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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-02 18:03:54 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-02 18:03:54 +0100
commit2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch)
treef286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/create_deg_func.html
parent351248d07f810ccb6c497633a02cd48ee35526e6 (diff)
Make tests more platform independent, update docs
Diffstat (limited to 'docs/reference/create_deg_func.html')
-rw-r--r--docs/reference/create_deg_func.html215
1 files changed, 77 insertions, 138 deletions
diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html
index 82583f1a..ca57addf 100644
--- a/docs/reference/create_deg_func.html
+++ b/docs/reference/create_deg_func.html
@@ -1,67 +1,12 @@
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@@ -98,6 +41,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
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+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
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@@ -112,34 +58,27 @@
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<h1>Create degradation functions for known analytical solutions</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/create_deg_func.R'><code>R/create_deg_func.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/create_deg_func.R" class="external-link"><code>R/create_deg_func.R</code></a></small>
<div class="hidden name"><code>create_deg_func.Rd</code></div>
</div>
@@ -147,83 +86,83 @@
<p>Create degradation functions for known analytical solutions</p>
</div>
- <pre class="usage"><span class='fu'>create_deg_func</span><span class='op'>(</span><span class='va'>spec</span>, use_of_ff <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"min"</span>, <span class='st'>"max"</span><span class='op'>)</span><span class='op'>)</span></pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>spec</th>
- <td><p>List of model specifications as contained in mkinmod objects</p></td>
- </tr>
- <tr>
- <th>use_of_ff</th>
- <td><p>Minimum or maximum use of formation fractions</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">create_deg_func</span><span class="op">(</span><span class="va">spec</span>, use_of_ff <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"min"</span>, <span class="st">"max"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+ </div>
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>spec</dt>
+<dd><p>List of model specifications as contained in mkinmod objects</p></dd>
+<dt>use_of_ff</dt>
+<dd><p>Minimum or maximum use of formation fractions</p></dd>
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
<p>Degradation function to be attached to mkinmod objects</p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
-<span class='va'>SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
- parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>FOCUS_D</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># to avoid warnings</span>
-<span class='va'>fit_1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='va'>fit_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='co'># \dontrun{</span>
-<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span>
- <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>
- analytical <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
- deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
- replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
-#&gt; 1 analytical 2 0.389 1.000 0.389 0 0
-#&gt; 2 deSolve 2 0.690 1.774 0.690 0 0
-#&gt; sys.child
-#&gt; 1 0
-#&gt; 2 0</div><div class='input'> <span class='va'>DFOP_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
- parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>
- analytical <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
- deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
- replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
-#&gt; 1 analytical 2 0.817 1.000 0.818 0 0
-#&gt; 2 deSolve 2 1.591 1.947 1.591 0 0
-#&gt; sys.child
-#&gt; 1 0
-#&gt; 2 0</div><div class='input'><span class='co'># }</span>
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
+<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
+<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
+<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># to avoid warnings</span></span>
+<span class="r-in"><span class="va">fit_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"><span class="co"># \dontrun{</span></span>
+<span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span>
+<span class="r-in"> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
+<span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
+<span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> test replications elapsed relative user.self sys.self user.child</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical 2 0.446 1.000 0.446 0 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve 2 0.756 1.695 0.756 0 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sys.child</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 0</span>
+<span class="r-in"> <span class="va">DFOP_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
+<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
+<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span>
+<span class="r-in"> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
+<span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
+<span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> test replications elapsed relative user.self sys.self user.child</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical 2 0.896 1.000 0.896 0 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve 2 1.685 1.881 1.685 0 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sys.child</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 0</span>
+<span class="r-in"><span class="co"># }</span></span>
+</code></pre></div>
+ </div>
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