From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 15 Feb 2021 17:36:12 +0100
Subject: Fully rebuild docs, rerun tests and check

---
 docs/dev/reference/mkinmod.html | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'docs/dev/reference/mkinmod.html')

diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 9a7dac6f..413f0ae1 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -78,7 +78,7 @@ mkinmod." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -127,7 +127,7 @@ mkinmod." />
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -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/Rtmpy4eiQb/file554e573761a7.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/Rtmp92fCb2/file133ad522561845.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: 0x55555cac8d00&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x5555572517f8&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>
-- 
cgit v1.2.1


From 0b754ffa91b9496bdd2f892cf3ca2bd887028dea Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 27 Jul 2021 18:22:01 +0200
Subject: Fix dimethenamid vignette problems and update docs

---
 docs/dev/reference/mkinmod.html | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

(limited to 'docs/dev/reference/mkinmod.html')

diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 413f0ae1..e57e7062 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -44,9 +44,7 @@
 variable, specifying the corresponding submodel as well as outgoing pathways
 (see examples).
 Print mkinmod objects in a way that the user finds his way to get to its
-components.
-This is a convenience function to set up the lists used as arguments for
-mkinmod." />
+components." />
 
 
 <meta name="robots" content="noindex">
@@ -78,7 +76,7 @@ mkinmod." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span>
       </span>
     </div>
 
@@ -155,8 +153,6 @@ variable, specifying the corresponding submodel as well as outgoing pathways
 (see examples).</p>
 <p>Print mkinmod objects in a way that the user finds his way to get to its
 components.</p>
-<p>This is a convenience function to set up the lists used as arguments for
-<code>mkinmod</code>.</p>
     </div>
 
     <pre class="usage"><span class='fu'>mkinmod</span><span class='op'>(</span>
@@ -348,7 +344,7 @@ 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/Rtmp92fCb2/file133ad522561845.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/RtmpPWWdbW/fileccff46a6d9773.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 +393,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x5555572517f8&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x5555645abab8&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>
-- 
cgit v1.2.1


From 137612045c23198f10d6e8612c32e266c2a6c00e Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 29 Jul 2021 12:17:56 +0200
Subject: Go back to 1.0.x version, update docs

---
 docs/dev/reference/mkinmod.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'docs/dev/reference/mkinmod.html')

diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index e57e7062..5db8e719 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -76,7 +76,7 @@ components." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.5</span>
       </span>
     </div>
 
@@ -344,7 +344,7 @@ 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/RtmpPWWdbW/fileccff46a6d9773.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/Rtmpjz6gts/filefa69f342e9d9d.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>
@@ -393,7 +393,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x5555645abab8&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x55556283eae8&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>
-- 
cgit v1.2.1


From 51fab94230e926cec690dc455964bd797a97b7c7 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 4 Aug 2021 16:37:52 +0200
Subject: Improve AIC table in vignette

---
 docs/dev/reference/mkinmod.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'docs/dev/reference/mkinmod.html')

diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 5db8e719..ac7c2daa 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -344,7 +344,7 @@ 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/Rtmpjz6gts/filefa69f342e9d9d.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/RtmpKZJMFk/file179ba717d15c81.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>
@@ -393,7 +393,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x55556283eae8&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x555559c54f78&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>
-- 
cgit v1.2.1


From c41381a961263c28d60976e68923157916c78b15 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 16 Sep 2021 15:31:13 +0200
Subject: Adapt and improve the dimethenamid vignette

Adapt to the corrected data and unify control parameters for saemix and
nlmixr with saem. Update docs
---
 docs/dev/reference/mkinmod.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'docs/dev/reference/mkinmod.html')

diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index ac7c2daa..6478cda4 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -76,7 +76,7 @@ components." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.5</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span>
       </span>
     </div>
 
@@ -344,7 +344,7 @@ 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/RtmpKZJMFk/file179ba717d15c81.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/RtmpTzKqT5/file7993c266a7f90.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>
@@ -393,7 +393,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x555559c54f78&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x555559365690&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>
-- 
cgit v1.2.1


From ff83d8b2ba623513d92ac90fac4a1b0ec98c2cb5 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 5 Oct 2021 17:33:52 +0200
Subject: Update docs

---
 docs/dev/reference/mkinmod.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'docs/dev/reference/mkinmod.html')

diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 6478cda4..60a0af96 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -344,7 +344,7 @@ 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/RtmpTzKqT5/file7993c266a7f90.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/RtmpWsX48Z/file1029f864aada00.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>
@@ -393,7 +393,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x555559365690&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x55555cc38878&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>
-- 
cgit v1.2.1