diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-11-01 14:16:21 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-11-01 14:16:21 +0100 |
| commit | 630e657f1794ea441afc9ff10663309fec5e847e (patch) | |
| tree | 6f09ad8413f0a8c23f0b21e5067b4fccb183056e | |
| parent | a787e5266628f859fd70454c5419721efa494887 (diff) | |
Update online docs
30 files changed, 275 insertions, 176 deletions
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 551e9c98..45ba1c77 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index e5bc5a21..2aa2f45a 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -63,12 +63,15 @@ <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -106,7 +109,7 @@ <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-09-16)</h4> + <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-01)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -340,6 +343,14 @@ <td align="right">1.957</td> <td align="right">3.633</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">2.020</td> +<td align="right">3.608</td> +</tr> </tbody> </table> </div> @@ -511,6 +522,15 @@ <td align="right">6.147</td> <td align="right">2.803</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">1.579</td> +<td align="right">5.973</td> +<td align="right">2.839</td> +</tr> </tbody> </table> </div> @@ -736,6 +756,18 @@ <td align="right">1.961</td> <td align="right">2.852</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.920</td> +<td align="right">1.295</td> +<td align="right">1.518</td> +<td align="right">3.060</td> +<td align="right">1.895</td> +<td align="right">2.740</td> +</tr> </tbody> </table> </div> diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index 49a579fc..ade86bc5 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -20,6 +20,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -32,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -42,7 +44,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -58,12 +60,18 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -80,7 +88,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> @@ -95,108 +103,108 @@ - </header><script src="compiled_models_files/header-attrs-2.6/header-attrs.js"></script><script src="compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><script src="compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> - <h4 class="author">Johannes Ranke</h4> + <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 class="date">2021-02-15</h4> + <h4 data-toc-skip class="date">2022-11-01</h4> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> </div> -<div id="how-to-benefit-from-compiled-models" class="section level2"> -<h2 class="hasAnchor"> -<a href="#how-to-benefit-from-compiled-models" class="anchor"></a>How to benefit from compiled models</h2> +<div class="section level2"> +<h2 id="how-to-benefit-from-compiled-models">How to benefit from compiled models<a class="anchor" aria-label="anchor" href="#how-to-benefit-from-compiled-models"></a> +</h2> <p>When using an mkin version equal to or greater than 0.9-36 and a C compiler is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. Starting from version 0.9.49.9, the <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of a compiler using</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/pkgbuild/man/has_compiler.html">has_compiler</a></span><span class="op">(</span><span class="op">)</span></code></pre></div> -<p>In previous versions, it used <code><a href="https://rdrr.io/r/base/Sys.which.html">Sys.which("gcc")</a></code> for this check.</p> +<code class="sourceCode R"><span><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/pkgbuild/man/has_compiler.html" class="external-link">has_compiler</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<p>In previous versions, it used <code>Sys.which("gcc")</code> for this check.</p> <p>On Linux, you need to have the essential build tools like make and gcc or clang installed. On Debian based linux distributions, these will be pulled in by installing the build-essential package.</p> <p>On MacOS, which I do not use personally, I have had reports that a compiler is available by default.</p> <p>On Windows, you need to install Rtools and have the path to its bin directory in your PATH variable. You do not need to modify the PATH variable when installing Rtools. Instead, I would recommend to put the line</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html">Sys.setenv</a></span><span class="op">(</span>PATH <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste</a></span><span class="op">(</span><span class="st">"C:/Rtools/bin"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv</a></span><span class="op">(</span><span class="st">"PATH"</span><span class="op">)</span>, sep<span class="op">=</span><span class="st">";"</span><span class="op">)</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html" class="external-link">Sys.setenv</a></span><span class="op">(</span>PATH <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"C:/Rtools/bin"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"PATH"</span><span class="op">)</span>, sep<span class="op">=</span><span class="st">";"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p>into your .Rprofile startup file. This is just a text file with some R code that is executed when your R session starts. It has to be named .Rprofile and has to be located in your home directory, which will generally be your Documents folder. You can check the location of the home directory used by R by issuing</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv</a></span><span class="op">(</span><span class="st">"HOME"</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"HOME"</span><span class="op">)</span></span></code></pre></div> </div> -<div id="comparison-with-other-solution-methods" class="section level2"> -<h2 class="hasAnchor"> -<a href="#comparison-with-other-solution-methods" class="anchor"></a>Comparison with other solution methods</h2> +<div class="section level2"> +<h2 id="comparison-with-other-solution-methods">Comparison with other solution methods<a class="anchor" aria-label="anchor" href="#comparison-with-other-solution-methods"></a> +</h2> <p>First, we build a simple degradation model for a parent compound with one metabolite, and we remove zero values from the dataset.</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> -<span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span> - parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, - m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> +<span> m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package. In the output of below code, the warnings about zero being removed from the FOCUS D dataset are suppressed. Since mkin version 0.9.49.11, an analytical solution is also implemented, which is included in the tests below.