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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:21:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:55:25 +0200
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tree00ca40222b1f4c9bcffca081982e006763e697d8 /docs/mkinfit.html
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+
+ <h1>
+ Fit a kinetic model to data with one or more state variables
+</h1>
+
+<div class="row">
+ <div class="span8">
+ <h2>Usage</h2>
+ <pre><span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="symbol">mkinmod</span><span class="keyword">,</span> <span class="symbol">observed</span><span class="keyword">,</span>
+ <span class="argument">parms.ini</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"auto"</span><span class="keyword">,</span>
+ <span class="argument">state.ini</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"auto"</span><span class="keyword">,</span>
+ <span class="argument">fixed_parms</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="argument">fixed_initials</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/names'>names</a></span><span class="keyword">(</span><span class="symbol">mkinmod</span><span class="keyword">$</span><span class="symbol">diffs</span><span class="keyword">)</span><span class="keyword">[</span><span class="keyword">-</span><span class="number">1</span><span class="keyword">]</span><span class="keyword">,</span>
+ <span class="argument">from_max_mean</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"auto"</span><span class="keyword">,</span> <span class="string">"analytical"</span><span class="keyword">,</span> <span class="string">"eigen"</span><span class="keyword">,</span> <span class="string">"deSolve"</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">method.ode</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"lsoda"</span><span class="keyword">,</span>
+ <span class="argument">use_compiled</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"auto"</span><span class="keyword">,</span>
+ <span class="argument">method.modFit</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"Port"</span><span class="keyword">,</span> <span class="string">"Marq"</span><span class="keyword">,</span> <span class="string">"SANN"</span><span class="keyword">,</span> <span class="string">"Nelder-Mead"</span><span class="keyword">,</span> <span class="string">"BFGS"</span><span class="keyword">,</span> <span class="string">"CG"</span><span class="keyword">,</span> <span class="string">"L-BFGS-B"</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">maxit.modFit</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"auto"</span><span class="keyword">,</span>
+ <span class="argument">control.modFit</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">transform_rates</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span>
+ <span class="argument">transform_fractions</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span>
+ <span class="argument">plot</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">quiet</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">err</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="argument">weight</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"none"</span><span class="keyword">,</span>
+ <span class="argument">scaleVar</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span>
+ <span class="argument">atol</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1e-8</span><span class="keyword">,</span> <span class="argument">rtol</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1e-10</span><span class="keyword">,</span> <span class="argument">n.outtimes</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">100</span><span class="keyword">,</span>
+ <span class="argument">reweight.method</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span>
+ <span class="argument">reweight.tol</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1e-8</span><span class="keyword">,</span> <span class="argument">reweight.max.iter</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">10</span><span class="keyword">,</span>
+ <span class="argument">trace_parms</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre>
+
+ <h2>Arguments</h2>
+ <dl>
+ <dt>mkinmod</dt>
+ <dd>
+ A list of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the kinetic model to be
+ fitted to the data, or one of the shorthand names (&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;,
+ &quot;HS&quot;, &quot;SFORB&quot;). If a shorthand name is given, a parent only degradation
+ model is generated for the variable with the highest value in
+ <code>observed</code>.
+ </dd>
+ <dt>observed</dt>
+ <dd>
+ The observed data. It has to be in the long format as described in
+ <code><a href='http://www.rdocumentation.org/packages/FME/topics/modFit'>modFit</a></code>, i.e. the first column called &quot;name&quot; must contain the
+ name of the observed variable for each data point. The second column must
+ contain the times of observation, named &quot;time&quot;. The third column must be
+ named &quot;value&quot; and contain the observed values. Optionally, a further column
+ can contain weights for each data point. Its name must be passed as a
+ further argument named <code>err</code> which is then passed on to
+ <code><a href='http://www.rdocumentation.org/packages/FME/topics/modFit'>modFit</a></code>.
+ </dd>
+ <dt>parms.ini</dt>
+ <dd>
+ A named vector of initial values for the parameters, including parameters
+ to be optimised and potentially also fixed parameters as indicated by
+ <code>fixed_parms</code>. If set to &quot;auto&quot;, initial values for rate constants
+ are set to default values. Using parameter names that are not in the model
+ gives an error.
