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Diffstat (limited to 'docs')
| -rw-r--r-- | docs/articles/FOCUS_L.html | 40 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 10 | ||||
| -rw-r--r-- | docs/news/index.html | 3 | ||||
| -rw-r--r-- | docs/reference/AIC.mmkin.html | 211 | ||||
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 12 | ||||
| -rw-r--r-- | docs/reference/logLik.mkinfit.html | 19 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 46 | ||||
| -rw-r--r-- | docs/reference/mkinmod.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 4 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 4 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 24 |
13 files changed, 305 insertions, 86 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 4d337e72..448a03bb 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -110,15 +110,15 @@ <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.1 -## Date of fit: Mon Nov 26 09:47:23 2018 -## Date of summary: Mon Nov 26 09:47:23 2018 +## Date of fit: Mon Nov 26 11:41:50 2018 +## Date of summary: Mon Nov 26 11:41:50 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.093 s +## Fitted with method Port using 37 model solutions performed in 0.094 s ## ## Weighting: none ## @@ -201,8 +201,8 @@ <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.1 -## Date of fit: Mon Nov 26 09:47:25 2018 -## Date of summary: Mon Nov 26 09:47:25 2018 +## Date of fit: Mon Nov 26 11:41:52 2018 +## Date of summary: Mon Nov 26 11:41:52 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -296,15 +296,15 @@ <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.1 -## Date of fit: Mon Nov 26 09:47:26 2018 -## Date of summary: Mon Nov 26 09:47:26 2018 +## Date of fit: Mon Nov 26 11:41:53 2018 +## Date of summary: Mon Nov 26 11:41:53 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.192 s +## Fitted with method Port using 81 model solutions performed in 0.193 s ## ## Weighting: none ## @@ -367,8 +367,8 @@ <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.1 -## Date of fit: Mon Nov 26 09:47:27 2018 -## Date of summary: Mon Nov 26 09:47:27 2018 +## Date of fit: Mon Nov 26 11:41:54 2018 +## Date of summary: Mon Nov 26 11:41:54 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -377,7 +377,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.831 s +## Fitted with method Port using 336 model solutions performed in 0.826 s ## ## Weighting: none ## @@ -459,8 +459,8 @@ <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.1 -## Date of fit: Mon Nov 26 09:47:28 2018 -## Date of summary: Mon Nov 26 09:47:28 2018 +## Date of fit: Mon Nov 26 11:41:55 2018 +## Date of summary: Mon Nov 26 11:41:55 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -469,7 +469,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.336 s +## Fitted with method Port using 137 model solutions performed in 0.337 s ## ## Weighting: none ## @@ -560,15 +560,15 @@ <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.1 -## Date of fit: Mon Nov 26 09:47:28 2018 -## Date of summary: Mon Nov 26 09:47:29 2018 +## Date of fit: Mon Nov 26 11:41:55 2018 +## Date of summary: Mon Nov 26 11:41:56 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.107 s +## Fitted with method Port using 46 model solutions performed in 0.108 s ## ## Weighting: none ## @@ -620,15 +620,15 @@ <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.1 -## Date of fit: Mon Nov 26 09:47:28 2018 -## Date of summary: Mon Nov 26 09:47:29 2018 +## Date of fit: Mon Nov 26 11:41:56 2018 +## Date of summary: Mon Nov 26 11:41:56 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.168 s +## Fitted with method Port using 66 model solutions performed in 0.16 s ## ## Weighting: none ## diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 083cdb79..8da95e4d 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -125,9 +125,9 @@ <a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.264 1.000 2.263 0 -## 1 deSolve, not compiled 3 17.642 7.792 17.634 0 -## 2 Eigenvalue based 3 2.801 1.237 2.799 0 +## 3 deSolve, compiled 3 2.302 1.000 2.301 0 +## 1 deSolve, not compiled 3 17.754 7.712 17.743 0 +## 2 Eigenvalue based 3 2.840 1.234 2.838 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -156,8 +156,8 @@ <a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.012 1.000 4.010 0 -## 1 deSolve, not compiled 3 37.606 9.373 37.589 0 +## 2 deSolve, compiled 3 4.116 1.000 4.114 0 +## 1 deSolve, not compiled 3 37.902 9.208 37.884 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> diff --git a/docs/news/index.html b/docs/news/index.html index 9f658dad..1b2455a8 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -122,7 +122,8 @@ <a href="#mkin-0-9-47-6-2018-11-26" class="anchor"></a>mkin 0.9.47.6 (2018-11-26)<small> Unreleased </small> </h1> <ul> -<li><p>Add the function ‘logLik.mkinfit.R’ which makes it possible to calculate an AIC for mkinfit objects</p></li> +<li><p>Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects</p></li> +<li><p>Add the function ‘AIC.mmkin’ to makeqit easy to compare columns of mmkin objects</p></li> <li><p>‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset</p></li> <li><p>‘max_twa_parent’: Support maximum time weighted average concentration calculations for the hockey stick (HS) model</p></li> <li><p>‘mkinpredict’: Make the function generic and create a method for mkinfit objects</p></li> diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html new file mode 100644 index 00000000..a2ce9885 --- /dev/null +++ b/docs/reference/AIC.mmkin.html @@ -0,0 +1,211 @@ +<!-- 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 AIC for a column of an mmkin object — AIC.mmkin • mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link 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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 AIC for a column of an mmkin object</h1> + + <div class="hidden name"><code>AIC.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + + <p>Provides a convenient way to compare different kineti models fitted to the + same dataset.</p> + + </div> + + <pre class="usage"><span class='co'># S3 method for mmkin</span> +<span class='fu'>AIC</span>(<span class='no'>object</span>, <span class='no'>...</span>, <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>2</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='mmkin.html'>mmkin</a></code>, containing only one column.</p></td> + </tr> + <tr> + <th>…</th> + <td><p>For compatibility with the generic method</p></td> + </tr> + <tr> + <th>k</th> + <td><p>As in the generic method</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>As in the generic method (a numeric value for single fits, or a dataframe if + there are several fits in the column).</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), + <span class='fu'>list</span>(<span class='st'>"FOCUS A"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_A</span>, + <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>)) + <span class='fu'>AIC</span>(<span class='no'>f</span>[<span class='fl'>1</span>, <span class='st'>"FOCUS A"</span>]) <span class='co'># We get a single number for a single fit</span></div><div class='output co'>#> [1] 55.32452</div><div class='input'> + <span class='co'># For FOCUS A, the models fit almost equally well, so the higher the number</span> + <span class='co'># of parameters, the higher (worse) the AIC</span> + <span class='fu'>AIC</span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#> df AIC +#> SFO 3 55.32452 +#> FOMC 4 57.32477 +#> DFOP 5 59.32452</div><div class='input'> <span class='fu'>AIC</span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>], <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>0</span>) <span class='co'># If we do not penalize additional parameters, we get nearly the same</span></div><div class='output co'>#> df AIC +#> SFO 3 49.32452 +#> FOMC 4 49.32477 +#> DFOP 5 49.32452</div><div class='input'> + <span class='co'># For FOCUS C, the more complex models fit better</span> + <span class='fu'>AIC</span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> df AIC +#> SFO 3 59.84675 +#> FOMC 4 44.70584 +#> DFOP 5 29.08369</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/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 51da42fc..b304c2fb 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.183 0.000 0.183 +#> 0.188 0.000 0.188 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555be28e50> -#> <environment: 0x55555bc4d2b0> +#> <bytecode: 0x55555bd98970> +#> <environment: 0x55555d417aa8> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555cd2fbb8> -#> <environment: 0x55555bc4d2b0> +#> <bytecode: 0x55555cd14308> +#> <environment: 0x55555d417aa8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Mon Nov 26 09:45:35 2018" +#> [1] "Mon Nov 26 11:40:00 2018" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index b1901703..33d9eb36 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -34,15 +34,15 @@ <meta property="og:description" content="This function simply calculates the product of the likelihood densities calculated using dnorm, i.e. assuming normal distribution. -The total number of estimated parameters returned with the value - of the likelihood is calculated as the sum of fitted degradation +The total number of estimated parameters returned with the value + of the likelihood is calculated as the sum of fitted degradation model parameters and the fitted error model parameters. For the case of unweighted least squares fitting, we calculate one constant standard deviation from the residuals using sd and add one to the number of fitted degradation model parameters. For the case of manual weighting, we use the weight given for each observation as standard deviation in calculating its likelihood - and the total number of estimated parameters is equal to the + and the total number of estimated parameters is equal to the number of fitted degradation model parameters. In the case of iterative reweighting, the variances obtained by this procedure are used in the likelihood calculations, and the number of @@ -142,15 +142,15 @@ In the case of iterative reweighting, the variances obtained by this <p>This function simply calculates the product of the likelihood densities calculated using <code>dnorm</code>, i.e. assuming normal distribution.