diff options
| -rw-r--r-- | docs/articles/FOCUS_D.html | 6 | ||||
| -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/logistic.solution.html | 50 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 42 | ||||
| -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/logistic.solution.Rd | 2 |
13 files changed, 85 insertions, 131 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 6a8500a0..4a080ac1 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -163,8 +163,8 @@ <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Feb 21 14:32:03 2019 -## Date of summary: Thu Feb 21 14:32:04 2019 +## Date of fit: Thu Feb 21 14:58:25 2019 +## Date of summary: Thu Feb 21 14:58:26 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -172,7 +172,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.735 s +## Fitted with method Port using 153 model solutions performed in 0.705 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 265dd96c..b9f72dbe 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -111,15 +111,15 @@ <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.2 -## Date of fit: Thu Feb 21 14:32:06 2019 -## Date of summary: Thu Feb 21 14:32:06 2019 +## Date of fit: Thu Feb 21 14:58:27 2019 +## Date of summary: Thu Feb 21 14:58:27 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.097 s +## Fitted with method Port using 37 model solutions performed in 0.096 s ## ## Weighting: none ## @@ -202,15 +202,15 @@ <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 3.5.2 -## Date of fit: Thu Feb 21 14:32:08 2019 -## Date of summary: Thu Feb 21 14:32:08 2019 +## Date of fit: Thu Feb 21 14:58:29 2019 +## Date of summary: Thu Feb 21 14:58:29 2019 ## ## 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 1.547 s +## Fitted with method Port using 611 model solutions performed in 1.507 s ## ## Weighting: none ## @@ -297,15 +297,15 @@ <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 3.5.2 -## Date of fit: Thu Feb 21 14:32:08 2019 -## Date of summary: Thu Feb 21 14:32:08 2019 +## Date of fit: Thu Feb 21 14:58:30 2019 +## Date of summary: Thu Feb 21 14:58:30 2019 ## ## 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 0.201 s +## Fitted with method Port using 81 model solutions performed in 0.197 s ## ## Weighting: none ## @@ -368,8 +368,8 @@ <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 3.5.2 -## Date of fit: Thu Feb 21 14:32:09 2019 -## Date of summary: Thu Feb 21 14:32:09 2019 +## Date of fit: Thu Feb 21 14:58:31 2019 +## Date of summary: Thu Feb 21 14:58:31 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -378,7 +378,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.86 s +## Fitted with method Port using 336 model solutions performed in 0.842 s ## ## Weighting: none ## @@ -460,8 +460,8 @@ <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 3.5.2 -## Date of fit: Thu Feb 21 14:32:10 2019 -## Date of summary: Thu Feb 21 14:32:11 2019 +## Date of fit: Thu Feb 21 14:58:32 2019 +## Date of summary: Thu Feb 21 14:58:32 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -470,7 +470,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.351 s +## Fitted with method Port using 137 model solutions performed in 0.346 s ## ## Weighting: none ## @@ -561,15 +561,15 @@ <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 3.5.2 -## Date of fit: Thu Feb 21 14:32:11 2019 -## Date of summary: Thu Feb 21 14:32:11 2019 +## Date of fit: Thu Feb 21 14:58:32 2019 +## Date of summary: Thu Feb 21 14:58:33 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.113 s +## Fitted with method Port using 46 model solutions performed in 0.111 s ## ## Weighting: none ## @@ -621,15 +621,15 @@ <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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 3.5.2 -## Date of fit: Thu Feb 21 14:32:11 2019 -## Date of summary: Thu Feb 21 14:32:11 2019 +## Date of fit: Thu Feb 21 14:58:33 2019 +## Date of summary: Thu Feb 21 14:58:33 2019 ## ## 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 0.165 s ## ## Weighting: none ## diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 3a37d114..e1149c67 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -126,14 +126,14 @@ <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 2.429 1.000 2.427 0 -## 1 deSolve, not compiled 3 17.826 7.339 17.815 0 -## 2 Eigenvalue based 3 2.968 1.222 2.967 0 +## 3 deSolve, compiled 3 2.329 1.000 2.327 0 +## 1 deSolve, not compiled 3 17.556 7.538 17.549 0 +## 2 Eigenvalue based 3 2.863 1.229 2.860 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 ## 2 0 0</code></pre> -<p>We see that using the compiled model is by a factor of around 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> +<p>We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> @@ -157,8 +157,8 @@ <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 4.234 1.000 4.232 0 -## 1 deSolve, not compiled 3 37.807 8.929 37.785 0 +## 2 deSolve, compiled 3 4.105 1.000 4.101 0 +## 1 deSolve, not compiled 3 37.400 9.111 37.381 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index dd088a0f..fe6fc125 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -280,7 +280,7 @@ #> #> $time #> User System verstrichen -#> 0.196 0.000 0.196 +#> 0.199 0.000 0.200 #> #> $mkinmod #> <mkinmod> model generated with @@ -469,8 +469,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x555559201470> -#> <environment: 0x555555ce4640> +#> <bytecode: 0x555559227548> +#> <environment: 0x555556ee4048> #> #> $cost_notrans #> function (P) @@ -492,8 +492,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555a3214d8> -#> <environment: 0x555555ce4640> +#> <bytecode: 0x55555a34ddf0> +#> <environment: 