+
+ It is possible to only specify a subset of the parameters that the model
+ needs. You can use the parameter lists &quot;bparms.ode&quot; from a previously
+ fitted model, which contains the differential equation parameters from this
+ model. This works nicely if the models are nested. An example is given
+ below.
+ </dd>
+ <dt>state.ini</dt>
+ <dd>
+ A named vector of initial values for the state variables of the model. In
+ case the observed variables are represented by more than one model
+ variable, the names will differ from the names of the observed variables
+ (see <code>map</code> component of <code><a href='mkinmod.html'>mkinmod</a></code>). The default is to set
+ the initial value of the first model variable to the mean of the time zero
+ values for the variable with the maximum observed value, and all others to 0.
+ If this variable has no time zero observations, its initial value is set to 100.
+ </dd>
+ <dt>fixed_parms</dt>
+ <dd>
+ The names of parameters that should not be optimised but rather kept at the
+ values specified in <code>parms.ini</code>.
+ </dd>
+ <dt>fixed_initials</dt>
+ <dd>
+ The names of model variables for which the initial state at time 0 should
+ be excluded from the optimisation. Defaults to all state variables except
+ for the first one.
+ </dd>
+ <dt>from_max_mean</dt>
+ <dd>
+ If this is set to TRUE, and the model has only one observed variable, then
+ data before the time of the maximum observed value (after averaging for each
+ sampling time) are discarded, and this time is subtracted from all
+ remaining time values, so the time of the maximum observed mean value is
+ the new time zero.
+ </dd>
+ <dt>solution_type</dt>
+ <dd>
+ If set to &quot;eigen&quot;, the solution of the system of differential equations is
+ based on the spectral decomposition of the coefficient matrix in cases that
+ this is possible. If set to &quot;deSolve&quot;, a numerical ode solver from package
+ <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/deSolve'>deSolve</a></code> is used. If set to &quot;analytical&quot;, an analytical
+ solution of the model is used. This is only implemented for simple
+ degradation experiments with only one state variable, i.e. with no
+ metabolites. The default is &quot;auto&quot;, which uses &quot;analytical&quot; if possible,
+ otherwise &quot;eigen&quot; if the model can be expressed using eigenvalues and
+ eigenvectors, and finally &quot;deSolve&quot; for the remaining models (time
+ dependence of degradation rates and metabolites). This argument is passed
+ on to the helper function <code><a href='mkinpredict.html'>mkinpredict</a></code>.
+ </dd>
+ <dt>method.ode</dt>
+ <dd>
+ The solution method passed via <code><a href='mkinpredict.html'>mkinpredict</a></code> to
+ <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/ode'>ode</a></code> in case the solution type is &quot;deSolve&quot;. The default
+ &quot;lsoda&quot; is performant, but sometimes fails to converge.
+ </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>
+ model is used, in the calls to <code><a href='mkinpredict.html'>mkinpredict</a></code> even if
+ a compiled verion is present.
+ </dd>
+ <dt>method.modFit</dt>
+ <dd>
+ The optimisation method passed to <code><a href='http://www.rdocumentation.org/packages/FME/topics/modFit'>modFit</a></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
+ in local minima and depends less on starting values for parameters than
+ the Levenberg Marquardt variant selected by &quot;Marq&quot;. However, &quot;Port&quot; needs
+ more iterations.
+
+ The former default &quot;Marq&quot; is the Levenberg Marquardt algorithm
+ <code><a href='http://www.rdocumentation.org/packages/minpack.lm/topics/nls.lm'>nls.lm</a></code> from the package <code>minpack.lm</code> and usually needs
+ the least number of iterations.
+
+ The &quot;Pseudo&quot; algorithm is not included because it needs finite parameter bounds
+ which are currently not supported.
+
+ The &quot;Newton&quot; algorithm is not included because its number of iterations
+ can not be controlled by <code>control.modFit</code> and it does not appear
+ to provide advantages over the other algorithms.
