Further corrections of the twa vignette

Static documentation rebuilt by pkgdown

5 files changed, 41 insertions, 41 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 70739ae6..b62afbf8 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 12:57:33 2019 
-## Date of summary: Wed Sep 18 12:57:33 2019 
+## Date of fit:     Wed Sep 18 13:17:00 2019 
+## Date of summary: Wed Sep 18 13:17:00 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 1.01 s
+## Fitted using 389 model solutions performed in 1.115 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 81659030..0d5667f5 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 12:57:35 2019 
-## Date of summary: Wed Sep 18 12:57:35 2019 
+## Date of fit:     Wed Sep 18 13:17:02 2019 
+## Date of summary: Wed Sep 18 13:17:02 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.287 s
+## Fitted using 133 model solutions performed in 0.297 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 12:57:37 2019 
-## Date of summary: Wed Sep 18 12:57:37 2019 
+## Date of fit:     Wed Sep 18 13:17:05 2019 
+## Date of summary: Wed Sep 18 13:17:05 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -231,7 +231,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.921 s
+## Fitted using 899 model solutions performed in 2.099 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 12:57:38 2019 
-## Date of summary: Wed Sep 18 12:57:38 2019 
+## Date of fit:     Wed Sep 18 13:17:06 2019 
+## Date of summary: Wed Sep 18 13:17:06 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 0.49 s
+## Fitted using 239 model solutions performed in 0.554 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 12:57:40 2019 
-## Date of summary: Wed Sep 18 12:57:40 2019 
+## Date of fit:     Wed Sep 18 13:17:07 2019 
+## Date of summary: Wed Sep 18 13:17:07 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 1.209 s
+## Fitted using 572 model solutions performed in 1.273 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 12:57:42 2019 
-## Date of summary: Wed Sep 18 12:57:42 2019 
+## Date of fit:     Wed Sep 18 13:17:09 2019 
+## Date of summary: Wed Sep 18 13:17:09 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 0.783 s
+## Fitted using 373 model solutions performed in 0.792 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 12:57:42 2019 
-## Date of summary: Wed Sep 18 12:57:43 2019 
+## Date of fit:     Wed Sep 18 13:17:10 2019 
+## Date of summary: Wed Sep 18 13:17:11 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.288 s
+## Fitted using 142 model solutions performed in 0.299 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 12:57:43 2019 
-## Date of summary: Wed Sep 18 12:57:43 2019 
+## Date of fit:     Wed Sep 18 13:17:10 2019 
+## Date of summary: Wed Sep 18 13:17:11 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 0.463 s
+## Fitted using 224 model solutions performed in 0.488 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index b15f1522..799349d9 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’ is include in the ‘mkin’ package (<a href="https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html">‘max_twa_parent’</a>. If the same is needed for metabolites, the function <a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html">‘max_twa’</a> 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 <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>
 <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 f1ed1f96..0c78d346 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -204,77 +204,77 @@
 ## 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 0.9.49.6 5.920
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 6.106
 ##                                                                         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 36.932
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 37.249
 ##                                                                        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 4.519
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.739
 ##                                                                         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 31.518
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.761
 ##                                                                         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 10.619
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.794
 ##                                                                        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  2.61
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.702
 ##                                                                        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 4.312
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.351
 ##                                                                        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  8.07
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.303
 ##                                                                         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 16.102
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.339
 ##                                                                       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 8.013
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  8.12
 ##                                                                        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 0.9.49.6 10.805</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  11.22</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://rdrr.io/r/base/save.html">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 89977591..99b05623 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   3.124    1.000     3.122        0
-## 1 deSolve, not compiled            3  28.822    9.226    28.807        0
-## 2      Eigenvalue based            3   4.416    1.414     4.413        0
+## 3     deSolve, compiled            3   3.153    1.000     3.152        0
+## 1 deSolve, not compiled            3  28.771    9.125    28.756        0
+## 2      Eigenvalue based            3   4.444    1.409     4.443        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   4.878    1.000     4.875        0
-## 1 deSolve, not compiled            3  53.602   10.989    53.568        0
+## 2     deSolve, compiled            3   4.978    1.000     4.975    0.000
+## 1 deSolve, not compiled            3  54.194   10.887    54.160    0.004
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</code></pre>