diff options
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 12 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 6 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 19 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 6 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 6 |
6 files changed, 27 insertions, 26 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 5bc23d98..982363a1 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.167 0.000 0.168 +#> 0.183 0.000 0.184 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bcec700> -#> <environment: 0x55555bc44168> +#> <bytecode: 0x55555bd7d1a0> +#> <environment: 0x55555bc8d4d8> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c9d13a8> -#> <environment: 0x55555bc44168> +#> <bytecode: 0x55555ca81b68> +#> <environment: 0x55555bc8d4d8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Wed Jul 18 15:15:52 2018" +#> [1] "Thu Sep 6 11:50:56 2018" #> #> $version #> [1] "0.9.47.2" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index aacdec88..cdfc4b5d 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -166,8 +166,8 @@ <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: 0.9.47.2 #> 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 +#> Date of fit: Thu Sep 6 11:51:05 2018 +#> Date of summary: Thu Sep 6 11:51:05 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 1.416 s +#> Fitted with method Port using 246 model solutions performed in 1.51 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 9e59c7e6..e99e7d9e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -325,13 +325,13 @@ <tr> <th>weight</th> <td><p>only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of "none", - "std", "mean", see details of <code>modCost</code>, or "tc" for the - two component error model of Rocke and Lorenzato.</p></td> + "std", "mean", see details of <code>modCost</code>, or "tc" for the + two component error model.</p></td> </tr> <tr> <th>tc</th> - <td><p>The two components of the Rocke and Lorenzato error model as used - for (initial) weighting</p></td> + <td><p>The two components of the error model as used for (initial) + weighting</p></td> </tr> <tr> <th>scaleVar</th> @@ -367,7 +367,8 @@ <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 an error model similar to + When using this method, the two components of an error model similar to + the one described by 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 @@ -432,15 +433,15 @@ <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: 0.9.47.2 #> 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 +#> Date of fit: Thu Sep 6 11:51:08 2018 +#> Date of summary: Thu Sep 6 11:51:08 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 0.134 s +#> Fitted with method Port using 64 model solutions performed in 0.142 s #> #> Weighting: none #> @@ -509,7 +510,7 @@ <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 -#> 0.863 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 +#> 0.895 0.000 0.898 </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/mkinpredict.html b/docs/reference/mkinpredict.html index d5357ef6..5e2e5449 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -326,12 +326,12 @@ <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 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.001 </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='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 -#> 0.035 0.000 0.035 </div></pre> +#> 0.035 0.000 0.034 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 4d9c511c..7fb56bd3 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,15 +206,15 @@ <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: 0.9.47.2 #> 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 +#> Date of fit: Thu Sep 6 11:51:18 2018 +#> Date of summary: Thu Sep 6 11:51:18 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 0.073 s +#> Fitted with method Port using 35 model solutions performed in 0.078 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index a2f7a338..bd8b5165 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <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: 0.9.47.2 #> 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 +#> Date of fit: Thu Sep 6 11:51:19 2018 +#> Date of summary: Thu Sep 6 11:51:19 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 0.639 s +#> Fitted with method Port using 153 model solutions performed in 0.612 s #> #> Weighting: none #> |