+ </dd>
+ <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><a href='http://www.rdocumentation.org/packages/FME/topics/modFit'>modFit</a></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><a href='http://www.rdocumentation.org/packages/FME/topics/modFit'>modFit</a></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
+ 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.
+ </dd>
+ <dt>transform_fractions</dt>
+ <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
+ 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
+ <code><a href='ilr.html'>ilr</a></code> transformation.
+ </dd>
+ <dt>plot</dt>
+ <dd>
+ Should the observed values and the numerical solutions be plotted at each
+ stage of the optimisation?
+ </dd>
+ <dt>quiet</dt>
+ <dd>
+ Suppress printing out the current model cost after each improvement?
+ </dd>
+ <dt>err </dt>
+ <dd>either <code>NULL</code>, or the name of the column with the
+ <em>error</em> estimates, used to weigh the residuals (see details of
+ <code><a href='http://www.rdocumentation.org/packages/FME/topics/modCost'>modCost</a></code>); if <code>NULL</code>, then the residuals are not weighed.
+ </dd>
+ <dt>weight</dt>
+ <dd>
+ only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of &quot;none&quot;,
+ &quot;std&quot;, &quot;mean&quot;, see details of <code><a href='http://www.rdocumentation.org/packages/FME/topics/modCost'>modCost</a></code>.
+ </dd>
+ <dt>scaleVar</dt>
+ <dd>
+ Will be passed to <code><a href='http://www.rdocumentation.org/packages/FME/topics/modCost'>modCost</a></code>. Default is not to scale Variables
+ according to the number of observations.
+ </dd>
+ <dt>atol</dt>
+ <dd>
+ Absolute error tolerance, passed to <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/ode'>ode</a></code>. Default is 1e-8,
+ lower than in <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/lsoda'>lsoda</a></code>.
+ </dd>
+ <dt>rtol</dt>
+ <dd>
+ Absolute error tolerance, passed to <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/ode'>ode</a></code>. Default is 1e-10,
+ much lower than in <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/lsoda'>lsoda</a></code>.
+ </dd>
+ <dt>n.outtimes</dt>
+ <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 default value is 100.
+ </dd>
+ <dt>reweight.method</dt>
+ <dd>
+ 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
+ estimated from the fit and used for weighting the residuals
+ 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>
+ <dt>reweight.tol</dt>
+ <dd>
+ Tolerance for convergence criterion for the variance components
+ in IRLS fits.
+ </dd>
+ <dt>reweight.max.iter</dt>
+ <dd>
+ Maximum iterations in IRLS fits.
+ </dd>
+ <dt>trace_parms</dt>
+ <dd>
+ Should a trace of the parameter values be listed?
+ </dd>
+ <dt>...</dt>
+ <dd>
+ Further arguments that will be passed to <code><a href='http://www.rdocumentation.org/packages/FME/topics/modFit'>modFit</a></code>.
+ </dd>
+ </dl>
+
+ <div class="Description">
+ <h2>Description</h2>
+
+ <p>This function uses the Flexible Modelling Environment package
+ <code><a href='http://www.rdocumentation.org/packages/FME/topics/FME'>FME</a></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><a href='http://www.rdocumentation.org/packages/stats/topics/nlminb'>nlminb</a></code>,
+ using the specified initial or fixed parameters and starting values.
+ 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
+ observed variable can optionally be iteratively reweighted until convergence
+ using the argument <code>reweight.method = &quot;obs&quot;</code>.</p>
+
+ </div>
+
+ <div class="Value">
+ <h2>Value</h2>
+
+ <p><dl>
+ 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>.
