diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-11-23 20:01:28 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-11-23 20:01:28 +0100 |
| commit | 5f9645570d8308f48a492d48f38acd0d08f7d636 (patch) | |
| tree | c9ecdfd23e311ed3d3f6f84f2e5ce0978694d44b /docs/reference | |
| parent | d566ba840f4351a3aeebf21aae0649caebe0e009 (diff) | |
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 12 | ||||
| -rw-r--r-- | docs/reference/index.html | 6 | ||||
| -rw-r--r-- | docs/reference/logLik.mkinfit.html | 202 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 50 | ||||
| -rw-r--r-- | docs/reference/mkinmod.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 6 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 6 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 24 |
10 files changed, 267 insertions, 57 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 0447e2d9..a74a3067 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.175 0.000 0.175 +#> 0.184 0.000 0.184 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd99510> -#> <environment: 0x55555bc57c88> +#> <bytecode: 0x55555be47f20> +#> <environment: 0x55555bc31c70> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555cb90200> -#> <environment: 0x55555bc57c88> +#> <bytecode: 0x55555cd8de90> +#> <environment: 0x55555bc31c70> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Tue Sep 18 15:16:36 2018" +#> [1] "Fri Nov 23 19:56:59 2018" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/index.html b/docs/reference/index.html index a7806970..c1d31aff 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -193,6 +193,12 @@ <p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p> </td> <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td> + </tr><tr> + + <td> + <p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p> + </td> + <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html new file mode 100644 index 00000000..1dda313f --- /dev/null +++ b/docs/reference/logLik.mkinfit.html @@ -0,0 +1,202 @@ +<!-- 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>Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • 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 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+ <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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/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>Calculated the log-likelihood of a fitted mkinfit object</h1> + + <div class="hidden name"><code>logLik.mkinfit.Rd</code></div> + </div> + + <div class="ref-description"> + + <p>This function simply calculates the product of the likelihood densities + calc</p> + + </div> + + <pre class="usage"><span class='co'># S3 method for mkinfit</span> +<span class='fu'>logLik</span>(<span class='no'>object</span>, <span class='no'>...</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>object</th> + <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + </tr> + <tr> + <th>…</th> + <td><p>For compatibility with the generic method</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>An object of class <code>logLik</code> with the number of + estimated parameters (degradation model parameters plus variance + model parameters) as attribute.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> <span class='no'>sfo_sfo</span> <span class='kw'><-</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + <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='no'>d_t</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> + <span class='no'>d_t</span>[<span class='fl'>23</span>:<span class='fl'>24</span>, <span class='st'>"value"</span>] <span class='kw'><-</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='fl'>NA</span>) <span class='co'># can't cope with zero values at the moment</span> + <span class='no'>f_nw</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>f_obs</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>f_tc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>AIC</span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>)</div><div class='output co'>#> df AIC +#> f_nw 5 204.4619 +#> f_obs 6 205.8727 +#> f_tc 6 143.8773</div></pre> + </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="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + + Johannes Ranke + + </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/mccall81_245T.html b/docs/reference/mccall81_245T.html index be77df76..9f937a12 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -158,8 +158,8 @@ <span class='kw'>anisole</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'> </div><div class='input'> <span class='no'>fit.1</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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.1</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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:16:48 2018 -#> Date of summary: Tue Sep 18 15:16:48 2018 +#> Date of fit: Fri Nov 23 19:57:18 2018 +#> Date of summary: Fri Nov 23 19:57:18 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -169,7 +169,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.602 s +#> Fitted with method Port using 574 model solutions performed in 3.661 s #> #> Weighting: none #> @@ -247,8 +247,8 @@ <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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:16:50 2018 -#> Date of summary: Tue Sep 18 15:16:50 2018 +#> Date of fit: Fri Nov 23 19:57:19 2018 +#> Date of summary: Fri Nov 23 19:57:19 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.513 s +#> Fitted with method Port using 246 model solutions performed in 1.549 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3c8442b6..9bbe3900 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -326,7 +326,7 @@ <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. The option "manual" is available for + two component error model. The option "manual" is available for the case that <code>err</code>!=<code>NULL</code>, but it is not necessary to specify it.</p></td> </tr> <tr> @@ -406,6 +406,8 @@ <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> +<p>Comparisons of models fitted to the same data can be made using <code>AIC</code> + by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</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></div> @@ -434,15 +436,15 @@ <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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:16:52 2018 -#> Date of summary: Tue Sep 18 15:16:52 2018 +#> Date of fit: Fri Nov 23 19:57:22 2018 +#> Date of summary: Fri Nov 23 19:57:22 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 0.158 s +#> Fitted with method Port using 64 model solutions performed in 0.155 s #> #> Weighting: none #> @@ -511,7 +513,7 @@ <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 -#> 1.011 0.000 1.012 </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 +#> 0.995 0.000 0.995 </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 @@ -586,7 +588,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.755 0.000 0.755 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.789 0.000 0.790 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</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.