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Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 50 |
1 files changed, 25 insertions, 25 deletions
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 "Port" 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 "auto", 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 "obs", 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>&#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 "mkinfit" and "modFit" in the class attribute. + <p>A list with "mkinfit" and "modFit" 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 "IORE" submodel for metabolites, fitting with + <p>When using the "IORE" submodel for metabolites, fitting with "transform_rates = TRUE" (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'><-</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'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:12:35 2016 -#> Date of summary: Fri Nov 4 17:12:35 2016 +#> Date of fit: Thu Nov 17 22:56:57 2016 +#> Date of summary: Thu Nov 17 22:56:57 2016 #> #> Equations: -#> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent +#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.147 s +#> Fitted with method Port using 64 model solutions performed in 0.158 s #> #> Weighting: none #> @@ -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'>#> <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'><-</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'>#> user system elapsed -#> 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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 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'>#> 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='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -450,7 +450,7 @@ #> m1 131.760712 437.69961 #> </div><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span> -<span class='co'># print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, </span> +<span class='co'># print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,</span> <span class='co'># solution_type = "deSolve")))</span> <span class='co'># coef(fit.deSolve)</span> <span class='co'># endpoints(fit.deSolve)</span> @@ -465,7 +465,7 @@ <span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D)</span> <span class='co'># # Use starting parameters from parent only FOMC fit</span> <span class='co'># fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)</span> -<span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, </span> +<span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D,</span> <span class='co'># parms.ini = fit.FOMC$bparms.ode, plot=TRUE)</span> <span class='co'># </span> <span class='co'># # Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span> |