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| -rw-r--r-- | docs/articles/FOCUS_L.html | 42 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 12 | ||||
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 12 | ||||
| -rw-r--r-- | docs/reference/logLik.mkinfit.html | 8 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 44 | ||||
| -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 | ||||
| -rw-r--r-- | man/logLik.mkinfit.Rd | 4 |
12 files changed, 89 insertions, 83 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 02b3f60e..4d337e72 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 09:29:29 2018 -## Date of summary: Mon Nov 26 09:29:29 2018 +## Date of fit: Mon Nov 26 09:47:23 2018 +## Date of summary: Mon Nov 26 09:47:23 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 0.094 s +## Fitted with method Port using 37 model solutions performed in 0.093 s ## ## Weighting: none ## @@ -201,15 +201,15 @@ <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 09:29:30 2018 -## Date of summary: Mon Nov 26 09:29:30 2018 +## Date of fit: Mon Nov 26 09:47:25 2018 +## Date of summary: Mon Nov 26 09:47:25 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.467 s +## Fitted with method Port using 611 model solutions performed in 1.475 s ## ## Weighting: none ## @@ -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 09:29:31 2018 -## Date of summary: Mon Nov 26 09:29:31 2018 +## Date of fit: Mon Nov 26 09:47:26 2018 +## Date of summary: Mon Nov 26 09:47:26 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 0.191 s +## Fitted with method Port using 81 model solutions performed in 0.192 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 09:29:32 2018 -## Date of summary: Mon Nov 26 09:29:32 2018 +## Date of fit: Mon Nov 26 09:47:27 2018 +## Date of summary: Mon Nov 26 09:47:27 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 0.828 s +## Fitted with method Port using 336 model solutions performed in 0.831 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 09:29:33 2018 -## Date of summary: Mon Nov 26 09:29:33 2018 +## Date of fit: Mon Nov 26 09:47:28 2018 +## Date of summary: Mon Nov 26 09:47:28 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 0.334 s +## Fitted with method Port using 137 model solutions performed in 0.336 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 09:29:34 2018 -## Date of summary: Mon Nov 26 09:29:34 2018 +## Date of fit: Mon Nov 26 09:47:28 2018 +## Date of summary: Mon Nov 26 09:47:29 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 0.108 s +## Fitted with method Port using 46 model solutions performed in 0.107 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 09:29:34 2018 -## Date of summary: Mon Nov 26 09:29:34 2018 +## Date of fit: Mon Nov 26 09:47:28 2018 +## Date of summary: Mon Nov 26 09:47:29 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 0.158 s +## Fitted with method Port using 66 model solutions performed in 0.168 s ## ## Weighting: none ## diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 93c800bf..083cdb79 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 2.268 1.000 2.267 0 -## 1 deSolve, not compiled 3 18.698 8.244 18.690 0 -## 2 Eigenvalue based 3 2.812 1.240 2.811 0 +## 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 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -156,12 +156,12 @@ <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 4.032 1.000 4.028 0 -## 1 deSolve, not compiled 3 39.759 9.861 39.741 0 +## 2 deSolve, compiled 3 4.012 1.000 4.010 0 +## 1 deSolve, not compiled 3 37.606 9.373 37.589 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.47.6 on</p> <pre><code>## R version 3.5.1 (2018-07-02) ## Platform: x86_64-pc-linux-gnu (64-bit) diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 33d90e5b..51da42fc 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.182 0.000 0.183 +#> 0.183 0.000 0.183 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555be42410> -#> <environment: 0x55555bc697f8> +#> <bytecode: 0x55555be28e50> +#> <environment: 0x55555bc4d2b0> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555cd2ca88> -#> <environment: 0x55555bc697f8> +#> <bytecode: 0x55555cd2fbb8> +#> <environment: 0x55555bc4d2b0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Mon Nov 26 09:27:40 2018" +#> [1] "Mon Nov 26 09:45:35 2018" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 5fd6c6d7..b1901703 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -41,7 +41,9 @@ 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. + observation as standard deviation in calculating its likelihood + 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 estimated parameters is obtained by the number of degradation model @@ -147,7 +149,9 @@ In the case of iterative reweighting, the variances obtained by this 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.</p> + observation as standard deviation in calculating its likelihood + 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 estimated parameters is obtained by the number of degradation model diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 2cd933e9..981c633a 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 09:27:59 2018 -#> Date of summary: Mon Nov 26 09:27:59 2018 +#> Date of fit: Mon Nov 26 09:45:54 2018 +#> Date of summary: Mon Nov 26 09:45:54 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 3.635 s +#> Fitted with method Port using 574 model solutions performed in 3.641 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 09:28:01 2018 -#> Date of summary: Mon Nov 26 09:28:01 2018 +#> Date of fit: Mon Nov 26 09:45:56 2018 +#> Date of summary: Mon Nov 26 09:45:56 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 1.623 s +#> Fitted with method Port using 246 model solutions performed in 1.627 