diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-21 18:16:52 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-21 18:16:52 +0100 |
| commit | 6ea7bc3614b9a303f7c38dd63b9f80b8d0ebd95e (patch) | |
| tree | c8d79386f9f01c8ddfe218435860d997ba6af01a | |
| parent | b88bc151196d66d876fbc11059fc8cd365ef5534 (diff) | |
Static documentation rebuilt by pkgdown
| -rw-r--r-- | docs/articles/FOCUS_D.html | 2 | ||||
| -rw-r--r-- | docs/articles/FOCUS_L.html | 56 | ||||
| -rw-r--r-- | docs/articles/FOCUS_Z.html | 2 | ||||
| -rw-r--r-- | docs/articles/compiled_models.html | 14 | ||||
| -rw-r--r-- | docs/articles/mkin.html | 2 | ||||
| -rw-r--r-- | docs/articles/twa.html | 2 | ||||
| -rw-r--r-- | docs/news/index.html | 6 | ||||
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 14 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 8 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 10 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 4 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 8 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 8 |
14 files changed, 71 insertions, 69 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index a8002acd..a83c2f44 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -80,7 +80,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-11</h4> + <h4 class="date">2018-03-21</h4> </div> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index a23876ec..08e144bd 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -80,7 +80,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-11</h4> + <h4 class="date">2018-03-21</h4> </div> @@ -102,16 +102,16 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.3 -## Date of fit: Sun Mar 11 22:11:58 2018 -## Date of summary: Sun Mar 11 22:11:58 2018 +## R version: 3.4.4 +## Date of fit: Wed Mar 21 18:16:03 2018 +## Date of summary: Wed Mar 21 18:16:03 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 0.235 s +## Fitted with method Port using 37 model solutions performed in 0.257 s ## ## Weighting: none ## @@ -193,16 +193,16 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.3 -## Date of fit: Sun Mar 11 22:12:01 2018 -## Date of summary: Sun Mar 11 22:12:01 2018 +## R version: 3.4.4 +## Date of fit: Wed Mar 21 18:16:05 2018 +## Date of summary: Wed Mar 21 18:16:05 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 1.458 s +## Fitted with method Port using 611 model solutions performed in 1.404 s ## ## Weighting: none ## @@ -288,16 +288,16 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.3 -## Date of fit: Sun Mar 11 22:12:01 2018 -## Date of summary: Sun Mar 11 22:12:01 2018 +## R version: 3.4.4 +## Date of fit: Wed Mar 21 18:16:06 2018 +## Date of summary: Wed Mar 21 18:16:06 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 0.158 s +## Fitted with method Port using 81 model solutions performed in 0.168 s ## ## Weighting: none ## @@ -359,9 +359,9 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.3 -## Date of fit: Sun Mar 11 22:12:02 2018 -## Date of summary: Sun Mar 11 22:12:02 2018 +## R version: 3.4.4 +## Date of fit: Wed Mar 21 18:16:06 2018 +## Date of summary: Wed Mar 21 18:16:06 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -370,7 +370,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.681 s +## Fitted with method Port using 336 model solutions performed in 0.719 s ## ## Weighting: none ## @@ -451,9 +451,9 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div> <pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.3 -## Date of fit: Sun Mar 11 22:12:03 2018 -## Date of summary: Sun Mar 11 22:12:03 2018 +## R version: 3.4.4 +## Date of fit: Wed Mar 21 18:16:07 2018 +## Date of summary: Wed Mar 21 18:16:07 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -462,7 +462,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.272 s +## Fitted with method Port using 137 model solutions performed in 0.283 s ## ## Weighting: none ## @@ -552,9 +552,9 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><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>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.3 -## Date of fit: Sun Mar 11 22:12:04 2018 -## Date of summary: Sun Mar 11 22:12:04 2018 +## R version: 3.4.4 +## Date of fit: Wed Mar 21 18:16:08 2018 +## Date of summary: Wed Mar 21 18:16:08 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -612,16 +612,16 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## parent 106 352</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><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>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.3 -## Date of fit: Sun Mar 11 22:12:04 2018 -## Date of summary: Sun Mar 11 22:12:04 2018 +## R version: 3.4.4 +## Date of fit: Wed Mar 21 18:16:08 2018 +## Date of summary: Wed Mar 21 18:16:08 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 0.13 s +## Fitted with method Port using 66 model solutions performed in 0.138 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html index 78a00062..a2b88caa 100644 --- a/docs/articles/FOCUS_Z.html +++ b/docs/articles/FOCUS_Z.html @@ -80,7 +80,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-11</h4> + <h4 class="date">2018-03-21</h4> </div> diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 8923acac..19cb806b 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -80,7 +80,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-11</h4> + <h4 class="date">2018-03-21</h4> </div> @@ -118,9 +118,9 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki }</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 1.978 1.000 1.976 0 -## 1 deSolve, not compiled 3 13.541 6.846 13.531 0 -## 2 Eigenvalue based 3 2.332 1.179 2.330 0 +## 3 deSolve, compiled 3 2.155 1.000 2.152 0 +## 1 deSolve, not compiled 3 15.124 7.018 15.109 0 +## 2 Eigenvalue based 3 2.576 1.195 2.574 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -149,14 +149,14 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki }</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 3.334 1.000 3.331 0 -## 1 deSolve, not compiled 3 29.917 8.973 29.888 0 +## 2 deSolve, compiled 3 3.419 1.000 3.415 0 +## 1 deSolve, not compiled 3 31.159 9.113 31.130 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> <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 0.9.46.3 on</p> -<pre><code>## R version 3.4.3 (2017-11-30) +<pre><code>## R