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authorJohannes Ranke <jranke@uni-bremen.de>2019-09-18 18:30:21 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-09-18 18:30:21 +0200
commit1c7b39f3c542de75a1ba685fec3c154bef8a3301 (patch)
tree4e8fffd9841c2f8bea9ba6012363ef9d831227ed /docs/articles
parentb2c75fa1f73167d3e3c9c7db1d561dd482090aab (diff)
Static documentation rebuilt by pkgdown
to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly
Diffstat (limited to 'docs/articles')
-rw-r--r--docs/articles/FOCUS_D.html6
-rw-r--r--docs/articles/FOCUS_L.html42
-rw-r--r--docs/articles/twa.html2
-rw-r--r--docs/articles/web_only/benchmarks.html20
-rw-r--r--docs/articles/web_only/compiled_models.html10
5 files changed, 40 insertions, 40 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index c22eb2c3..53164ffd 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -170,8 +170,8 @@
<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://rdrr.io/r/base/summary.html">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 17:55:05 2019
-## Date of summary: Wed Sep 18 17:55:06 2019
+## Date of fit: Wed Sep 18 18:24:07 2019
+## Date of summary: Wed Sep 18 18:24:08 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +179,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted using 389 model solutions performed in 1.003 s
+## Fitted using 389 model solutions performed in 1.014 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 428ca84f..50c83db6 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -116,15 +116,15 @@
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 17:55:08 2019
-## Date of summary: Wed Sep 18 17:55:08 2019
+## Date of fit: Wed Sep 18 18:24:09 2019
+## Date of summary: Wed Sep 18 18:24:09 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.293 s
+## Fitted using 133 model solutions performed in 0.287 s
##
## Error model: Constant variance
##
@@ -218,8 +218,8 @@
## finite result is doubtful</code></pre>
<pre><code>## mkin version used for fitting: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 17:55:10 2019
-## Date of summary: Wed Sep 18 17:55:10 2019
+## Date of fit: Wed Sep 18 18:24:12 2019
+## Date of summary: Wed Sep 18 18:24:12 2019
##
##
## Warning: Optimisation did not converge:
@@ -231,7 +231,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 899 model solutions performed in 1.914 s
+## Fitted using 899 model solutions performed in 1.954 s
##
## Error model: Constant variance
##
@@ -323,15 +323,15 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 17:55:11 2019
-## Date of summary: Wed Sep 18 17:55:11 2019
+## Date of fit: Wed Sep 18 18:24:13 2019
+## Date of summary: Wed Sep 18 18:24:13 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 0.511 s
+## Fitted using 239 model solutions performed in 0.497 s
##
## Error model: Constant variance
##
@@ -399,8 +399,8 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 17:55:12 2019
-## Date of summary: Wed Sep 18 17:55:12 2019
+## Date of fit: Wed Sep 18 18:24:14 2019
+## Date of summary: Wed Sep 18 18:24:14 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -409,7 +409,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 572 model solutions performed in 1.217 s
+## Fitted using 572 model solutions performed in 1.215 s
##
## Error model: Constant variance
##
@@ -499,8 +499,8 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 17:55:14 2019
-## Date of summary: Wed Sep 18 17:55:14 2019
+## Date of fit: Wed Sep 18 18:24:16 2019
+## Date of summary: Wed Sep 18 18:24:16 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -509,7 +509,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 373 model solutions performed in 0.803 s
+## Fitted using 373 model solutions performed in 0.778 s
##
## Error model: Constant variance
##
@@ -605,15 +605,15 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 17:55:15 2019
-## Date of summary: Wed Sep 18 17:55:15 2019
+## Date of fit: Wed Sep 18 18:24:17 2019
+## Date of summary: Wed Sep 18 18:24:17 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 142 model solutions performed in 0.301 s
+## Fitted using 142 model solutions performed in 0.293 s
##
## Error model: Constant variance
##
@@ -670,15 +670,15 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 17:55:15 2019
-## Date of summary: Wed Sep 18 17:55:15 2019
+## Date of fit: Wed Sep 18 18:24:17 2019
+## Date of summary: Wed Sep 18 18:24:17 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 0.458 s
+## Fitted using 224 model solutions performed in 0.46 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 799349d9..2d44a89d 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -130,7 +130,7 @@
<p><span class="math display">\[f_\textrm{twa} = \frac{1}{t} \left(
\frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
\frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]</span></p>
-<p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <a href="https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html">‘max_twa_parent’</a> function. If the same is needed for metabolites, the function <a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html">‘max_twa’</a> from the ‘pfm’ package can be used.</p>
+<p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for metabolites, the function <code><a href="https://rdrr.io/pkg/pfm/man/max_twa.html">pfm::max_twa()</a></code> from the ‘pfm’ package can be used.</p>
<div id="refs" class="references">
<div id="ref-FOCUSkinetics2014">
<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 144c4c29..d46e738a 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -204,70 +204,70 @@
## 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 0.9.49.6 5.940
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.970
## 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 0.9.49.6 36.631
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.524
## 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 0.9.49.6 4.507
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.607
## 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 0.9.49.6 31.282
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.617
## 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 0.9.49.6 10.727
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.543
## 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 0.9.49.6 2.634
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.579
## 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 0.9.49.6 4.295
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.341
## 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 0.9.49.6 8.13
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.101
## 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 0.9.49.6 16.064
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.211
## 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 0.9.49.6 8.034
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.041
## 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
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 6594c3e6..1876e2b3 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -165,9 +165,9 @@
## 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 3.143 1.000 3.141 0
-## 1 deSolve, not compiled 3 28.853 9.180 28.839 0
-## 2 Eigenvalue based 3 4.427 1.409 4.425 0
+## 3 deSolve, compiled 3 3.129 1.000 3.127 0
+## 1 deSolve, not compiled 3 28.841 9.217 28.827 0
+## 2 Eigenvalue based 3 4.433 1.417 4.430 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -216,8 +216,8 @@
## 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 4.956 1.000 4.952 0
-## 1 deSolve, not compiled 3 53.338 10.762 53.312 0
+## 2 deSolve, compiled 3 4.860 1.000 4.857 0
+## 1 deSolve, not compiled 3 53.877 11.086 53.850 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>

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