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authorJohannes Ranke <jranke@uni-bremen.de>2019-02-22 20:51:13 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-02-22 20:51:13 +0100
commitdd6c4a8f895fd470345e7ae773299daaa4de7aef (patch)
tree03ee92fe3280f126ba7a2a21af2fec190458ccb9 /docs/reference/mkinfit.html
parentf12b9bcc5bded392eee51810fac5f94c2ae7d9c2 (diff)
Implement the NAFTA evaluation scheme
Diffstat (limited to 'docs/reference/mkinfit.html')
-rw-r--r--docs/reference/mkinfit.html46
1 files changed, 23 insertions, 23 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index addb23e5..dfdddb25 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -438,15 +438,15 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:49:53 2019
-#&gt; Date of summary: Fri Feb 22 09:49:53 2019
+#&gt; Date of fit: Fri Feb 22 20:46:59 2019
+#&gt; Date of summary: Fri Feb 22 20:46:59 2019
#&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 0.159 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.185 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -515,7 +515,7 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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 verstrichen
-#&gt; 1.015 0.000 1.016 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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; 1.071 0.000 1.072 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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
@@ -590,7 +590,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.821 0.000 0.822 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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; 0.852 0.000 0.852 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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
@@ -628,8 +628,8 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:05 2019
-#&gt; Date of summary: Fri Feb 22 09:50:05 2019
+#&gt; Date of fit: Fri Feb 22 20:47:11 2019
+#&gt; Date of summary: Fri Feb 22 20:47:11 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -637,7 +637,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.853 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.864 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -745,8 +745,8 @@
#&gt; 120 m1 33.31 28.78984 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:07 2019
-#&gt; Date of summary: Fri Feb 22 09:50:07 2019
+#&gt; Date of fit: Fri Feb 22 20:47:14 2019
+#&gt; Date of summary: Fri Feb 22 20:47:14 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -754,7 +754,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.535 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.584 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -867,8 +867,8 @@
#&gt; 120 m1 33.31 28.80898 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:08 2019
-#&gt; Date of summary: Fri Feb 22 09:50:08 2019
+#&gt; Date of fit: Fri Feb 22 20:47:15 2019
+#&gt; Date of summary: Fri Feb 22 20:47:15 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -876,7 +876,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.717 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.716 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -985,8 +985,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:09 2019
-#&gt; Date of summary: Fri Feb 22 09:50:09 2019
+#&gt; Date of fit: Fri Feb 22 20:47:16 2019
+#&gt; Date of summary: Fri Feb 22 20:47:16 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -994,7 +994,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.796 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.83 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1105,8 +1105,8 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:11 2019
-#&gt; Date of summary: Fri Feb 22 09:50:11 2019
+#&gt; Date of fit: Fri Feb 22 20:47:17 2019
+#&gt; Date of summary: Fri Feb 22 20:47:17 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1114,7 +1114,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.325 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.286 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1223,8 +1223,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:14 2019
-#&gt; Date of summary: Fri Feb 22 09:50:14 2019
+#&gt; Date of fit: Fri Feb 22 20:47:21 2019
+#&gt; Date of summary: Fri Feb 22 20:47:21 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1232,7 +1232,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.303 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.38 s
#&gt;
#&gt; Weighting: manual
#&gt;

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