version 3.4.4 (2018-03-15) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 9 (stretch)</code></pre> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 7b26b3f1..12ff2e98 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -80,7 +80,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-11</h4> + <h4 class="date">2018-03-21</h4> </div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 7f4c941e..551cf03f 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -80,7 +80,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-11</h4> + <h4 class="date">2018-03-21</h4> </div> diff --git a/docs/news/index.html b/docs/news/index.html index f311efe5..c4605ae1 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -107,9 +107,9 @@ </div> <div class="contents"> - <div id="mkin-0-9-47-1-2017-02-06" class="section level1"> + <div id="mkin-0-9-47-1-2018-02-06" class="section level1"> <h1 class="hasAnchor"> -<a href="#mkin-0-9-47-1-2017-02-06" class="anchor"></a>mkin 0.9.47.1 (2017-02-06)</h1> +<a href="#mkin-0-9-47-1-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)</h1> <ul> <li><p>Skip some test on CRAN and winbuilder to avoid timeouts</p></li> <li><p>‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014</p></li> @@ -594,7 +594,7 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-47-1-2017-02-06">0.9.47.1</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> <li><a href="#mkin-0-9-46-1-2017-09-14">0.9.46.1</a></li> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index e554432f..2a3b1c78 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -263,7 +263,7 @@ #> #> $time #> user system elapsed -#> 0.234 0.000 0.234 +#> 0.242 0.000 0.244 #> #> $mkinmod #> <mkinmod> model generated with @@ -452,8 +452,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5555578e66e0> -#> <environment: 0x555559cd9780> +#> <bytecode: 0x5555578ff9d0> +#> <environment: 0x555559a0da40> #> #> $cost_notrans #> function (P) @@ -475,8 +475,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555acf3f50> -#> <environment: 0x555559cd9780> +#> <bytecode: 0x555559b90d60> +#> <environment: 0x555559a0da40> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -543,13 +543,13 @@ #> 99.17407 #> #> $date -#> [1] "Sun Mar 11 22:10:21 2018" +#> [1] "Wed Mar 21 18:14:20 2018" #> #> $version #> [1] "0.9.47.1" #> #> $Rversion -#> [1] "3.4.3" +#> [1] "3.4.4" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 80cac442..cb70e68c 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -150,9 +150,9 @@ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <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: 0.9.47.1 -#> R version used for fitting: 3.4.3 -#> Date of fit: Sun Mar 11 22:10:30 2018 -#> Date of summary: Sun Mar 11 22:10:30 2018 +#> R version used for fitting: 3.4.4 +#> Date of fit: Wed Mar 21 18:14:30 2018 +#> Date of summary: Wed Mar 21 18:14:30 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -162,7 +162,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.318 s +#> Fitted with method Port using 246 model solutions performed in 1.403 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 991df1cc..8ac8295f 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -413,16 +413,16 @@ <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <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: 0.9.47.1 -#> R version used for fitting: 3.4.3 -#> Date of fit: Sun Mar 11 22:10:32 2018 -#> Date of summary: Sun Mar 11 22:10:32 2018 +#> R version used for fitting: 3.4.4 +#> Date of fit: Wed Mar 21 18:14:33 2018 +#> Date of summary: Wed Mar 21 18:14:33 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 0.135 s +#> Fitted with method Port using 64 model solutions performed in 0.14 s #> #> Weighting: none #> @@ -491,7 +491,7 @@ <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 elapsed -#> 0.829 0.000 0.829 </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 +#> 0.834 0.000 0.835 </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 044b2d92..4768215b 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -306,7 +306,7 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.002 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.003 0.000 0.003 </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 @@ -316,7 +316,7 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.029 0.000 0.029 </div></pre> +#> 0.033 0.000 0.032 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 65c37898..6c99f07b 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -134,7 +134,9 @@ <tr> <th>cores</th> <td><p>The number of cores to be used for multicore processing. This is only - used when the <code>cluster</code> argument is <code>NULL</code>.</p></td> + used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines, + cores > 1 is not supported, you need to use the <code>cluster</code> argument + to use multiple logical processors.</p></td> </tr> <tr> <th>cluster</th> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index e462fd17..37b8fff8 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -190,16 +190,16 @@ <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: 0.9.47.1 -#> R version used for fitting: 3.4.3 -#> Date of fit: Sun Mar 11 22:10:41 2018 -#> Date of summary: Sun Mar 11 22:10:41 2018 +#> R version used for fitting: 3.4.4 +#> Date of fit: Wed Mar 21 18:14:42 2018 +#> Date of summary: Wed Mar 21 18:14:42 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 0.07 s +#> Fitted with method Port using 35 model solutions performed in 0.072 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 5c89f8e2..fb03cdac 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -184,9 +184,9 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>m1</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'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <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: 0.9.47.1 -#> R version used for fitting: 3.4.3 -#> Date of fit: Sun Mar 11 22:10:42 2018 -#> Date of summary: Sun Mar 11 22:10:42 2018 +#> R version used for fitting: 3.4.4 +#> Date of fit: Wed Mar 21 18:14:43 2018 +#> Date of summary: Wed Mar 21 18:14:43 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -194,7 +194,7 @@ 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 0.564 s +#> Fitted with method Port using 153 model solutions performed in 0.585 s #> #> Weighting: none #> |