Merge branch 'master' into nlmixr

23 files changed, 7 insertions, 7 deletions

diff --git a/docs/news/index.html b/docs/news/index.html
index 2905c120..0ac20352 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -141,9 +141,9 @@
       <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="mkin-104-unreleased" class="section level1">
+    <div id="mkin-104-2021-04-20" class="section level1">
 <h1 class="page-header" data-toc-text="1.0.4">
-<a href="#mkin-104-unreleased" class="anchor"></a>mkin 1.0.4 (Unreleased)</h1>
+<a href="#mkin-104-2021-04-20" class="anchor"></a>mkin 1.0.4 (2021-04-20)</h1>
 <ul>
 <li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li>
 <li><p>‘plot.mkinfit’: Use xlab and xlim for the residual plot if show_residuals is TRUE</p></li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 3f97ea94..554b3bdc 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   web_only/NAFTA_examples: NAFTA_examples.html
   web_only/benchmarks: benchmarks.html
   web_only/compiled_models: compiled_models.html
-last_built: 2021-04-20T14:34Z
+last_built: 2021-07-27T13:38Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index 49fb9af1..22eb54d3 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index 745d583d..8512d4f8 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
index eba202e9..da0a093b 100644
--- a/docs/reference/Rplot003.png
+++ b/docs/reference/Rplot003.png
diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png
index a4f878c8..31771c20 100644
--- a/docs/reference/Rplot004.png
+++ b/docs/reference/Rplot004.png
diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png
index a4f878c8..31771c20 100644
--- a/docs/reference/Rplot005.png
+++ b/docs/reference/Rplot005.png
diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png
index ff8a5d83..4c728f4e 100644
--- a/docs/reference/Rplot006.png
+++ b/docs/reference/Rplot006.png
diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png
index b9454c86..422ab6a0 100644
--- a/docs/reference/mixed-1.png
+++ b/docs/reference/mixed-1.png
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 1e8ad60d..441e573e 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
    parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>,
    m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span>,
    name <span class='op'>=</span> <span class='st'>"SFO_SFO"</span>, dll_dir <span class='op'>=</span> <span class='va'>DLL_dir</span>, unload <span class='op'>=</span> <span class='cn'>TRUE</span>, overwrite <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/Rtmp17EVw2/file269cfd5cc541a9.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
+</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/RtmpkoTT3P/filecc29e29e1b974.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
 <span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></span><span class='op'>(</span><span class='va'>SFO_SFO.2</span>, file <span class='op'>=</span> <span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span>
 <span class='co'># Terminate the R session here if you would like to check, and then do</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span>
@@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x55555c17ae90&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x55555a57f6c8&gt;</div><div class='input'>
 <span class='co'># If we have several parallel metabolites</span>
 <span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
 <span class='va'>m_synth_DFOP_par</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png
index f6bb2131..701a6d6a 100644
--- a/docs/reference/mmkin-1.png
+++ b/docs/reference/mmkin-1.png
diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png
index 50102a3d..5277b389 100644
--- a/docs/reference/mmkin-2.png
+++ b/docs/reference/mmkin-2.png
diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png
index 9aa7f0db..2659cd61 100644
--- a/docs/reference/mmkin-3.png
+++ b/docs/reference/mmkin-3.png
diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png
index f4f413d1..ae16ee79 100644
--- a/docs/reference/mmkin-4.png
+++ b/docs/reference/mmkin-4.png
diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png
index 48ab2c50..2b9dc831 100644
--- a/docs/reference/mmkin-5.png
+++ b/docs/reference/mmkin-5.png
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index caba300e..d7989c6b 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -235,9 +235,9 @@ plotting.</p></div>
 
 <span class='va'>time_default</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   4.656   0.403   1.734 </div><div class='input'><span class='va'>time_1</span>
+#&gt;   4.491   0.397   1.634 </div><div class='input'><span class='va'>time_1</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   5.627   0.004   5.631 </div><div class='input'>
+#&gt;   5.491   0.000   5.492 </div><div class='input'>
 <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
 #&gt;   parent_M1 parent_sink       M1_M2     M1_sink 
diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png
index c41adc27..365aaef0 100644
--- a/docs/reference/nlme-1.png
+++ b/docs/reference/nlme-1.png
diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png
index c0d8e857..40841404 100644
--- a/docs/reference/nlme-2.png
+++ b/docs/reference/nlme-2.png
diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png
index 90ede880..95adfafb 100644
--- a/docs/reference/nlme.mmkin-1.png
+++ b/docs/reference/nlme.mmkin-1.png
diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png
index 0d140fd1..53b6fc76 100644
--- a/docs/reference/nlme.mmkin-2.png
+++ b/docs/reference/nlme.mmkin-2.png
diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png
index 8a60b52b..e87d15e5 100644
--- a/docs/reference/nlme.mmkin-3.png
+++ b/docs/reference/nlme.mmkin-3.png
diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png
index 65660abe..be3c664a 100644
--- a/docs/reference/plot.mixed.mmkin-1.png
+++ b/docs/reference/plot.mixed.mmkin-1.png
diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png
index 28168495..933d477b 100644
--- a/docs/reference/plot.mixed.mmkin-2.png
+++ b/docs/reference/plot.mixed.mmkin-2.png