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-rw-r--r--docs/reference/mkinpredict.html253
1 files changed, 126 insertions, 127 deletions
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 21c13156..e48a0cdb 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -251,7 +251,8 @@ is 1e-10, much lower than in <code>lsoda</code>.</p></td>
<th>map_output</th>
<td><p>Boolean to specify if the output should list values for
the observed variables (default) or for all state variables (if set to
-FALSE).</p></td>
+FALSE). Setting this to FALSE has no effect for analytical solutions,
+as these always return mapped output.</p></td>
</tr>
<tr>
<th>...</th>
@@ -262,7 +263,7 @@ solver is used.</p></td>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>A matrix in the same format as the output of <code>ode</code>.</p>
+ <p>A matrix with the numeric solution in wide format</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'>
@@ -270,149 +271,147 @@ solver is used.</p></td>
<span class='co'># Compare solution types</span>
<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt; time degradinol
-#&gt; 1 0 100.0000000
-#&gt; 2 1 74.0818221
-#&gt; 3 2 54.8811636
-#&gt; 4 3 40.6569660
-#&gt; 5 4 30.1194212
-#&gt; 6 5 22.3130160
-#&gt; 7 6 16.5298888
-#&gt; 8 7 12.2456428
-#&gt; 9 8 9.0717953
-#&gt; 10 9 6.7205513
-#&gt; 11 10 4.9787068
-#&gt; 12 11 3.6883167
-#&gt; 13 12 2.7323722
-#&gt; 14 13 2.0241911
-#&gt; 15 14 1.4995577
-#&gt; 16 15 1.1108997
-#&gt; 17 16 0.8229747
-#&gt; 18 17 0.6096747
-#&gt; 19 18 0.4516581
-#&gt; 20 19 0.3345965
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 0 0 100.0000000
+#&gt; 1 1 74.0818221
+#&gt; 2 2 54.8811636
+#&gt; 3 3 40.6569660
+#&gt; 4 4 30.1194212
+#&gt; 5 5 22.3130160
+#&gt; 6 6 16.5298888
+#&gt; 7 7 12.2456428
+#&gt; 8 8 9.0717953
+#&gt; 9 9 6.7205513
+#&gt; 10 10 4.9787068
+#&gt; 11 11 3.6883167
+#&gt; 12 12 2.7323722
+#&gt; 13 13 2.0241911
+#&gt; 14 14 1.4995577
+#&gt; 15 15 1.1108997
+#&gt; 16 16 0.8229747
+#&gt; 17 17 0.6096747
+#&gt; 18 18 0.4516581
+#&gt; 19 19 0.3345965
+#&gt; 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt; time degradinol
-#&gt; 1 0 100.0000000
-#&gt; 2 1 74.0818221
-#&gt; 3 2 54.8811636
-#&gt; 4 3 40.6569660
-#&gt; 5 4 30.1194212
-#&gt; 6 5 22.3130160
-#&gt; 7 6 16.5298888
-#&gt; 8 7 12.2456428
-#&gt; 9 8 9.0717953
-#&gt; 10 9 6.7205513
-#&gt; 11 10 4.9787068
-#&gt; 12 11 3.6883167
-#&gt; 13 12 2.7323722
-#&gt; 14 13 2.0241911
-#&gt; 15 14 1.4995577
-#&gt; 16 15 1.1108996
-#&gt; 17 16 0.8229747
-#&gt; 18 17 0.6096747
-#&gt; 19 18 0.4516581
-#&gt; 20 19 0.3345965
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 0 0 100.0000000
+#&gt; 1 1 74.0818221
+#&gt; 2 2 54.8811636
+#&gt; 3 3 40.6569660
+#&gt; 4 4 30.1194212
+#&gt; 5 5 22.3130160
+#&gt; 6 6 16.5298888
+#&gt; 7 7 12.2456428
+#&gt; 8 8 9.0717953
+#&gt; 9 9 6.7205513
+#&gt; 10 10 4.9787068
+#&gt; 11 11 3.6883167
+#&gt; 12 12 2.7323722
+#&gt; 13 13 2.0241911
+#&gt; 14 14 1.4995577
+#&gt; 15 15 1.1108996
+#&gt; 16 16 0.8229747
+#&gt; 17 17 0.6096747
+#&gt; 18 18 0.4516581
+#&gt; 19 19 0.3345965
+#&gt; 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; time degradinol
-#&gt; 1 0 100.0000000
-#&gt; 2 1 74.0818221
-#&gt; 3 2 54.8811636
-#&gt; 4 3 40.6569660
-#&gt; 5 4 30.1194212
-#&gt; 6 5 22.3130160
-#&gt; 7 6 16.5298888
-#&gt; 8 7 12.2456428
-#&gt; 9 8 9.0717953
-#&gt; 10 9 6.7205513
-#&gt; 11 10 4.9787068
-#&gt; 12 11 3.6883167
-#&gt; 13 12 2.7323722
-#&gt; 14 13 2.0241911
-#&gt; 15 14 1.4995577
-#&gt; 16 15 1.1108996
-#&gt; 17 16 0.8229747
-#&gt; 18 17 0.6096747
-#&gt; 19 18 0.4516581
-#&gt; 20 19 0.3345965
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 0 0 100.0000000
+#&gt; 1 1 74.0818221
+#&gt; 2 2 54.8811636
+#&gt; 3 3 40.6569660
+#&gt; 4 4 30.1194212
+#&gt; 5 5 22.3130160
+#&gt; 6 6 16.5298888
+#&gt; 7 7 12.2456428
+#&gt; 8 8 9.0717953
+#&gt; 9 9 6.7205513
+#&gt; 10 10 4.9787068
+#&gt; 11 11 3.6883167
+#&gt; 12 12 2.7323722
+#&gt; 13 13 2.0241911
+#&gt; 14 14 1.4995577
+#&gt; 15 15 1.1108996
+#&gt; 16 16 0.8229747
+#&gt; 17 17 0.6096747
+#&gt; 18 18 0.4516581
+#&gt; 19 19 0.3345965
+#&gt; 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#&gt; time degradinol
-#&gt; 1 0 100.0000000
-#&gt; 2 1 74.0818221
-#&gt; 3 2 54.8811636
-#&gt; 4 3 40.6569660
-#&gt; 5 4 30.1194212
-#&gt; 6 5 22.3130160
-#&gt; 7 6 16.5298888
-#&gt; 8 7 12.2456428
-#&gt; 9 8 9.0717953
-#&gt; 10 9 6.7205513
-#&gt; 11 10 4.9787068
-#&gt; 12 11 3.6883167
-#&gt; 13 12 2.7323722
-#&gt; 14 13 2.0241911
-#&gt; 15 14 1.4995577
-#&gt; 16 15 1.1108997
-#&gt; 17 16 0.8229747
-#&gt; 18 17 0.6096747
-#&gt; 19 18 0.4516581
-#&gt; 20 19 0.3345965
-#&gt; 21 20 0.2478752</div><div class='input'>
+#&gt; 0 0 100.0000000
+#&gt; 1 1 74.0818221
+#&gt; 2 2 54.8811636
+#&gt; 3 3 40.6569660
+#&gt; 4 4 30.1194212
+#&gt; 5 5 22.3130160