</p> -<p>The total number of estimated parameters returned with the value - of the likelihood is calculated as the sum of fitted degradation +<p>The total number of estimated parameters returned with the value + of the likelihood is calculated as the sum of fitted degradation model parameters and the fitted error model parameters.</p> <p>For the case of unweighted least squares fitting, we calculate one constant standard deviation from the residuals using <code>sd</code> and add one to the number of fitted degradation model parameters.</p> <p>For the case of manual weighting, we use the weight given for each observation as standard deviation in calculating its likelihood - and the total number of estimated parameters is equal to the + and the total number of estimated parameters is equal to the number of fitted degradation model parameters.</p> <p>In the case of iterative reweighting, the variances obtained by this procedure are used in the likelihood calculations, and the number of @@ -183,6 +183,11 @@ In the case of iterative reweighting, the variances obtained by this estimated parameters (degradation model parameters plus variance model parameters) as attribute.</p> + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <div class='dont-index'><p>Compare the AIC of columns of <code><a href='mmkin.html'>mmkin</a></code> objects using + <code><a href='AIC.mmkin.html'>AIC.mmkin</a></code>.</p></div> + <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>( @@ -207,6 +212,8 @@ In the case of iterative reweighting, the variances obtained by this <li><a href="#arguments">Arguments</a></li> <li><a href="#value">Value</a></li> + + <li><a href="#see-also">See also</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 981c633a..96082932 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: Mon Nov 26 09:45:54 2018 -#> Date of summary: Mon Nov 26 09:45:54 2018 +#> Date of fit: Mon Nov 26 11:40:20 2018 +#> Date of summary: Mon Nov 26 11:40:20 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 3.641 s +#> Fitted with method Port using 574 model solutions performed in 3.702 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: Mon Nov 26 09:45:56 2018 -#> Date of summary: Mon Nov 26 09:45:56 2018 +#> Date of fit: Mon Nov 26 11:40:22 2018 +#> Date of summary: Mon Nov 26 11:40:22 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 1.627 s +#> Fitted with method Port using 246 model solutions performed in 1.646 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 883dda22..77c69f4e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -436,15 +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: Mon Nov 26 09:45:59 2018 -#> Date of summary: Mon Nov 26 09:45:59 2018 +#> Date of fit: Mon Nov 26 11:40:24 2018 +#> Date of summary: Mon Nov 26 11:40:24 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 0.155 s +#> Fitted with method Port using 64 model solutions performed in 0.156 s #> #> Weighting: none #> @@ -513,7 +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 -#> 0.974 0.000 0.975 </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 +#> 0.989 0.000 0.990 </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 @@ -588,7 +588,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.79 0.00 0.79 </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 +#> 0.799 0.000 0.800 </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 @@ -626,8 +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: Mon Nov 26 09:46:10 2018 -#> Date of summary: Mon Nov 26 09:46:10 2018 +#> Date of fit: Mon Nov 26 11:40:36 2018 +#> Date of summary: Mon Nov 26 11:40:36 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -635,7 +635,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.889 s +#> Fitted with method Port using 186 model solutions performed in 0.839 s #> #> Weighting: none #> @@ -743,8 +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: Mon Nov 26 09:46:13 2018 -#> Date of summary: Mon Nov 26 09:46:13 2018 +#> Date of fit: Mon Nov 26 11:40:39 2018 +#> Date of summary: Mon Nov 26 11:40:39 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -752,7 +752,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.441 s +#> Fitted with method Port using 551 model solutions performed in 2.48 s #> #> Weighting: none #> @@ -865,8 +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: Mon Nov 26 09:46:14 2018 -#> Date of summary: Mon Nov 26 09:46:14 2018 +#> Date of fit: Mon Nov 26 11:40:40 2018 +#> Date of summary: Mon Nov 26 11:40:40 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -874,7 +874,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.679 s +#> Fitted with method Port using 155 model solutions performed in 0.694 s #> #> Weighting: mean #> @@ -983,8 +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: Mon Nov 26 09:46:15 2018 -#> Date of summary: Mon Nov 26 09:46:15 2018 +#> Date of fit: Mon Nov 26 11:40:41 2018 +#> Date of summary: Mon Nov 26 11:40:41 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -992,7 +992,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.771 s +#> Fitted with method Port using 174 model solutions performed in 0.778 s #> #> Weighting: manual #> @@ -1103,8 +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: Mon Nov 26 09:46:16 2018 -#> Date of summary: Mon Nov 26 09:46:16 2018 +#> Date of fit: Mon Nov 26 11:40:42 2018 +#> Date of summary: Mon Nov 26 11:40:42 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1112,7 +1112,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.2 s +#> Fitted with method Port using 270 model solutions performed in 1.225 s #> #> Weighting: manual #> @@ -1221,8 +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: Mon Nov 26 09:46:19 2018 -#> Date of summary: Mon Nov 26 09:46:19 2018 +#> Date of fit: Mon Nov 26 11:40:45 2018 +#> Date of summary: Mon Nov 26 11:40:45 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1230,7 +1230,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.079 s +#> Fitted with method Port using 692 model solutions performed in 3.119 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index d947aff5..0d644bc4 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 file74b35b9de5b.c 2> file74b35b9de5b.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file4252799a8f5a.c 2> file4252799a8f5a.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 88858539..bfe71be5 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -323,7 +323,7 @@ <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 -#> 0.005 0.000 0.005 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.003 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 @@ -333,7 +333,7 @@ <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'>"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 -#> 0.039 0.000 0.039 </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 49117199..92f12c2a 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 -#> 0.037 0.036 7.001 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 21.838 0.000 21.852 </div><div class='input'> +#> 0.050 0.037 6.958 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 22.101 0.000 22.114 </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 e63ab87e..554a28e3 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,8 +206,8 @@ <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: Mon Nov 26 09:47:09 2018 -#> Date of summary: Mon Nov 26 09:47:09 2018 +#> Date of fit: Mon Nov 26 11:41:36 2018 +#> Date of summary: Mon Nov 26 11:41:36 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index c0ff16fd..e6a42993 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: Mon Nov 26 09:47:17 2018 -#> Date of summary: Mon Nov 26 09:47:17 2018 +#> Date of fit: Mon Nov 26 11:41:44 2018 +#> Date of summary: Mon Nov 26 11:41:44 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 0.673 s +#> Fitted with method Port using 153 model solutions performed in 0.686 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: Mon Nov 26 09:47:18 2018 -#> Date of summary: Mon Nov 26 09:47:18 2018 +#> Date of fit: Mon Nov 26 11:41:45 2018 +#> Date of summary: Mon Nov 26 11:41:45 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 1.529 s +#> Fitted with method Port using 350 model solutions performed in 1.558 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: Mon Nov 26 09:47:20 2018 -#> Date of summary: Mon Nov 26 09:47:20 2018 +#> Date of fit: Mon Nov 26 11:41:46 2018 +#> Date of summary: Mon Nov 26 11:41:46 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 0.847 s +#> Fitted with method Port using 186 model solutions performed in 0.828 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: Mon Nov 26 09:47:20 2018 -#> Date of summary: Mon Nov 26 09:47:20 2018 +#> Date of fit: Mon Nov 26 11:41:47 2018 +#> Date of summary: Mon Nov 26 11:41:47 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 0.457 s +#> Fitted with method Port using 104 model solutions performed in 0.464 s #> #> Weighting: none #> |