Address failures of CRAN checks, improve NEWSv0.9.49.5

Static documentation rebuilt by pkgdown

8 files changed, 46 insertions, 46 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 88a3fa6a..ed41e555 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">2019-07-03</h4>
+            <h4 class="date">2019-07-04</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:     Wed Jul  3 16:39:00 2019 
-## Date of summary: Wed Jul  3 16:39:00 2019 
+## Date of fit:     Thu Jul  4 08:04:23 2019 
+## Date of summary: Thu Jul  4 08:04:24 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,7 +177,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 0.977 s
+## Fitted using 389 model solutions performed in 0.982 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 1b54252f..0060bd69 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">2019-07-03</h4>
+            <h4 class="date">2019-07-04</h4>
       
       
       <div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -114,15 +114,15 @@
 <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:     Wed Jul  3 16:39:02 2019 
-## Date of summary: Wed Jul  3 16:39:02 2019 
+## Date of fit:     Thu Jul  4 08:04:26 2019 
+## Date of summary: Thu Jul  4 08:04:26 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.279 s
+## Fitted using 133 model solutions performed in 0.278 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -216,8 +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:     Wed Jul  3 16:39:04 2019 
-## Date of summary: Wed Jul  3 16:39:04 2019 
+## Date of fit:     Thu Jul  4 08:04:28 2019 
+## Date of summary: Thu Jul  4 08:04:28 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -229,7 +229,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.874 s
+## Fitted using 899 model solutions performed in 1.876 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -321,15 +321,15 @@
 <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://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:     Wed Jul  3 16:39:05 2019 
-## Date of summary: Wed Jul  3 16:39:05 2019 
+## Date of fit:     Thu Jul  4 08:04:29 2019 
+## Date of summary: Thu Jul  4 08:04:29 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 0.485 s
+## Fitted using 239 model solutions performed in 0.486 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -397,8 +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:     Wed Jul  3 16:39:07 2019 
-## Date of summary: Wed Jul  3 16:39:07 2019 
+## Date of fit:     Thu Jul  4 08:04:30 2019 
+## Date of summary: Thu Jul  4 08:04:30 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -497,8 +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:     Wed Jul  3 16:39:08 2019 
-## Date of summary: Wed Jul  3 16:39:09 2019 
+## Date of fit:     Thu Jul  4 08:04:32 2019 
+## Date of summary: Thu Jul  4 08:04:32 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -507,7 +507,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.772 s
+## Fitted using 373 model solutions performed in 0.773 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -603,8 +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:     Wed Jul  3 16:39:09 2019 
-## Date of summary: Wed Jul  3 16:39:10 2019 
+## Date of fit:     Thu Jul  4 08:04:33 2019 
+## Date of summary: Thu Jul  4 08:04:33 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -668,15 +668,15 @@
 <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://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:     Wed Jul  3 16:39:10 2019 
-## Date of summary: Wed Jul  3 16:39:10 2019 
+## Date of fit:     Thu Jul  4 08:04:33 2019 
+## Date of summary: Thu Jul  4 08:04:33 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 0.452 s
+## Fitted using 224 model solutions performed in 0.453 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index df694259..8ad4a8e9 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">2019-07-03</h4>
+            <h4 class="date">2019-07-04</h4>
       
       
       <div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 34b85796..98e5efdf 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">2019-07-03</h4>
+            <h4 class="date">2019-07-04</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 b82e1e01..4a856b71 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">2019-07-03</h4>
+            <h4 class="date">2019-07-04</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 c1922b64..3f6ff8b9 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">2019-07-03</h4>
+            <h4 class="date">2019-07-04</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 c68db93b..005834cc 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">2019-07-03</h4>
+            <h4 class="date">2019-07-04</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 5.820
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.843
 ##                                                                         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 35.917
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.863
 ##                                                                        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 4.415
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.417
 ##                                                                         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 30.588
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.484
 ##                                                                         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 10.317
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.307
 ##                                                                        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 2.556
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.538
 ##                                                                        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 4.213
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.196
 ##                                                                        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 7.851
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.853
 ##                                                                         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 15.645
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.643
 ##                                                                       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 7.734
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.733
 ##                                                                        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 10.489</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.511</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 b30488a0..3fc54cfa 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">2019-07-03</h4>
+            <h4 class="date">2019-07-04</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   3.043    1.000     3.042        0
-## 1 deSolve, not compiled            3  28.630    9.408    28.616        0
-## 2      Eigenvalue based            3   4.291    1.410     4.289        0
+## 3     deSolve, compiled            3   3.061    1.000     3.059        0
+## 1 deSolve, not compiled            3  28.502    9.311    28.487        0
+## 2      Eigenvalue based            3   4.321    1.412     4.318        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   4.800    1.000     4.795    0.002
-## 1 deSolve, not compiled            3  53.371   11.119    53.346    0.000
+## 2     deSolve, compiled            3   4.818    1.000     4.814        0
+## 1 deSolve, not compiled            3  53.275   11.057    53.249        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</code></pre>