diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-07-18 15:18:30 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-07-18 15:58:46 +0200 |
| commit | 0b98c459c30a0629a728acf6b311de035c55fb64 (patch) | |
| tree | f146faf4802da38862aa14b0268265f3fad9ba34 /docs/reference | |
| parent | d3ed95f2a0a43ed74b02ea90e35d043ed4e1e72f (diff) | |
Correct references to the Rocke and Lorenzato model
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y.
Rebuild static documentation.
Diffstat (limited to 'docs/reference')
42 files changed, 291 insertions, 79 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index cd8f29e9..c1177306 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index deb418c2..5bc23d98 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.179 0.000 0.184 +#> 0.167 0.000 0.168 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555b9b9d58> -#> <environment: 0x55555be59518> +#> <bytecode: 0x55555bcec700> +#> <environment: 0x55555bc44168> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c2673f8> -#> <environment: 0x55555be59518> +#> <bytecode: 0x55555c9d13a8> +#> <environment: 0x55555bc44168> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,13 +558,13 @@ #> 99.17407 #> #> $date -#> [1] "Wed Jun 6 01:21:24 2018" +#> [1] "Wed Jul 18 15:15:52 2018" #> #> $version -#> [1] "0.9.47.1" +#> [1] "0.9.47.2" #> #> $Rversion -#> [1] "3.5.0" +#> [1] "3.5.1" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 78caf48d..6888c0ba 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index c854c11c..624f3908 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 89ee9ae9..c089e5e7 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 182c7003..e6846a38 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index aa84e14b..42ff6926 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 4b8f1c92..9f7db6c1 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -65,7 +65,7 @@ The form given here differs slightly from the original reference by Gustafson </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index d06a839e..87ee2d20 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index c037a8d2..18c8a751 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -178,7 +178,7 @@ <span class='fu'>print</span>(<span class='fu'>data.frame</span>(<span class='fu'>coef</span>(<span class='no'>fit.fomc</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore.deS</span>), <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>paste</span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)))</div><div class='output co'>#> coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS. -#> model par 1 85.87489063 85.874891 85.874890 +#> model par 1 85.87489063 85.874890 85.874890 #> model par 2 0.05192238 -4.826631 -4.826631 #> model par 3 0.65096665 1.949403 1.949403</div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 32ef9f29..ac26f950 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index aee32558..bb782104 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 063234b3..9d71c18c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index b10998fb..46cb10e1 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -64,7 +64,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 90b6fd9d..091e65ea 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 8f337595..34edfc08 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 5785b5aa..d9705ce3 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -352,9 +352,9 @@ </tr><tr> <td> - <p><code><a href="sigma_rl.html">sigma_rl()</a></code> </p> + <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p> </td> - <td><p>Two component error model of Rocke and Lorenzato</p></td> + <td><p>Two component error model</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 7b3ef8ea..447d9fda 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -65,7 +65,7 @@ guidance." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 3326a225..aacdec88 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -164,10 +164,10 @@ <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 -#> R version used for fitting: 3.5.0 -#> Date of fit: Wed Jun 6 01:21:34 2018 -#> Date of summary: Wed Jun 6 01:21:34 2018 + <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.2 +#> R version used for fitting: 3.5.1 +#> Date of fit: Wed Jul 18 15:16:02 2018 +#> Date of summary: Wed Jul 18 15:16:02 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -177,7 +177,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.452 s +#> Fitted with method Port using 246 model solutions performed in 1.416 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 7f4431f5..2bf67d39 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index d52f582b..3e0f10f7 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 43cd51f7..3f4a84ec 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index e6fd8807..44fc1e51 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -62,7 +62,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index d0b54098..9e59c7e6 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -367,11 +367,14 @@ <code>reweight.tol</code> or up to the maximum number of iterations specified by <code>reweight.max.iter</code>. The second reweighting method is called "tc" (two-component error model). - When using this method, the two components of the error model according - to Rocke and Lorenzato (1995) are estimated from the fit and the resulting + When using this method, the two components an error model similar to + Rocke and Lorenzato (1995) are estimated from the fit and the resulting variances are used for weighting the residuals in each iteration until convergence of these components or up to the maximum number of iterations - specified.</p></td> + specified. Note that this method deviates from the model by Rocke and + Lorenzato, as their model implies that the errors follow a lognormal + distribution for large values, not a normal distribution as assumed by this + method.</p></td> </tr> <tr> <th>reweight.tol</th> @@ -427,17 +430,17 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <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: 3.5.0 -#> Date of fit: Wed Jun 6 01:21:36 2018 -#> Date of summary: Wed Jun 6 01:21:36 2018 +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.2 +#> R version used for fitting: 3.5.1 +#> Date of fit: Wed Jul 18 15:16:04 2018 +#> Date of summary: Wed Jul 18 15:16:04 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 0.143 s +#> Fitted with method Port using 64 model solutions performed in 0.134 s #> #> Weighting: none #> @@ -506,7 +509,7 @@ <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 verstrichen -#> 0.927 0.000 0.929 </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 +#> 0.863 0.000 0.864 </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 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 04050367..a9c6bb26 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -66,7 +66,7 @@ For the definition of model types and their parameters, the equations given </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 5a843c0e..33eeefbd 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 3a55ceae..71437181 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 946e0dfc..d5357ef6 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -321,7 +321,7 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.004 0.000 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index c288bf7c..e73b4905 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 9f98a077..85345135 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 74b6adad..2a060628 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 525a8453..07fc4854 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -66,7 +66,7 @@ If the current plot device is a tikz device, </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index a554a489..829105bd 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -65,7 +65,7 @@ If the current plot device is a tikz device, </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index ade048f0..70c4f768 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 64d3a03c..141dd1c9 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 06b3c049..18f3b78f 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html index bb9fd396..c8fc3bf9 100644 --- a/docs/reference/sigma_rl.html +++ b/docs/reference/sigma_rl.html @@ -63,7 +63,7 @@ $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html new file mode 100644 index 00000000..8bf1d5f6 --- /dev/null +++ b/docs/reference/sigma_twocomp.html @@ -0,0 +1,203 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Two component error model — sigma_twocomp • mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> + +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + + + +<meta property="og:title" content="Two component error model — sigma_twocomp" /> + +<meta property="og:description" content="Function describing the standard deviation of the measurement error + in dependence of the measured value \(y\): +$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$ +This is the error model used for example by Werner et al. (1978). The model + proposed by Rocke and Lorenzato (1995) can be written in this form as well, + but assumes approximate lognormal distribution of errors for high values of y." /> +<meta name="twitter:card" content="summary" /> + + + +<!-- mathjax --> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Two component error model</h1> + + <div class="hidden name"><code>sigma_twocomp.Rd</code></div> + </div> + + <div class="ref-description"> + + <p>Function describing the standard deviation of the measurement error + in dependence of the measured value \(y\):</p> +<p>$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$</p> +<p>This is the error model used for example by Werner et al. (1978). The model + proposed by Rocke and Lorenzato (1995) can be written in this form as well, + but assumes approximate lognormal distribution of errors for high values of y.</p> + + </div> + + <pre class="usage"><span class='fu'>sigma_twocomp</span>(<span class='no'>y</span>, <span class='no'>sigma_low</span>, <span class='no'>rsd_high</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>y</th> + <td><p>The magnitude of the observed value</p></td> + </tr> + <tr> + <th>sigma_low</th> + <td><p>The asymptotic minimum of the standard deviation for low observed values</p></td> + </tr> + <tr> + <th>rsd_high</th> + <td><p>The coefficient describing the increase of the standard deviation with + the magnitude of the observed value</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The standard deviation of the response variable.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) + Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry + 24(11), 1895-1898.</p> +<p>Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for + measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + + + </body> +</html> + diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index c8919f1c..4d9c511c 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -204,17 +204,17 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 -#> R version used for fitting: 3.5.0 -#> Date of fit: Wed Jun 6 01:21:46 2018 -#> Date of summary: Wed Jun 6 01:21:46 2018 + <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.47.2 +#> R version used for fitting: 3.5.1 +#> Date of fit: Wed Jul 18 15:16:13 2018 +#> Date of summary: Wed Jul 18 15:16:13 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.075 s +#> Fitted with method Port using 35 model solutions performed in 0.073 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 6e0ac227..9d9404e5 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -39,7 +39,10 @@ Variance component 'a' is based on a normal distribution with standard deviation Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 - for the increase of the standard deviation with y. + for the increase of the standard deviation with y. Note that this is a simplified version + of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the + measured values approximates lognormal distribution for high values, whereas we are using + normally distributed error components all along. Initial concentrations for metabolites and all values where adding the variance component resulted in a value below the assumed limit of detection of 0.1 were set to NA. As an example, the first dataset has the title SFO_lin_a and is based on the SFO model @@ -73,7 +76,7 @@ Compare also the code in the example section to see the degradation models." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -142,7 +145,10 @@ Compare also the code in the example section to see the degradation models." /> Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 - for the increase of the standard deviation with y.</p> + for the increase of the standard deviation with y. Note that this is a simplified version + of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the + measured values approximates lognormal distribution for high values, whereas we are using + normally distributed error components all along.</p> <p>Initial concentrations for metabolites and all values where adding the variance component resulted in a value below the assumed limit of detection of 0.1 were set to <code>NA</code>.</p> <p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 090b0c22..5b683283 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 3adb3a10..a2f7a338 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</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'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 -#> R version used for fitting: 3.5.0 -#> Date of fit: Wed Jun 6 01:21:47 2018 -#> Date of summary: Wed Jun 6 01:21:47 2018 +<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.47.2 +#> R version used for fitting: 3.5.1 +#> Date of fit: Wed Jul 18 15:16:15 2018 +#> Date of summary: Wed Jul 18 15:16:15 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.628 s +#> Fitted with method Port using 153 model solutions performed in 0.639 s #> #> Weighting: none #> |