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index addd9c30..883dda22 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -436,8 +436,8 @@ <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 09:28:04 2018 -#> Date of summary: Mon Nov 26 09:28:04 2018 +#> Date of fit: Mon Nov 26 09:45:59 2018 +#> Date of summary: Mon Nov 26 09:45:59 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -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 -#> 1.009 0.000 1.009 </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 +#> 0.974 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 #> 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 -#> 0.909 0.000 0.910 </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 +#> 0.79 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 #> 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 09:28:16 2018 -#> Date of summary: Mon Nov 26 09:28:16 2018 +#> Date of fit: Mon Nov 26 09:46:10 2018 +#> Date of summary: Mon Nov 26 09:46:10 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 0.927 s +#> Fitted with method Port using 186 model solutions performed in 0.889 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 09:28:18 2018 -#> Date of summary: Mon Nov 26 09:28:18 2018 +#> Date of fit: Mon Nov 26 09:46:13 2018 +#> Date of summary: Mon Nov 26 09:46:13 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 2.509 s +#> Fitted with method Port using 551 model solutions performed in 2.441 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 09:28:19 2018 -#> Date of summary: Mon Nov 26 09:28:19 2018 +#> Date of fit: Mon Nov 26 09:46:14 2018 +#> Date of summary: Mon Nov 26 09:46:14 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 0.68 s +#> Fitted with method Port using 155 model solutions performed in 0.679 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 09:28:20 2018 -#> Date of summary: Mon Nov 26 09:28:20 2018 +#> Date of fit: Mon Nov 26 09:46:15 2018 +#> Date of summary: Mon Nov 26 09:46:15 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 0.775 s +#> Fitted with method Port using 174 model solutions performed in 0.771 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 09:28:22 2018 -#> Date of summary: Mon Nov 26 09:28:22 2018 +#> Date of fit: Mon Nov 26 09:46:16 2018 +#> Date of summary: Mon Nov 26 09:46:16 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 1.203 s +#> Fitted with method Port using 270 model solutions performed in 1.2 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 09:28:25 2018 -#> Date of summary: Mon Nov 26 09:28:25 2018 +#> Date of fit: Mon Nov 26 09:46:19 2018 +#> Date of summary: Mon Nov 26 09:46:19 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 3.078 s +#> Fitted with method Port using 692 model solutions performed in 3.079 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 448c0e8e..d947aff5 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 file775a236112e7.c 2> file775a236112e7.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file74b35b9de5b.c 2> file74b35b9de5b.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 84e6591b..88858539 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -323,12 +323,12 @@ <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'>"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>( +#> 0.005 0.000 0.005 </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 -#> 0.001 0.000 0.002 </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 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index a27cf5db..49117199 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 -#> 0.038 0.036 6.851 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 21.780 0.000 21.791 </div><div class='input'> +#> 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'> <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 7f510c67..e63ab87e 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 09:29:14 2018 -#> Date of summary: Mon Nov 26 09:29:14 2018 +#> Date of fit: Mon Nov 26 09:47:09 2018 +#> Date of summary: Mon Nov 26 09:47:09 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 24b50890..c0ff16fd 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 09:29:22 2018 -#> Date of summary: Mon Nov 26 09:29:22 2018 +#> Date of fit: Mon Nov 26 09:47:17 2018 +#> Date of summary: Mon Nov 26 09:47:17 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 0.683 s +#> Fitted with method Port using 153 model solutions performed in 0.673 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 09:29:24 2018 -#> Date of summary: Mon Nov 26 09:29:24 2018 +#> Date of fit: Mon Nov 26 09:47:18 2018 +#> Date of summary: Mon Nov 26 09:47:18 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 1.594 s +#> Fitted with method Port using 350 model solutions performed in 1.529 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 09:29:25 2018 -#> Date of summary: Mon Nov 26 09:29:25 2018 +#> Date of fit: Mon Nov 26 09:47:20 2018 +#> Date of summary: Mon Nov 26 09:47:20 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 0.819 s +#> Fitted with method Port using 186 model solutions performed in 0.847 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 09:29:26 2018 -#> Date of summary: Mon Nov 26 09:29:26 2018 +#> Date of fit: Mon Nov 26 09:47:20 2018 +#> Date of summary: Mon Nov 26 09:47:20 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 0.486 s +#> Fitted with method Port using 104 model solutions performed in 0.457 s #> #> Weighting: none #> diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd index 78c4e4c2..8080f3db 100644 --- a/man/logLik.mkinfit.Rd +++ b/man/logLik.mkinfit.Rd @@ -16,7 +16,9 @@ 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. + observation as standard deviation in calculating its likelihood + 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 |