+</dl></p>
+
+ </div>
+
+ <div class="Note">
+ <h2>Note</h2>
+
+ <p>The implementation of iteratively reweighted least squares is inspired by the
+ work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei
+ Gao). A similar implemention can also be found in CAKE 2.0, which is the
+ other GUI derivative of mkin, sponsored by Syngenta.</p>
+
+ </div>
+
+ <div class="Note">
+ <h2>Note</h2>
+
+ <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>
+
+ </div>
+
+ <h2 id="examples">Examples</h2>
+ <pre class="examples"><div class='input'><span class="comment"># Use shorthand notation for parent only degradation</span>
+<span class="symbol">fit</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="string">"FOMC"</span><span class="keyword">,</span> <span class="symbol">FOCUS_2006_C</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span>
+<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">)</span></div>
+<div class='output'>mkin version: 0.9.44.9000
+R version: 3.3.1
+Date of fit: Sat Sep 10 05:53:02 2016
+Date of summary: Sat Sep 10 05:53:02 2016
+
+Equations:
+d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
+
+Model predictions using solution type analytical
+
+Fitted with method Port using 64 model solutions performed in 0.16 s
+
+Weighting: none
+
+Starting values for parameters to be optimised:
+ value type
+parent_0 85.1 state
+alpha 1.0 deparm
+beta 10.0 deparm
+
+Starting values for the transformed parameters actually optimised:
+ value lower upper
+parent_0 85.100000 -Inf Inf
+log_alpha 0.000000 -Inf Inf
+log_beta 2.302585 -Inf Inf
+
+Fixed parameter values:
+None
+
+Optimised, transformed parameters with symmetric confidence intervals:
+ Estimate Std. Error Lower Upper
+parent_0 85.87000 2.2460 80.38000 91.3700
+log_alpha 0.05192 0.1605 -0.34080 0.4446
+log_beta 0.65100 0.2801 -0.03452 1.3360
+
+Parameter correlation:
+ parent_0 log_alpha log_beta
+parent_0 1.0000 -0.2033 -0.3624
+log_alpha -0.2033 1.0000 0.9547
+log_beta -0.3624 0.9547 1.0000
+
+Residual standard error: 2.275 on 6 degrees of freedom
+
+Backtransformed parameters:
+Confidence intervals for internally transformed parameters are asymmetric.
+t-test (unrealistically) based on the assumption of normal distribution
+for estimators of untransformed parameters.
+ Estimate t value Pr(&gt;t) Lower Upper
+parent_0 85.870 38.230 1.069e-08 80.3800 91.370
+alpha 1.053 6.231 3.953e-04 0.7112 1.560
+beta 1.917 3.570 5.895e-03 0.9661 3.806
+
+Chi2 error levels in percent:
+ err.min n.optim df
+All data 6.657 3 6
+parent 6.657 3 6
+
+Estimated disappearance times:
+ DT50 DT90 DT50back
+parent 1.785 15.15 4.56
+
+Data:
+ time variable observed predicted residual
+ 0 parent 85.1 85.875 -0.7749
+ 1 parent 57.9 55.191 2.7091
+ 3 parent 29.9 31.845 -1.9452
+ 7 parent 14.6 17.012 -2.4124
+ 14 parent 9.7 9.241 0.4590
+ 28 parent 6.6 4.754 1.8460
+ 63 parent 4.0 2.102 1.8977
+ 91 parent 3.9 1.441 2.4590
+ 119 parent 0.6 1.092 -0.4919
+</div>
+<div class='input'>
+<span class="comment"># One parent compound, one metabolite, both single first order.</span>
+<span class="comment"># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span>
+<span class="symbol">SFO_SFO</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span>
+ <span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"m1"</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span></div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'><span class="comment"># Fit the model to the FOCUS example dataset D using defaults</span>
+<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span><span class="keyword">(</span><span class="symbol">fit</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO</span><span class="keyword">,</span> <span class="symbol">FOCUS_2006_D</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"eigen"</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span><span class="keyword">)</span><span class="keyword">)</span></div>
+<div class='output'> user system elapsed
+ 1.272 1.360 1.044
+</div>
+<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">)</span></div>
+<div class='output'> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+ 99.59848 -3.03822 -2.98030 -5.24750
+</div>
+<div class='input'><span class="functioncall"><a href='endpoints.html'>endpoints</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">)</span></div>
+<div class='output'>$ff
+parent_sink parent_m1 m1_sink
+ 0.485524 0.514476 1.000000
+
+$SFORB
+logical(0)
+
+$distimes
+ DT50 DT90
+parent 7.022929 23.32967
+m1 131.760712 437.69961
+
+</div>
