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-rw-r--r--docs/reference/mkinfit.html50
1 files changed, 26 insertions, 24 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 3c8442b6..9bbe3900 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -326,7 +326,7 @@
<th>weight</th>
<td><p>only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of "none",
"std", "mean", see details of <code>modCost</code>, or "tc" for the
- two component error model. The option "manual" is available for
+ two component error model. The option "manual" is available for
the case that <code>err</code>!=<code>NULL</code>, but it is not necessary to specify it.</p></td>
</tr>
<tr>
@@ -406,6 +406,8 @@
<div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
<code><a href='mkinparplot.html'>mkinparplot</a></code>.</p>
+<p>Comparisons of models fitted to the same data can be made using <code>AIC</code>
+ by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p>
<p>Fitting of several models to several datasets in a single call to
<code><a href='mmkin.html'>mmkin</a></code>.</p></div>
@@ -434,15 +436,15 @@
<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 used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:16:52 2018
-#&gt; Date of summary: Tue Sep 18 15:16:52 2018
+#&gt; Date of fit: Fri Nov 23 19:57:22 2018
+#&gt; Date of summary: Fri Nov 23 19:57:22 2018
#&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 0.158 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.155 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -511,7 +513,7 @@
<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 verstrichen
-#&gt; 1.011 0.000 1.012 </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; 0.995 0.000 0.995 </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
@@ -586,7 +588,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.755 0.000 0.755 </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; 0.789 0.000 0.790 </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
@@ -624,8 +626,8 @@
<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 used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:04 2018
-#&gt; Date of summary: Tue Sep 18 15:17:04 2018
+#&gt; Date of fit: Fri Nov 23 19:57:34 2018
+#&gt; Date of summary: Fri Nov 23 19:57:34 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -633,7 +635,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.823 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.825 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -741,8 +743,8 @@
#&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'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:06 2018
-#&gt; Date of summary: Tue Sep 18 15:17:06 2018
+#&gt; Date of fit: Fri Nov 23 19:57:36 2018
+#&gt; Date of summary: Fri Nov 23 19:57:36 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -750,7 +752,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.374 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.528 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -863,8 +865,8 @@
#&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'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:07 2018
-#&gt; Date of summary: Tue Sep 18 15:17:07 2018
+#&gt; Date of fit: Fri Nov 23 19:57:37 2018
+#&gt; Date of summary: Fri Nov 23 19:57:37 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -872,7 +874,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.636 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.687 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -981,8 +983,8 @@
<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 used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:08 2018
-#&gt; Date of summary: Tue Sep 18 15:17:08 2018
+#&gt; Date of fit: Fri Nov 23 19:57:38 2018
+#&gt; Date of summary: Fri Nov 23 19:57:38 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -990,7 +992,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.717 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.781 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1101,8 +1103,8 @@
<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 used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:09 2018
-#&gt; Date of summary: Tue Sep 18 15:17:09 2018
+#&gt; Date of fit: Fri Nov 23 19:57:39 2018
+#&gt; Date of summary: Fri Nov 23 19:57:39 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1110,7 +1112,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.181 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.201 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1219,8 +1221,8 @@
<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 used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:13 2018
-#&gt; Date of summary: Tue Sep 18 15:17:13 2018
+#&gt; Date of fit: Fri Nov 23 19:57:43 2018
+#&gt; Date of summary: Fri Nov 23 19:57:43 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1228,7 +1230,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.077 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.087 s
#&gt;
#&gt; Weighting: manual
#&gt;

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