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authorJohannes Ranke <jranke@uni-bremen.de>2016-11-17 22:58:28 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2016-11-17 22:58:28 +0100
commit98d684becd9495d370e1bcc8f9c7ca758caa4dd8 (patch)
tree94c5e18f755d1c3328fad3fe517fe28b45c2df2f /docs/reference/mkinfit.html
parent3f6ce570824616f5be0d6289ed65910d455dd266 (diff)
Static documentation rebuilt by pkgdown::build_site()
Diffstat (limited to 'docs/reference/mkinfit.html')
-rw-r--r--docs/reference/mkinfit.html50
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diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 32083843..891bc18b 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -82,11 +82,11 @@
<p>This function uses the Flexible Modelling Environment package
- <code>FME</code> to create a function calculating the model cost, i.e. the
+ <code>FME</code> to create a function calculating the model cost, i.e. the
deviation between the kinetic model and the observed data. This model cost is
- then minimised using the Port algorithm <code>nlminb</code>,
+ then minimised using the Port algorithm <code>nlminb</code>,
using the specified initial or fixed parameters and starting values.
- Per default, parameters in the kinetic models are internally transformed in order
+ Per default, parameters in the kinetic models are internally transformed in order
to better satisfy the assumption of a normal distribution of their estimators.
In each step of the optimsation, the kinetic model is solved using the
function <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the residuals for each
@@ -200,13 +200,13 @@
</dd>
<dt>use_compiled</dt>
<dd>
- If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code>
+ If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code>
model is used, in the calls to <code><a href='mkinpredict.html'>mkinpredict</a></code> even if
- a compiled verion is present.
+ a compiled verion is present.
</dd>
<dt>method.modFit</dt>
<dd>
- The optimisation method passed to <code>modFit</code>.
+ The optimisation method passed to <code>modFit</code>.
In order to optimally deal with problems where local minima occur, the
&quot;Port&quot; algorithm is now used per default as it is less prone to get trapped
@@ -228,20 +228,20 @@
<dt>maxit.modFit</dt>
<dd>
Maximum number of iterations in the optimisation. If not &quot;auto&quot;, this will
- be passed to the method called by <code>modFit</code>, overriding
+ be passed to the method called by <code>modFit</code>, overriding
what may be specified in the next argument <code>control.modFit</code>.
</dd>
<dt>control.modFit</dt>
<dd>
Additional arguments passed to the optimisation method used by
- <code>modFit</code>.
+ <code>modFit</code>.
</dd>
<dt>transform_rates</dt>
<dd>
Boolean specifying if kinetic rate constants should be transformed in the
model specification used in the fitting for better compliance with the
- assumption of normal distribution of the estimator. If TRUE, also
- alpha and beta parameters of the FOMC model are log-transformed, as well
+ assumption of normal distribution of the estimator. If TRUE, also
+ alpha and beta parameters of the FOMC model are log-transformed, as well
as k1 and k2 rate constants for the DFOP and HS models and the break point
tb of the HS model.
If FALSE, zero is used as a lower bound for the rates in the optimisation.
@@ -250,7 +250,7 @@
<dd>
Boolean specifying if formation fractions constants should be transformed in the
model specification used in the fitting for better compliance with the
- assumption of normal distribution of the estimator. The default (TRUE) is
+ assumption of normal distribution of the estimator. The default (TRUE) is
to do transformations. If TRUE, the g parameter of the DFOP and HS
models are also transformed, as they can also be seen as compositional
data. The transformation used for these transformations is the
@@ -294,7 +294,7 @@
<dd>
The length of the dataseries that is produced by the model prediction
function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy of
- the numerical solver if that is used (see <code>solution_type</code> argument.
+ the numerical solver if that is used (see <code>solution_type</code> argument.
The default value is 100.
</dd>
<dt>reweight.method</dt>
@@ -302,9 +302,9 @@
The method used for iteratively reweighting residuals, also known
as iteratively reweighted least squares (IRLS). Default is NULL,
the other method implemented is called &quot;obs&quot;, meaning that each
- observed variable is assumed to have its own variance, this is
+ observed variable is assumed to have its own variance, this is
estimated from the fit and used for weighting the residuals
- in each iteration until convergence of this estimate up to
+ in each iteration until convergence of this estimate up to
<code>reweight.tol</code> or up to the maximum number of iterations
specified by <code>reweight.max.iter</code>.
</dd>
@@ -323,20 +323,20 @@
</dd>
<dt>&amp;#8230;</dt>
<dd>
- Further arguments that will be passed to <code>modFit</code>.
+ Further arguments that will be passed to <code>modFit</code>.
</dd>
</dl>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>A list with &quot;mkinfit&quot; and &quot;modFit&quot; in the class attribute.
+ <p>A list with &quot;mkinfit&quot; and &quot;modFit&quot; in the class attribute.
A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
<code><a href='mkinparplot.html'>mkinparplot</a></code>.</p>
- <p>Fitting of several models to several datasets in a single call to
+ <p>Fitting of several models to several datasets in a single call to
<code><a href='mmkin.html'>mmkin</a></code>.</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
@@ -348,7 +348,7 @@
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
- <p>When using the &quot;IORE&quot; submodel for metabolites, fitting with
+ <p>When using the &quot;IORE&quot; submodel for metabolites, fitting with
&quot;transform_rates = TRUE&quot; (the default) often leads to failures of the
numerical ODE solver. In this situation it may help to switch off the
internal rate transformation.</p>
@@ -359,15 +359,15 @@
<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 4 17:12:35 2016
-#&gt; Date of summary: Fri Nov 4 17:12:35 2016
+#&gt; Date of fit: Thu Nov 17 22:56:57 2016
+#&gt; Date of summary: Thu Nov 17 22:56:57 2016
#&gt;
#&gt; Equations:
-#&gt; d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
+#&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 0.147 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.158 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -436,7 +436,7 @@
<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; 1.208 1.256 0.935 </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; 1.168 1.260 0.924 </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; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -450,7 +450,7 @@
#&gt; m1 131.760712 437.69961
#&gt; </div><div class='input'><span class='co'>## Not run: ------------------------------------</span>
<span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span>
-<span class='co'># print(system.time(fit.deSolve &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, </span>
+<span class='co'># print(system.time(fit.deSolve &lt;- mkinfit(SFO_SFO, FOCUS_2006_D,</span>
<span class='co'># solution_type = "deSolve")))</span>
<span class='co'># coef(fit.deSolve)</span>
<span class='co'># endpoints(fit.deSolve)</span>
@@ -465,7 +465,7 @@
<span class='co'># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D)</span>
<span class='co'># # Use starting parameters from parent only FOMC fit</span>
<span class='co'># fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)</span>
-<span class='co'># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D, </span>
+<span class='co'># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D,</span>
<span class='co'># parms.ini = fit.FOMC$bparms.ode, plot=TRUE)</span>
<span class='co'># </span>
<span class='co'># # Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>

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