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| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-11 22:12:51 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-11 22:12:51 +0100 |
| commit | d185c26e4909efbae9dc4210ed9eac4b2600910e (patch) | |
| tree | 7ac9660d439a6de997dac800d09c82404027ef9a /docs/reference/mkinfit.html | |
| parent | a0bbfd3291aaa1a55438b8746c1e3cfb58ce4172 (diff) | |
Static docs rebuilt again, with current pkgdown
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 23 |
1 files changed, 19 insertions, 4 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 10052053..991df1cc 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -27,6 +27,20 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" /> + +<meta property="og:description" content="This function uses the Flexible Modelling Environment package + FME 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 nlminb, + 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 mkinpredict. The variance of the residuals for each + observed variable can optionally be iteratively reweighted until convergence + using the argument reweight.method = "obs"." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -400,15 +414,15 @@ <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 used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:20 2018 -#> Date of summary: Fri Mar 9 23:08:20 2018 +#> Date of fit: Sun Mar 11 22:10:32 2018 +#> Date of summary: Sun Mar 11 22:10:32 2018 #> #> Equations: #> 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 0.148 s +#> Fitted with method Port using 64 model solutions performed in 0.135 s #> #> Weighting: none #> @@ -477,7 +491,7 @@ <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 -#> 0.839 0.000 0.840 </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 +#> 0.829 0.000 0.829 </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 @@ -585,3 +599,4 @@ </body> </html> + |