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| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | docs/articles/FOCUS_L.html | 38 | ||||
| -rw-r--r-- | docs/articles/compiled_models.html | 10 | ||||
| -rw-r--r-- | docs/news/index.html | 6 | ||||
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 12 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 6 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 8 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 6 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 6 |
10 files changed, 49 insertions, 49 deletions
@@ -1,4 +1,4 @@ -# mkin 0.9.47.2 (2018-07-09) +# mkin 0.9.47.2 (2018-07-19) - 'sigma_twocomp': Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly. diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 4b324b7e..a42c6e38 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: 0.9.47.2 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 11:51:22 2018 -## Date of summary: Thu Sep 6 11:51:22 2018 +## Date of fit: Thu Sep 6 13:35:50 2018 +## Date of summary: Thu Sep 6 13:35:50 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 0.085 s +## Fitted with method Port using 37 model solutions performed in 0.086 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: 0.9.47.2 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 11:51:24 2018 -## Date of summary: Thu Sep 6 11:51:24 2018 +## Date of fit: Thu Sep 6 13:35:52 2018 +## Date of summary: Thu Sep 6 13:35:52 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 1.348 s +## Fitted with method Port using 611 model solutions performed in 1.35 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: 0.9.47.2 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 11:51:25 2018 -## Date of summary: Thu Sep 6 11:51:25 2018 +## Date of fit: Thu Sep 6 13:35:52 2018 +## Date of summary: Thu Sep 6 13:35:53 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 0.182 s +## Fitted with method Port using 81 model solutions performed in 0.175 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: 0.9.47.2 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 11:51:26 2018 -## Date of summary: Thu Sep 6 11:51:26 2018 +## Date of fit: Thu Sep 6 13:35:53 2018 +## Date of summary: Thu Sep 6 13:35:53 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 0.749 s +## Fitted with method Port using 336 model solutions performed in 0.746 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: 0.9.47.2 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 11:51:27 2018 -## Date of summary: Thu Sep 6 11:51:27 2018 +## Date of fit: Thu Sep 6 13:35:54 2018 +## Date of summary: Thu Sep 6 13:35:55 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 0.329 s +## Fitted with method Port using 137 model solutions performed in 0.324 s ## ## Weighting: none ## @@ -560,8 +560,8 @@ <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: 0.9.47.2 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 11:51:27 2018 -## Date of summary: Thu Sep 6 11:51:27 2018 +## Date of fit: Thu Sep 6 13:35:55 2018 +## Date of summary: Thu Sep 6 13:35:55 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -620,8 +620,8 @@ <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: 0.9.47.2 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 11:51:27 2018 -## Date of summary: Thu Sep 6 11:51:27 2018 +## Date of fit: Thu Sep 6 13:35:55 2018 +## Date of summary: Thu Sep 6 13:35:55 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 17387187..16059fcb 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/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 2.112 1.000 2.110 0 -## 1 deSolve, not compiled 3 16.633 7.875 16.624 0 -## 2 Eigenvalue based 3 2.637 1.249 2.635 0 +## 3 deSolve, compiled 3 2.218 1.000 2.217 0 +## 1 deSolve, not compiled 3 16.654 7.509 16.646 0 +## 2 Eigenvalue based 3 2.724 1.228 2.722 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 3.720 1.000 3.718 0 -## 1 deSolve, not compiled 3 34.677 9.322 34.661 0 +## 2 deSolve, compiled 3 3.780 1.000 3.777 0 +## 1 deSolve, not compiled 3 35.169 9.304 35.152 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 95995810..71390917 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -117,9 +117,9 @@ </div> - <div id="mkin-0-9-47-2-2018-07-09" class="section level1"> + <div id="mkin-0-9-47-2-2018-07-19" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-47-2-2018-07-09" class="anchor"></a>mkin 0.9.47.2 (2018-07-09)<small> 2018-07-19 </small> +<a href="#mkin-0-9-47-2-2018-07-19" class="anchor"></a>mkin 0.9.47.2 (2018-07-19)<small> 2018-07-19 </small> </h1> <ul> <li><p>‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.</p></li> @@ -639,7 +639,7 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-47-2-2018-07-09">0.9.47.2</a></li> + <li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li> <li><a href="#mkin-0-9-47-1-2018-02-06">0.9.47.1</a></li> <li><a href="#mkin-0-9-46-3-2017-11-16">0.9.46.3</a></li> <li><a href="#mkin-0-9-46-2-2017-10-10">0.9.46.2</a></li> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 982363a1..8771b53b 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 0.184 +#> 0.171 0.001 0.171 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd7d1a0> -#> <environment: 0x55555bc8d4d8> +#> <bytecode: 0x55555bd7f970> +#> <environment: 0x55555bc8fca8> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555ca81b68> -#> <environment: 0x55555bc8d4d8> +#> <bytecode: 0x55555ca84338> +#> <environment: 0x55555bc8fca8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Sep 6 11:50:56 2018" +#> [1] "Thu Sep 6 13:35:24 2018" #> #> $version #> [1] "0.9.47.2" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index cdfc4b5d..9894f8eb 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -166,8 +166,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.2 #> R version used for fitting: 3.5.1 -#> Date of fit: Thu Sep 6 11:51:05 2018 -#> Date of summary: Thu Sep 6 11:51:05 2018 +#> Date of fit: Thu Sep 6 13:35:34 2018 +#> Date of summary: Thu Sep 6 13:35:34 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -177,7 +177,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.51 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 e99e7d9e..f9c6c117 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -433,15 +433,15 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.2 #> R version used for fitting: 3.5.1 -#> Date of fit: Thu Sep 6 11:51:08 2018 -#> Date of summary: Thu Sep 6 11:51:08 2018 +#> Date of fit: Thu Sep 6 13:35:36 2018 +#> Date of summary: Thu Sep 6 13:35:36 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 0.142 s +#> Fitted with method Port using 64 model solutions performed in 0.144 s #> #> Weighting: none #> @@ -510,7 +510,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> User System verstrichen -#> 0.895 0.000 0.898 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.919 0.000 0.920 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5e2e5449..59b67a5d 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -326,12 +326,12 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.002 0.000 0.001 </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 -#> 0.035 0.000 0.034 </div></pre> +#> 0.037 0.000 0.038 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 7fb56bd3..7b7b0a31 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,15 +206,15 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.47.2 #> R version used for fitting: 3.5.1 -#> Date of fit: Thu Sep 6 11:51:18 2018 -#> Date of summary: Thu Sep 6 11:51:18 2018 +#> Date of fit: Thu Sep 6 13:35:46 2018 +#> Date of summary: Thu Sep 6 13:35:46 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 0.078 s +#> Fitted with method Port using 35 model solutions performed in 0.075 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index bd8b5165..1b94d319 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.47.2 #> R version used for fitting: 3.5.1 -#> Date of fit: Thu Sep 6 11:51:19 2018 -#> Date of summary: Thu Sep 6 11:51:19 2018 +#> Date of fit: Thu Sep 6 13:35:48 2018 +#> Date of summary: Thu Sep 6 13:35:48 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 0.612 s +#> Fitted with method Port using 153 model solutions performed in 0.619 s #> #> Weighting: none #> |