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-rw-r--r--docs/articles/FOCUS_D.html13
-rw-r--r--docs/articles/FOCUS_L.html77
-rw-r--r--docs/articles/mkin.html2
-rw-r--r--docs/articles/twa.html2
-rw-r--r--docs/articles/web_only/FOCUS_Z.html2
-rw-r--r--docs/articles/web_only/NAFTA_examples.html2
-rw-r--r--docs/articles/web_only/benchmarks.html24
-rw-r--r--docs/articles/web_only/compiled_models.html12
8 files changed, 71 insertions, 63 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 698ccebc..be1f40f5 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -168,8 +168,8 @@
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:18 2019
-## Date of summary: Tue Jun 4 15:03:18 2019
+## Date of fit: Wed Jun 5 15:10:49 2019
+## Date of summary: Wed Jun 5 15:10:50 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,10 +177,11 @@
##
## Model predictions using solution type deSolve
##
-## Fitted using 389 model solutions performed in 0.978 s
+## Fitted using 389 model solutions performed in 0.984 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 75b2cf10..4388edd2 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -114,18 +114,19 @@
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:20 2019
-## Date of summary: Tue Jun 4 15:03:20 2019
+## Date of fit: Wed Jun 5 15:10:52 2019
+## Date of summary: Wed Jun 5 15:10:52 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.28 s
+## Fitted using 133 model solutions performed in 0.277 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -215,8 +216,8 @@
## finite result is doubtful</code></pre>
<pre><code>## mkin version used for fitting: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:22 2019
-## Date of summary: Tue Jun 4 15:03:22 2019
+## Date of fit: Wed Jun 5 15:10:54 2019
+## Date of summary: Wed Jun 5 15:10:54 2019
##
##
## Warning: Optimisation did not converge:
@@ -228,10 +229,11 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 899 model solutions performed in 1.868 s
+## Fitted using 899 model solutions performed in 1.877 s
+##
+## Error model: Constant variance
##
-## Error model:
-## Constant variance
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -319,18 +321,19 @@
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:23 2019
-## Date of summary: Tue Jun 4 15:03:23 2019
+## Date of fit: Wed Jun 5 15:10:55 2019
+## Date of summary: Wed Jun 5 15:10:55 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 239 model solutions performed in 0.484 s
+## Fitted using 239 model solutions performed in 0.492 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -394,8 +397,8 @@
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:25 2019
-## Date of summary: Tue Jun 4 15:03:25 2019
+## Date of fit: Wed Jun 5 15:10:56 2019
+## Date of summary: Wed Jun 5 15:10:56 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,10 +407,11 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 572 model solutions performed in 1.193 s
+## Fitted using 572 model solutions performed in 1.183 s
+##
+## Error model: Constant variance
##
-## Error model:
-## Constant variance
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -493,8 +497,8 @@
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:26 2019
-## Date of summary: Tue Jun 4 15:03:27 2019
+## Date of fit: Wed Jun 5 15:10:58 2019
+## Date of summary: Wed Jun 5 15:10:58 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,10 +507,11 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 373 model solutions performed in 0.767 s
+## Fitted using 373 model solutions performed in 0.773 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -598,8 +603,8 @@
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:27 2019
-## Date of summary: Tue Jun 4 15:03:28 2019
+## Date of fit: Wed Jun 5 15:10:59 2019
+## Date of summary: Wed Jun 5 15:10:59 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -608,8 +613,9 @@
##
## Fitted using 142 model solutions performed in 0.288 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -662,18 +668,19 @@
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:28 2019
-## Date of summary: Tue Jun 4 15:03:28 2019
+## Date of fit: Wed Jun 5 15:10:59 2019
+## Date of summary: Wed Jun 5 15:10:59 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 224 model solutions performed in 0.449 s
+## Fitted using 224 model solutions performed in 0.453 s
+##
+## Error model: Constant variance
##
-## Error model:
-## Constant variance
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 09b1b8ea..5977d642 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -88,7 +88,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index ede27942..f98026e7 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -88,7 +88,7 @@
<h1>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>twa.Rmd</code></div>
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 555400df..542deb14 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 7f3cc76b..4cd16437 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -88,7 +88,7 @@
<h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>NAFTA_examples.Rmd</code></div>
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 43f8d238..507bdb61 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -88,7 +88,7 @@
<h1>Benchmark timings for mkin on various systems</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@@ -202,77 +202,77 @@
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.805
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.828
## t2
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.748
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.869
## t3
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.403
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.412
## t4
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.613
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.497
## t5
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.309
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.329
## t6
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.546
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.548
## t7
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.214
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.192
## t8
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.871
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.827
## t9
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.738
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.653
## t10
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.763
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.762
## t11
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.527</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.512</code></pre>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div>
</div>
</div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index f3062c66..5f0301fc 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -88,7 +88,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -163,9 +163,9 @@
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
## = TRUE): Observations with value of zero were removed from the data</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 3.053 1.000 3.052 0
-## 1 deSolve, not compiled 3 28.457 9.321 28.442 0
-## 2 Eigenvalue based 3 4.296 1.407 4.293 0
+## 3 deSolve, compiled 3 3.041 1.000 3.039 0
+## 1 deSolve, not compiled 3 28.429 9.349 28.415 0
+## 2 Eigenvalue based 3 4.291 1.411 4.288 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -214,8 +214,8 @@
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
## value of zero were removed from the data</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.828 1.000 4.825 0
-## 1 deSolve, not compiled 3 53.153 11.009 53.125 0
+## 2 deSolve, compiled 3 4.927 1.000 4.924 0
+## 1 deSolve, not compiled 3 53.138 10.785 53.108 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>

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