0x555556ee4048> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -560,7 +560,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Feb 21 14:30:10 2019" +#> [1] "Thu Feb 21 14:56:32 2019" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index b0ab72d7..310f1c5a 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -202,54 +202,8 @@ <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>), <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]] - <span class='no'>m</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>)</div><div class='output co'>#> Model cost at call 1 : 789.6044 -#> Model cost at call 2 : 789.6043 -#> Model cost at call 7 : 716.9934 -#> Model cost at call 12 : 697.1186 -#> Model cost at call 15 : 697.1185 -#> Model cost at call 16 : 697.1184 -#> Model cost at call 17 : 661.1574 -#> Model cost at call 20 : 661.1573 -#> Model cost at call 22 : 620.0542 -#> Model cost at call 25 : 620.0541 -#> Model cost at call 29 : 616.6874 -#> Model cost at call 32 : 616.6874 -#> Model cost at call 33 : 616.6874 -#> Model cost at call 34 : 615.1671 -#> Model cost at call 37 : 615.1671 -#> Model cost at call 39 : 612.0795 -#> Model cost at call 42 : 612.0795 -#> Model cost at call 43 : 612.0795 -#> Model cost at call 44 : 605.9119 -#> Model cost at call 45 : 593.0433 -#> Model cost at call 46 : 548.0815 -#> Model cost at call 47 : 504.9062 -#> Model cost at call 50 : 504.9061 -#> Model cost at call 51 : 504.9061 -#> Model cost at call 53 : 485.929 -#> Model cost at call 55 : 485.929 -#> Model cost at call 56 : 485.929 -#> Model cost at call 58 : 485.241 -#> Model cost at call 60 : 485.241 -#> Model cost at call 61 : 485.2409 -#> Model cost at call 62 : 485.2409 -#> Model cost at call 63 : 484.0717 -#> Model cost at call 69 : 483.9062 -#> Model cost at call 74 : 483.5646 -#> Model cost at call 79 : 483.4908 -#> Model cost at call 84 : 483.4859 -#> Model cost at call 85 : 483.4859 -#> Model cost at call 89 : 483.4848 -#> Model cost at call 90 : 483.4836 -#> Model cost at call 92 : 483.4836 -#> Model cost at call 94 : 483.4836 -#> Model cost at call 97 : 483.4833 -#> Model cost at call 100 : 483.4833 -#> Model cost at call 105 : 483.4832 -#> Model cost at call 108 : 483.4832 -#> Model cost at call 114 : 483.4832 -#> Model cost at call 128 : 483.4832 -#> Optimisation by method Port successfully terminated.</div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower + <span class='no'>m</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower #> parent_0 1.057896e+02 2.3743105248 44.5559374 6.656664e-16 1.006602e+02 #> kmax 6.398190e-02 0.0193490291 3.3067243 2.836921e-03 3.329058e-02 #> k0 1.612775e-04 0.0009640761 0.1672871 4.348592e-01 3.972250e-10 diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index dcfc499f..bed8ed8e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -160,8 +160,8 @@ <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:31 2019 -#> Date of summary: Thu Feb 21 14:30:31 2019 +#> Date of fit: Thu Feb 21 14:56:53 2019 +#> Date of summary: Thu Feb 21 14:56:53 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -171,7 +171,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.822 s +#> Fitted with method Port using 574 model solutions performed in 3.873 s #> #> Weighting: none #> @@ -249,8 +249,8 @@ <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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:32 2019 -#> Date of summary: Thu Feb 21 14:30:32 2019 +#> Date of fit: Thu Feb 21 14:56:55 2019 +#> Date of summary: Thu Feb 21 14:56:55 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -260,7 +260,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.601 s +#> Fitted with method Port using 246 model solutions performed in 1.633 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index d09b9232..4f071574 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -438,8 +438,8 @@ <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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:35 2019 -#> Date of summary: Thu Feb 21 14:30:35 2019 +#> Date of fit: Thu Feb 21 14:56:58 2019 +#> Date of summary: Thu Feb 21 14:56:58 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -515,7 +515,7 @@ <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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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 -#> 1.017 0.004 1.022 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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 +#> 1.036 0.000 1.036 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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 @@ -590,7 +590,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.845 0.000 0.846 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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 +#> 0.830 0.000 0.832 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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 @@ -628,8 +628,8 @@ <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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:47 2019 -#> Date of summary: Thu Feb 21 14:30:47 2019 +#> Date of fit: Thu Feb 21 14:57:10 2019 +#> Date of summary: Thu Feb 21 14:57:10 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -745,8 +745,8 @@ #> 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:50 2019 -#> Date of summary: Thu Feb 21 14:30:50 2019 +#> Date of fit: Thu Feb 21 14:57:13 2019 +#> Date of summary: Thu Feb 21 14:57:13 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -754,7 +754,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.529 s +#> Fitted with method Port using 551 model solutions