7372 -144.1391
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#&gt; Level: ds
#&gt; Structure: Diagonal
-#&gt; parent_0 log_k_parent_sink Residual
-#&gt; StdDev: 0.004139378 0.6800778 2.489396
+#&gt; parent_0 log_k_parent_sink Residual
+#&gt; StdDev: 0.9374809 0.7098104 3.835429
#&gt;
#&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1
-#&gt; Value Std.Error DF t-value p-value
-#&gt; parent_0 101.74884 0.6456057 44 157.60213 0
-#&gt; log_k_parent_sink -3.05575 0.4015812 44 -7.60929 0
+#&gt; Value Std.Error DF t-value p-value
+#&gt; parent_0 101.76838 1.1445465 45 88.91589 0
+#&gt; log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0
#&gt; Correlation:
#&gt; prnt_0
-#&gt; log_k_parent_sink 0.026
+#&gt; log_k_parent_sink 0.034
#&gt;
#&gt; Standardized Within-Group Residuals:
#&gt; Min Q1 Med Q3 Max
-#&gt; -2.13168782 -0.68780415 0.08282907 0.85913228 2.95298904
+#&gt; -2.61693660 -0.21853517 0.05740766 0.57209378 3.04598387
#&gt;
-#&gt; Number of Observations: 48
+#&gt; Number of Observations: 49
#&gt; Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span>(<span class='no'>m_nlme</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0</span>:<span class='fl'>1</span>), <span class='kw'>layout</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>1</span>))</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'># augPred does not seem to work on fits with more than one state
# variable
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index a6716c0f..c7db9c23 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html
index 6a46dad0..a50ca352 100644
--- a/docs/dev/reference/parms.html
+++ b/docs/dev/reference/parms.html
@@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html
index ad16a81b..da28bff1 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-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -234,8 +234,8 @@ 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: 0x55555e4213d8&gt;
-#&gt; &lt;environment: 0x55555c47cdf0&gt;
+#&gt; &lt;bytecode: 0x55555bbf17c0&gt;
+#&gt; &lt;environment: 0x55555bbec4e0&gt;
#&gt; Nb of parameters: 4
#&gt; parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
#&gt; distribution:
@@ -266,10 +266,10 @@ variances of the deviations of the parameters from these mean values.</p>
<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 05:55:50 2020"
+#&gt; [1] "Wed May 27 07:45:07 2020"
#&gt; ..
#&gt; Minimisation finished
-#&gt; [1] "Wed May 27 06:01:54 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] "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; -----------------------------------
#&gt; ---- Data ----
#&gt; -----------------------------------
@@ -333,8 +333,8 @@ 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: 0x55555e4213d8&gt;
-#&gt; &lt;environment: 0x55555c47cdf0&gt;
+#&gt; &lt;bytecode: 0x55555bbf17c0&gt;
+#&gt; &lt;environment: 0x55555bbec4e0&gt;
#&gt; Nb of parameters: 4
#&gt; parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
#&gt; distribution:
diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html
index d0858eda..b0994d33 100644
--- a/docs/dev/reference/transform_odeparms.html
+++ b/docs/dev/reference/transform_odeparms.html
@@ -77,7 +77,7 @@ the ilr transformation is used." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-danger" 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">0.9.50.3</span>
</span>
</div>
@@ -241,7 +241,7 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit<
#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='co'># Compare to the version without transforming rate parameters</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</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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='error'>Error in if (cost &lt; cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.003 0 0.003</span></div><div class='input'><span class='no'>fit.2.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</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='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; <span class='error'>Error in print(fit.2.s$par, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; <span class='error'>Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span>
+<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='error'>Error in if (cost &lt; cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0.002 0.002</span></div><div class='input'><span class='no'>fit.2.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; <span class='error'>Error in print(fit.2.s$par, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; <span class='error'>Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span>
<span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span>
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>initials</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>)

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