aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/mkinfit.html
diff options
context:
space:
mode:
Diffstat (limited to 'docs/reference/mkinfit.html')
-rw-r--r--docs/reference/mkinfit.html71
1 files changed, 43 insertions, 28 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 99b10f43..a912b065 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -49,13 +49,28 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../reference/index.html">Function reference</a>
</li>
-<li>
- <a href="../articles/index.html">Articles</a>
-</li>
-<li>
- <a href="../news/index.html">News</a>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ </ul>
</li>
</ul>
@@ -359,15 +374,15 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</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'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:36:12 2016
-#&gt; Date of summary: Fri Nov 18 15:36:12 2016
+#&gt; Date of fit: Fri Nov 18 16:45:39 2016
+#&gt; Date of summary: Fri Nov 18 16:45:39 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.157 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.146 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -436,7 +451,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</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='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; user system elapsed
-#&gt; 1.264 1.216 0.945 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 1.220 1.216 0.920 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -513,7 +528,7 @@
#&gt; Model cost at call 152 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; user system elapsed
-#&gt; 0.712 0.036 0.702 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.724 0.048 0.722 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -556,8 +571,8 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:36:22 2016
-#&gt; Date of summary: Fri Nov 18 15:36:22 2016
+#&gt; Date of fit: Fri Nov 18 16:45:50 2016
+#&gt; Date of summary: Fri Nov 18 16:45:50 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -565,7 +580,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.752 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.872 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -677,8 +692,8 @@
#&gt; 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:36:24 2016
-#&gt; Date of summary: Fri Nov 18 15:36:24 2016
+#&gt; Date of fit: Fri Nov 18 16:45:52 2016
+#&gt; Date of summary: Fri Nov 18 16:45:52 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -686,7 +701,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 486 model solutions performed in 2.047 s
+#&gt; Fitted with method Port using 486 model solutions performed in 2.009 s
#&gt;
#&gt; Weighting: none then iterative reweighting method obs
#&gt;
@@ -798,8 +813,8 @@
#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:36:25 2016
-#&gt; Date of summary: Fri Nov 18 15:36:25 2016
+#&gt; Date of fit: Fri Nov 18 16:45:53 2016
+#&gt; Date of summary: Fri Nov 18 16:45:53 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -807,7 +822,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.653 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.647 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -920,8 +935,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:36:26 2016
-#&gt; Date of summary: Fri Nov 18 15:36:26 2016
+#&gt; Date of fit: Fri Nov 18 16:45:54 2016
+#&gt; Date of summary: Fri Nov 18 16:45:54 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -929,7 +944,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.708 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.749 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1042,8 +1057,8 @@
<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:36:27 2016
-#&gt; Date of summary: Fri Nov 18 15:36:27 2016
+#&gt; Date of fit: Fri Nov 18 16:45:55 2016
+#&gt; Date of summary: Fri Nov 18 16:45:55 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1164,8 +1179,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:36:30 2016
-#&gt; Date of summary: Fri Nov 18 15:36:30 2016
+#&gt; Date of fit: Fri Nov 18 16:45:58 2016
+#&gt; Date of summary: Fri Nov 18 16:45:58 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1173,7 +1188,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 648 model solutions performed in 2.694 s
+#&gt; Fitted with method Port using 648 model solutions performed in 2.738 s
#&gt;
#&gt; Weighting: manual then iterative reweighting method obs
#&gt;

Contact - Imprint