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authorJohannes Ranke <jranke@uni-bremen.de>2020-04-03 17:40:55 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-04-03 17:40:55 +0200
commit8c19fc5261dc53dc7880b3f54f8f2adf413de996 (patch)
tree193aad4a3b2920ad6bff1d54cd18e992ac179bdd /docs/reference/mkinpredict.html
parent312255078d2529f485a81df2a53d5928622ae81f (diff)
parent47ba9ea512b82fb8b31da8ec5558f3c0952d86d4 (diff)
Merge branch 'master' into mxkin
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log
Diffstat (limited to 'docs/reference/mkinpredict.html')
-rw-r--r--docs/reference/mkinpredict.html78
1 files changed, 51 insertions, 27 deletions
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 0eca973c..fe5bc975 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -71,7 +71,7 @@ kinetic parameters and initial values for the state variables." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span>
</span>
</div>
@@ -140,24 +140,49 @@ kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, u
kinetic parameters and initial values for the state variables.</p>
</div>
- <pre class="usage"><span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
- <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
- <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+ <pre class="usage"><span class='fu'>mkinpredict</span>(
+ <span class='no'>x</span>,
+ <span class='no'>odeparms</span>,
+ <span class='no'>odeini</span>,
+ <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+ <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+ <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='no'>...</span>
+)
<span class='co'># S3 method for mkinmod</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
- <span class='kw'>odeini</span> <span class='kw'>=</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'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
- <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
- <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+<span class='fu'>mkinpredict</span>(
+ <span class='no'>x</span>,
+ <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>odeini</span> <span class='kw'>=</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'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+ <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+ <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='no'>...</span>
+)
<span class='co'># S3 method for mkinfit</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>,
- <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
- <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
- <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>mkinpredict</span>(
+ <span class='no'>x</span>,
+ <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>,
+ <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>,
+ <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+ <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+ <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='no'>...</span>
+)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -350,7 +375,7 @@ solver is used.</p></td>
<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>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
+#&gt; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></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='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
@@ -360,7 +385,7 @@ solver is used.</p></td>
<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>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.021 0.000 0.022 </div><div class='input'>
+#&gt; 0.021 0.000 0.021 </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>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
@@ -372,10 +397,10 @@ solver is used.</p></td>
#&gt; Sum of squared residuals at call 9: 279.9294
#&gt; Sum of squared residuals at call 12: 200.3629
#&gt; Sum of squared residuals at call 13: 200.3629
-#&gt; Sum of squared residuals at call 18: 197.9039
-#&gt; Sum of squared residuals at call 23: 197.9039
-#&gt; Sum of squared residuals at call 25: 196.6754
-#&gt; Sum of squared residuals at call 27: 196.6754
+#&gt; Sum of squared residuals at call 18: 197.904
+#&gt; Sum of squared residuals at call 22: 197.904
+#&gt; Sum of squared residuals at call 25: 196.6753
+#&gt; Sum of squared residuals at call 27: 196.6753
#&gt; Sum of squared residuals at call 32: 196.5742
#&gt; Sum of squared residuals at call 33: 196.5742
#&gt; Sum of squared residuals at call 34: 196.5742
@@ -390,14 +415,13 @@ solver is used.</p></td>
#&gt; Sum of squared residuals at call 58: 196.5334
#&gt; Sum of squared residuals at call 59: 196.5334
#&gt; Sum of squared residuals at call 65: 196.5334
-#&gt; Sum of squared residuals at call 73: 196.5334
#&gt; Negative log-likelihood at call 75: 26.64668</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='input'> <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 1.179955
-#&gt; 3 0.2 77.59404 2.312580
-#&gt; 4 0.3 75.25515 3.399419
-#&gt; 5 0.4 72.98675 4.441969
-#&gt; 6 0.5 70.78673 5.441679</div><div class='input'> # }
+#&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'> # }
</div></pre>
</div>

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