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authorJohannes Ranke <jranke@uni-bremen.de>2018-09-06 13:38:06 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-09-06 13:38:06 +0200
commite1ccb85d60802be5e4848ceec0637483753ad8c3 (patch)
tree66c5a914acdacb62f47afd23ddca17e98f75c854 /docs
parentb4ac7f030fdb467ee995a7e12314d80633a72668 (diff)
Fixed publication date in NEWS, docs rebuilt
Diffstat (limited to 'docs')
-rw-r--r--docs/articles/FOCUS_L.html38
-rw-r--r--docs/articles/compiled_models.html10
-rw-r--r--docs/news/index.html6
-rw-r--r--docs/reference/Extract.mmkin.html12
-rw-r--r--docs/reference/mccall81_245T.html6
-rw-r--r--docs/reference/mkinfit.html8
-rw-r--r--docs/reference/mkinpredict.html4
-rw-r--r--docs/reference/summary.mkinfit.html6
-rw-r--r--docs/reference/transform_odeparms.html6
9 files changed, 48 insertions, 48 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 4b324b7e..a42c6e38 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -110,15 +110,15 @@
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.2
## R version used for fitting: 3.5.1
-## Date of fit: Thu Sep 6 11:51:22 2018
-## Date of summary: Thu Sep 6 11:51:22 2018
+## Date of fit: Thu Sep 6 13:35:50 2018
+## Date of summary: Thu Sep 6 13:35:50 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.085 s
+## Fitted with method Port using 37 model solutions performed in 0.086 s
##
## Weighting: none
##
@@ -201,15 +201,15 @@
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.2
## R version used for fitting: 3.5.1
-## Date of fit: Thu Sep 6 11:51:24 2018
-## Date of summary: Thu Sep 6 11:51:24 2018
+## Date of fit: Thu Sep 6 13:35:52 2018
+## Date of summary: Thu Sep 6 13:35:52 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.348 s
+## Fitted with method Port using 611 model solutions performed in 1.35 s
##
## Weighting: none
##
@@ -296,15 +296,15 @@
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.2
## R version used for fitting: 3.5.1
-## Date of fit: Thu Sep 6 11:51:25 2018
-## Date of summary: Thu Sep 6 11:51:25 2018
+## Date of fit: Thu Sep 6 13:35:52 2018
+## Date of summary: Thu Sep 6 13:35:53 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.182 s
+## Fitted with method Port using 81 model solutions performed in 0.175 s
##
## Weighting: none
##
@@ -367,8 +367,8 @@
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.2
## R version used for fitting: 3.5.1
-## Date of fit: Thu Sep 6 11:51:26 2018
-## Date of summary: Thu Sep 6 11:51:26 2018
+## Date of fit: Thu Sep 6 13:35:53 2018
+## Date of summary: Thu Sep 6 13:35:53 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.749 s
+## Fitted with method Port using 336 model solutions performed in 0.746 s
##
## Weighting: none
##
@@ -459,8 +459,8 @@
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.2
## R version used for fitting: 3.5.1
-## Date of fit: Thu Sep 6 11:51:27 2018
-## Date of summary: Thu Sep 6 11:51:27 2018
+## Date of fit: Thu Sep 6 13:35:54 2018
+## Date of summary: Thu Sep 6 13:35:55 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.329 s
+## Fitted with method Port using 137 model solutions performed in 0.324 s
##
## Weighting: none
##
@@ -560,8 +560,8 @@
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.2
## R version used for fitting: 3.5.1
-## Date of fit: Thu Sep 6 11:51:27 2018
-## Date of summary: Thu Sep 6 11:51:27 2018
+## Date of fit: Thu Sep 6 13:35:55 2018
+## Date of summary: Thu Sep 6 13:35:55 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -620,8 +620,8 @@
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.2
## R version used for fitting: 3.5.1
-## Date of fit: Thu Sep 6 11:51:27 2018
-## Date of summary: Thu Sep 6 11:51:27 2018
+## Date of fit: Thu Sep 6 13:35:55 2018
+## Date of summary: Thu Sep 6 13:35:55 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 17387187..16059fcb 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -125,9 +125,9 @@
<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.112 1.000 2.110 0
-## 1 deSolve, not compiled 3 16.633 7.875 16.624 0
-## 2 Eigenvalue based 3 2.637 1.249 2.635 0
+## 3 deSolve, compiled 3 2.218 1.000 2.217 0
+## 1 deSolve, not compiled 3 16.654 7.509 16.646 0
+## 2 Eigenvalue based 3 2.724 1.228 2.722 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -156,8 +156,8 @@
<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 3.720 1.000 3.718 0
-## 1 deSolve, not compiled 3 34.677 9.322 34.661 0
+## 2 deSolve, compiled 3 3.780 1.000 3.777 0
+## 1 deSolve, not compiled 3 35.169 9.304 35.152 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/news/index.html b/docs/news/index.html
