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authorJohannes Ranke <jranke@uni-bremen.de>2021-07-27 15:44:39 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-07-27 15:44:39 +0200
commit6bc7a6d3e4a849a4b4da49979c577646a541989e (patch)
treeb5b49147e85692342727a2d8203fbb310a4eb0bb /docs
parent25648577b6d5a4521da7c9d2eb174d292d2d85af (diff)
Publication date for 1.0.4 in NEWS, update docs
Diffstat (limited to 'docs')
-rw-r--r--docs/news/index.html4
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/Rplot001.pngbin27637 -> 27644 bytes
-rw-r--r--docs/reference/Rplot002.pngbin59394 -> 59381 bytes
-rw-r--r--docs/reference/Rplot003.pngbin33192 -> 59145 bytes
-rw-r--r--docs/reference/Rplot004.pngbin23509 -> 23487 bytes
-rw-r--r--docs/reference/Rplot005.pngbin23509 -> 23487 bytes
-rw-r--r--docs/reference/Rplot006.pngbin22129 -> 22144 bytes
-rw-r--r--docs/reference/mixed-1.pngbin219876 -> 220057 bytes
-rw-r--r--docs/reference/mkinmod.html4
-rw-r--r--docs/reference/mmkin-1.pngbin110844 -> 111120 bytes
-rw-r--r--docs/reference/mmkin-2.pngbin107612 -> 108016 bytes
-rw-r--r--docs/reference/mmkin-3.pngbin96248 -> 96433 bytes
-rw-r--r--docs/reference/mmkin-4.pngbin66653 -> 66723 bytes
-rw-r--r--docs/reference/mmkin-5.pngbin65046 -> 65113 bytes
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/nlme-1.pngbin70244 -> 68943 bytes
-rw-r--r--docs/reference/nlme-2.pngbin94239 -> 94409 bytes
-rw-r--r--docs/reference/nlme.mmkin-1.pngbin124827 -> 124937 bytes
-rw-r--r--docs/reference/nlme.mmkin-2.pngbin169698 -> 169884 bytes
-rw-r--r--docs/reference/nlme.mmkin-3.pngbin172809 -> 172866 bytes
-rw-r--r--docs/reference/plot.mixed.mmkin-1.pngbin84976 -> 85300 bytes
-rw-r--r--docs/reference/plot.mixed.mmkin-2.pngbin174061 -> 174113 bytes
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
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