+#&gt; 6 6 16.5298888
+#&gt; 7 7 12.2456428
+#&gt; 8 8 9.0717953
+#&gt; 9 9 6.7205513
+#&gt; 10 10 4.9787068
+#&gt; 11 11 3.6883167
+#&gt; 12 12 2.7323722
+#&gt; 13 13 2.0241911
+#&gt; 14 14 1.4995577
+#&gt; 15 15 1.1108997
+#&gt; 16 16 0.8229747
+#&gt; 17 17 0.6096747
+#&gt; 18 18 0.4516581
+#&gt; 19 19 0.3345965
+#&gt; 20 20 0.2478752</div><div class='input'>
<span class='co'># Compare integration methods to analytical solution</span>
<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
- <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
- <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
- <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
- <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 21 20 0.2480043</div><div class='input'><span class='co'># rk4 is not as precise here</span>
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2480043 </div><div class='input'><span class='co'># rk4 is not as precise here</span>
<span class='co'># The number of output times used to make a lot of difference until the</span>
<span class='co'># default for atol was adjusted</span>
<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
- <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 201 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
- <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 2001 20 0.2478752</div><div class='input'>
-<span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span>
+ <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'>
+<span class='co'># Comparison of the performance of solution types</span>
<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
- <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(
- <span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
+ <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(<span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>order</span> <span class='kw'>=</span> <span class='st'>"relative"</span>, <span class='kw'>columns</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"test"</span>, <span class='st'>"relative"</span>, <span class='st'>"elapsed"</span>),
+ <span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>f_parent_to_m1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_m1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,],
<span class='kw'>deSolve_compiled</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>f_parent_to_m1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_m1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,],
- <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
- <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,],
- <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>10</span>)
-}</div><div class='output co'>#&gt; <span class='message'>Lade nötiges Paket: rbenchmark</span></div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
-#&gt; 3 deSolve 10 0.229 28.625 0.229 0 0
-#&gt; 2 deSolve_compiled 10 0.008 1.000 0.008 0 0
-#&gt; 1 eigen 10 0.026 3.250 0.025 0 0
-#&gt; sys.child
-#&gt; 3 0
-#&gt; 2 0
-#&gt; 1 0</div><div class='input'>
-<span class='co'># Since mkin 0.9.49.11 we also have analytical solutions for some models, including SFO-SFO</span>
-<span class='co'># deSolve = mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),</span>
-<span class='co'># c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),</span>
-<span class='co'># solution_type = "analytical", use_compiled = FALSE)[201,],</span>
-
+ <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>f_parent_to_m1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_m1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,],
+ <span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>f_parent_to_m1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_m1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,])
+}</div><div class='output co'>#&gt; test relative elapsed
+#&gt; 4 analytical 1.00 0.004
+#&gt; 2 deSolve_compiled 1.25 0.005
+#&gt; 1 eigen 5.00 0.020
+#&gt; 3 deSolve 54.25 0.217</div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='co'># Predict from a fitted model</span>
<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt; time parent m1
-#&gt; 1 0.0 82.49216 0.000000
-#&gt; 2 0.1 80.00563 1.179963
-#&gt; 3 0.2 77.59404 2.312596
-#&gt; 4 0.3 75.25515 3.399443
-#&gt; 5 0.4 72.98675 4.442000
-#&gt; 6 0.5 70.78673 5.441717</div><div class='input'># }
+ <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)
+ <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt; time parent m1
+#&gt; 0 0.0 82.49216 0.000000
+#&gt; 0.1 0.1 80.00562 1.236198
+#&gt; 0.2 0.2 77.59404 2.422818
+#&gt; 0.3 0.3 75.25514 3.561476
+#&gt; 0.4 0.4 72.98675 4.653740
+#&gt; 0.5 0.5 70.78673 5.701130</div><div class='input'># }
</div></pre>
</div>

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