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -624,8 +626,8 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</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'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:04 2018 -#> Date of summary: Tue Sep 18 15:17:04 2018 +#> Date of fit: Fri Nov 23 19:57:34 2018 +#> Date of summary: Fri Nov 23 19:57:34 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -633,7 +635,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.823 s +#> Fitted with method Port using 186 model solutions performed in 0.825 s #> #> Weighting: none #> @@ -741,8 +743,8 @@ #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:06 2018 -#> Date of summary: Tue Sep 18 15:17:06 2018 +#> Date of fit: Fri Nov 23 19:57:36 2018 +#> Date of summary: Fri Nov 23 19:57:36 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -750,7 +752,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.374 s +#> Fitted with method Port using 551 model solutions performed in 2.528 s #> #> Weighting: none #> @@ -863,8 +865,8 @@ #> 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:07 2018 -#> Date of summary: Tue Sep 18 15:17:07 2018 +#> Date of fit: Fri Nov 23 19:57:37 2018 +#> Date of summary: Fri Nov 23 19:57:37 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -872,7 +874,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.636 s +#> Fitted with method Port using 155 model solutions performed in 0.687 s #> #> Weighting: mean #> @@ -981,8 +983,8 @@ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:08 2018 -#> Date of summary: Tue Sep 18 15:17:08 2018 +#> Date of fit: Fri Nov 23 19:57:38 2018 +#> Date of summary: Fri Nov 23 19:57:38 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -990,7 +992,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.717 s +#> Fitted with method Port using 174 model solutions performed in 0.781 s #> #> Weighting: manual #> @@ -1101,8 +1103,8 @@ <span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:09 2018 -#> Date of summary: Tue Sep 18 15:17:09 2018 +#> Date of fit: Fri Nov 23 19:57:39 2018 +#> Date of summary: Fri Nov 23 19:57:39 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1110,7 +1112,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.181 s +#> Fitted with method Port using 270 model solutions performed in 1.201 s #> #> Weighting: manual #> @@ -1219,8 +1221,8 @@ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) <span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:13 2018 -#> Date of summary: Tue Sep 18 15:17:13 2018 +#> Date of fit: Fri Nov 23 19:57:43 2018 +#> Date of summary: Fri Nov 23 19:57:43 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1228,7 +1230,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.077 s +#> Fitted with method Port using 692 model solutions performed in 3.087 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index af364403..3148efd8 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -229,7 +229,7 @@ For the definition of model types and their parameters, the equations given <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file20267955fc75.c 2> file20267955fc75.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file140043d42642.c 2> file140043d42642.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 91e9289d..baa67000 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -323,17 +323,17 @@ <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 -#> 0.003 0.000 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.004 0.000 0.004 </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 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.002 </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 -#> 0.034 0.000 0.034 </div><div class='input'> +#> 0.039 0.000 0.040 </div><div class='input'> </div><div class='input'> <span class='co'># Predict from a fitted model</span> <span class='no'>f</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_C</span>)</div><div class='output co'>#> Model cost at call 1 : 552.5739 #> Model cost at call 3 : 552.5739 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index ad011b75..8bc7b18c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -189,8 +189,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 0.054 0.027 6.836 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 20.444 0.000 20.459 </div><div class='input'> +#> 0.029 0.039 6.854 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 22.091 0.000 22.106 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f8e09b45..9428f187 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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:59 2018 -#> Date of summary: Tue Sep 18 15:17:59 2018 +#> Date of fit: Fri Nov 23 19:58:33 2018 +#> Date of summary: Fri Nov 23 19:58:33 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 0.071 s +#> Fitted with method Port using 35 model solutions performed in 0.081 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index f2602792..aa82269a 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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:18:06 2018 -#> Date of summary: Tue Sep 18 15:18:06 2018 +#> Date of fit: Fri Nov 23 19:58:40 2018 +#> Date of summary: Fri Nov 23 19:58:40 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 0.662 s +#> Fitted with method Port using 153 model solutions performed in 0.688 s #> #> Weighting: none #> @@ -276,8 +276,8 @@ The transformation of sets of formation fractions is fragile, as it supposes </div><div class='input'><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</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:18:08 2018 -#> Date of summary: Tue Sep 18 15:18:08 2018 +#> Date of fit: Fri Nov 23 19:58:42 2018 +#> Date of summary: Fri Nov 23 19:58:42 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 350 model solutions performed in 1.342 s +#> Fitted with method Port using 350 model solutions performed in 1.608 s #> #> Weighting: none #> @@ -364,8 +364,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</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.ff</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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:18:09 2018 -#> Date of summary: Tue Sep 18 15:18:09 2018 +#> Date of fit: Fri Nov 23 19:58:43 2018 +#> Date of summary: Fri Nov 23 19:58:43 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.737 s +#> Fitted with method Port using 186 model solutions performed in 0.821 s #> #> Weighting: none #> @@ -448,8 +448,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</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.ff.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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:18:10 2018 -#> Date of summary: Tue Sep 18 15:18:10 2018 +#> Date of fit: Fri Nov 23 19:58:44 2018 +#> Date of summary: Fri Nov 23 19:58:44 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.414 s +#> Fitted with method Port using 104 model solutions performed in 0.46 s #> #> Weighting: none #> |