performed in 2.543 s #> #> Weighting: none #> @@ -867,8 +867,8 @@ #> 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:51 2019 -#> Date of summary: Thu Feb 21 14:30:51 2019 +#> Date of fit: Thu Feb 21 14:57:14 2019 +#> Date of summary: Thu Feb 21 14:57:14 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -876,7 +876,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.707 s +#> Fitted with method Port using 155 model solutions performed in 0.718 s #> #> Weighting: mean #> @@ -985,8 +985,8 @@ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:52 2019 -#> Date of summary: Thu Feb 21 14:30:52 2019 +#> Date of fit: Thu Feb 21 14:57:15 2019 +#> Date of summary: Thu Feb 21 14:57:15 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -994,7 +994,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.792 s +#> Fitted with method Port using 174 model solutions performed in 0.8 s #> #> Weighting: manual #> @@ -1105,8 +1105,8 @@ <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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:53 2019 -#> Date of summary: Thu Feb 21 14:30:53 2019 +#> Date of fit: Thu Feb 21 14:57:16 2019 +#> Date of summary: Thu Feb 21 14:57:16 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1114,7 +1114,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.243 s +#> Fitted with method Port using 270 model solutions performed in 1.248 s #> #> Weighting: manual #> @@ -1223,8 +1223,8 @@ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:57 2019 -#> Date of summary: Thu Feb 21 14:30:57 2019 +#> Date of fit: Thu Feb 21 14:57:19 2019 +#> Date of summary: Thu Feb 21 14:57:19 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1232,7 +1232,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.27 s +#> Fitted with method Port using 692 model solutions performed in 3.287 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 0710e6de..17d8400d 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -231,7 +231,7 @@ 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 file33652d0fd552.c 2> file33652d0fd552.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file522976635fac.c 2> file522976635fac.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 8c5bf22b..414d97a8 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -330,12 +330,12 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( +#> 0.001 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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 -#> 0.047 0.000 0.047 </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 75da28c7..7352fb74 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -191,8 +191,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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 -#> 0.039 0.040 7.082 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 22.650 0.004 22.666 </div><div class='input'> +#> 0.044 0.036 7.245 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 22.796 0.004 22.814 </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 242d9f63..53b94948 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -208,8 +208,8 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:31:48 2019 -#> Date of summary: Thu Feb 21 14:31:48 2019 +#> Date of fit: Thu Feb 21 14:58:11 2019 +#> Date of summary: Thu Feb 21 14:58:11 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 939fa7b4..3dbacbe8 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -202,8 +202,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:31:57 2019 -#> Date of summary: Thu Feb 21 14:31:57 2019 +#> Date of fit: Thu Feb 21 14:58:19 2019 +#> Date of summary: Thu Feb 21 14:58:19 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -211,7 +211,7 @@ 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 0.849 s +#> Fitted with method Port using 153 model solutions performed in 0.765 s #> #> Weighting: none #> @@ -278,8 +278,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:31:59 2019 -#> Date of summary: Thu Feb 21 14:31:59 2019 +#> Date of fit: Thu Feb 21 14:58:21 2019 +#> Date of summary: Thu Feb 21 14:58:21 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -287,7 +287,7 @@ 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 1.649 s +#> Fitted with method Port using 350 model solutions performed in 1.58 s #> #> Weighting: none #> @@ -366,8 +366,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:32:00 2019 -#> Date of summary: Thu Feb 21 14:32:00 2019 +#> Date of fit: Thu Feb 21 14:58:22 2019 +#> Date of summary: Thu Feb 21 14:58:22 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -375,7 +375,7 @@ 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 0.976 s +#> Fitted with method Port using 186 model solutions performed in 0.872 s #> #> Weighting: none #> @@ -450,8 +450,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 3.5.2 -#> Date of fit: Thu Feb 21 14:32:01 2019 -#> Date of summary: Thu Feb 21 14:32:01 2019 +#> Date of fit: Thu Feb 21 14:58:23 2019 +#> Date of summary: Thu Feb 21 14:58:23 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -459,7 +459,7 @@ 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 0.512 s +#> Fitted with method Port using 104 model solutions performed in 0.473 s #> #> Weighting: none #> diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd index 798e78d1..396e09ef 100644 --- a/man/logistic.solution.Rd +++ b/man/logistic.solution.Rd @@ -61,7 +61,7 @@ logistic.solution(t, parent.0, kmax, k0, r) sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07), n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]] - m <- mkinfit("logistic", d_2_1) + m <- mkinfit("logistic", d_2_1, quiet = TRUE) plot_sep(m) summary(m)$bpar } |