+<div class='input'><span class="comment">## Not run: ------------------------------------</span>
+<span class="comment"># # deSolve is slower when no C compiler (gcc) was available during model generation</span>
+<span class="comment"># print(system.time(fit.deSolve &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, </span>
+<span class="comment"># solution_type = "deSolve")))</span>
+<span class="comment"># coef(fit.deSolve)</span>
+<span class="comment"># endpoints(fit.deSolve)</span>
+<span class="comment">## ---------------------------------------------</span>
+
+<span class="comment"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span>
+<span class="comment">## Not run: ------------------------------------</span>
+<span class="comment"># FOMC_SFO &lt;- mkinmod(</span>
+<span class="comment"># parent = mkinsub("FOMC", "m1"),</span>
+<span class="comment"># m1 = mkinsub("SFO"))</span>
+<span class="comment"># # Fit the model to the FOCUS example dataset D using defaults</span>
+<span class="comment"># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D)</span>
+<span class="comment"># # Use starting parameters from parent only FOMC fit</span>
+<span class="comment"># fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)</span>
+<span class="comment"># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D, </span>
+<span class="comment"># parms.ini = fit.FOMC$bparms.ode, plot=TRUE)</span>
+<span class="comment"># </span>
+<span class="comment"># # Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
+<span class="comment"># SFORB_SFO &lt;- mkinmod(</span>
+<span class="comment"># parent = list(type = "SFORB", to = "m1", sink = TRUE),</span>
+<span class="comment"># m1 = list(type = "SFO"))</span>
+<span class="comment"># # Fit the model to the FOCUS example dataset D using defaults</span>
+<span class="comment"># fit.SFORB_SFO &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D)</span>
+<span class="comment"># fit.SFORB_SFO.deSolve &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve")</span>
+<span class="comment"># # Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
+<span class="comment"># fit.SFORB = mkinfit("SFORB", FOCUS_2006_D)</span>
+<span class="comment"># fit.SFORB_SFO &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)</span>
+<span class="comment">## ---------------------------------------------</span>
+
+<span class="comment">## Not run: ------------------------------------</span>
+<span class="comment"># # Weighted fits, including IRLS</span>
+<span class="comment"># SFO_SFO.ff &lt;- mkinmod(parent = mkinsub("SFO", "m1"),</span>
+<span class="comment"># m1 = mkinsub("SFO"), use_of_ff = "max")</span>
+<span class="comment"># f.noweight &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span>
+<span class="comment"># summary(f.noweight)</span>
+<span class="comment"># f.irls &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs")</span>
+<span class="comment"># summary(f.irls)</span>
+<span class="comment"># f.w.mean &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean")</span>
+<span class="comment"># summary(f.w.mean)</span>
+<span class="comment"># f.w.value &lt;- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value")</span>
+<span class="comment"># summary(f.w.value)</span>
+<span class="comment">## ---------------------------------------------</span>
+
+<span class="comment">## Not run: ------------------------------------</span>
+<span class="comment"># # Manual weighting</span>
+<span class="comment"># dw &lt;- FOCUS_2006_D</span>
+<span class="comment"># errors &lt;- c(parent = 2, m1 = 1)</span>
+<span class="comment"># dw$err.man &lt;- errors[FOCUS_2006_D$name]</span>
+<span class="comment"># f.w.man &lt;- mkinfit(SFO_SFO.ff, dw, err = "err.man")</span>
+<span class="comment"># summary(f.w.man)</span>
+<span class="comment"># f.w.man.irls &lt;- mkinfit(SFO_SFO.ff, dw, err = "err.man",</span>
+<span class="comment"># reweight.method = "obs")</span>
+<span class="comment"># summary(f.w.man.irls)</span>
+<span class="comment">## ---------------------------------------------</span></div></pre>
+ </div>
+ <div class="span4 sidebar">
+ <!-- <ul>
+ <li>mkinfit</li>
+ </ul>
+ <ul>
+ <li> optimize </li>
+ </ul> -->
+
+ <h2>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
+ <code><a href='mmkin.html'>mmkin</a></code>.</p>
+
+
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+
+ </div>
+</div>
+
+ <footer>
+ <p class="pull-right"><a href="#">Back to top</a></p>
+<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
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