index 95995810..71390917 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -117,9 +117,9 @@
</div>
- <div id="mkin-0-9-47-2-2018-07-09" class="section level1">
+ <div id="mkin-0-9-47-2-2018-07-19" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-47-2-2018-07-09" class="anchor"></a>mkin 0.9.47.2 (2018-07-09)<small> 2018-07-19 </small>
+<a href="#mkin-0-9-47-2-2018-07-19" class="anchor"></a>mkin 0.9.47.2 (2018-07-19)<small> 2018-07-19 </small>
</h1>
<ul>
<li><p>‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.</p></li>
@@ -639,7 +639,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#mkin-0-9-47-2-2018-07-09">0.9.47.2</a></li>
+ <li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li>
<li><a href="#mkin-0-9-47-1-2018-02-06">0.9.47.1</a></li>
<li><a href="#mkin-0-9-46-3-2017-11-16">0.9.46.3</a></li>
<li><a href="#mkin-0-9-46-2-2017-10-10">0.9.46.2</a></li>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 982363a1..8771b53b 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.183 0.000 0.184
+#&gt; 0.171 0.001 0.171
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -467,8 +467,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555bd7d1a0&gt;
-#&gt; &lt;environment: 0x55555bc8d4d8&gt;
+#&gt; &lt;bytecode: 0x55555bd7f970&gt;
+#&gt; &lt;environment: 0x55555bc8fca8&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555ca81b68&gt;
-#&gt; &lt;environment: 0x55555bc8d4d8&gt;
+#&gt; &lt;bytecode: 0x55555ca84338&gt;
+#&gt; &lt;environment: 0x55555bc8fca8&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -558,7 +558,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Thu Sep 6 11:50:56 2018"
+#&gt; [1] "Thu Sep 6 13:35:24 2018"
#&gt;
#&gt; $version
#&gt; [1] "0.9.47.2"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index cdfc4b5d..9894f8eb 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -166,8 +166,8 @@
<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>)
<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Thu Sep 6 11:51:05 2018
-#&gt; Date of summary: Thu Sep 6 11:51:05 2018
+#&gt; Date of fit: Thu Sep 6 13:35:34 2018
+#&gt; Date of summary: Thu Sep 6 13:35:34 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -177,7 +177,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.51 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.549 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index e99e7d9e..f9c6c117 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -433,15 +433,15 @@
<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'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Thu Sep 6 11:51:08 2018
-#&gt; Date of summary: Thu Sep 6 11:51:08 2018
+#&gt; Date of fit: Thu Sep 6 13:35:36 2018
+#&gt; Date of summary: Thu Sep 6 13:35:36 2018
#&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 with method Port using 64 model solutions performed in 0.142 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.144 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -510,7 +510,7 @@
<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'>print</span>(<span class='fu'>system.time</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; User System verstrichen
-#&gt; 0.895 0.000 0.898 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.919 0.000 0.920 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 5e2e5449..59b67a5d 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -326,12 +326,12 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.035 0.000 0.034 </div></pre>
+#&gt; 0.037 0.000 0.038 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 7fb56bd3..7b7b0a31 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,15 +206,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Thu Sep 6 11:51:18 2018
-#&gt; Date of summary: Thu Sep 6 11:51:18 2018
+#&gt; Date of fit: Thu Sep 6 13:35:46 2018
+#&gt; Date of summary: Thu Sep 6 13:35:46 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.078 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.075 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index bd8b5165..1b94d319 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='no'>fit</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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Thu Sep 6 11:51:19 2018
-#&gt; Date of summary: Thu Sep 6 11:51:19 2018
+#&gt; Date of fit: Thu Sep 6 13:35:48 2018
+#&gt; Date of summary: Thu Sep 6 13:35:48 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.612 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.619 s
#&gt;
#&gt; Weighting: none
#&gt;

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