</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> - <span class="va">b.1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span><span class="op">(</span> - <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, - solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, - use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, - <span class="st">"Eigenvalue based"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, - solution_type <span class="op">=</span> <span class="st">"eigen"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, - <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, - solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, - <span class="st">"analytical"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, - solution_type <span class="op">=</span> <span class="st">"analytical"</span>, - use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, - replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, - columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span><span class="op">)</span> - <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">b.1</span><span class="op">)</span> -<span class="op">}</span> <span class="kw">else</span> <span class="op">{</span> - <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span> -<span class="op">}</span></code></pre></div> -<pre><code>## test replications relative elapsed -## 4 analytical 1 1.000 0.182 -## 3 deSolve, compiled 1 1.824 0.332 -## 2 Eigenvalue based 1 2.082 0.379 -## 1 deSolve, not compiled 1 46.181 8.405</code></pre> +<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">b.1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span> +<span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="st">"Eigenvalue based"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"eigen"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="st">"analytical"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>,</span> +<span> columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span><span class="op">)</span></span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">b.1</span><span class="op">)</span></span> +<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> +<span><span class="op">}</span></span></code></pre></div> +<pre><code><span><span class="co">## test replications relative elapsed</span></span> +<span><span class="co">## 4 analytical 1 1.000 0.186</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.656 0.308</span></span> +<span><span class="co">## 2 Eigenvalue based 1 2.102 0.391</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 38.968 7.248</span></span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> -<div id="model-without-analytical-solution" class="section level2"> -<h2 class="hasAnchor"> -<a href="#model-without-analytical-solution" class="anchor"></a>Model without analytical solution</h2> +<div class="section level2"> +<h2 id="model-without-analytical-solution">Model without analytical solution<a class="anchor" aria-label="anchor" href="#model-without-analytical-solution"></a> +</h2> <p>This evaluation is also taken from the example section of mkinfit. No analytical solution is available for this system, and now Eigenvalue based solution is possible, so only deSolve using with or without compiled code is available.</p> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> - <span class="va">FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span> - parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>, - m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span> - - <span class="va">b.2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span><span class="op">(</span> - <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, - use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, - <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, - replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, - columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span><span class="op">)</span> - <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">)</span> - <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html">round</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">[</span><span class="st">"1"</span>, <span class="st">"relative"</span><span class="op">]</span><span class="op">)</span> -<span class="op">}</span> <span class="kw">else</span> <span class="op">{</span> - <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="cn">NA</span> - <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="st">"R package benchmark is not available"</span><span class="op">)</span> -<span class="op">}</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> -<pre><code>## test replications relative elapsed -## 2 deSolve, compiled 1 1.000 0.541 -## 1 deSolve, not compiled 1 29.091 15.738</code></pre> +<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> +<span> m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span> <span class="va">b.2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span> +<span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>,</span> +<span> columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span><span class="op">)</span></span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">)</span></span> +<span> <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">[</span><span class="st">"1"</span>, <span class="st">"relative"</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> +<span> <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="cn">NA</span></span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package benchmark is not available"</span><span class="op">)</span></span> +<span><span class="op">}</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> +<pre><code><span><span class="co">## test replications relative elapsed</span></span> +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.452</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 29.431 13.303</span></span></code></pre> <p>Here we get a performance benefit of a factor of 29 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.0.3.9000 on</p> -<pre><code>## R version 4.0.3 (2020-10-10) -## Platform: x86_64-pc-linux-gnu (64-bit) -## Running under: Debian GNU/Linux bullseye/sid</code></pre> -<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> +<p>This vignette was built with mkin 1.2.0 on</p> +<pre><code><span><span class="co">## R version 4.2.2 (2022-10-31)</span></span> +<span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> +<span><span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></span></code></pre> +<pre><code><span><span class="co">## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</span></span></code></pre> </div> </div> @@ -211,11 +219,13 @@ <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> @@ -224,5 +234,7 @@ + + </body> </html> diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html index 0c08905a..50a57d1b 100644 --- a/docs/dev/articles/web_only/multistart.html +++ b/docs/dev/articles/web_only/multistart.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -109,7 +109,7 @@ <h1 data-toc-skip>Short demo of the multistart method</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-10-28)</h4> + <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-11-01)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> <div class="hidden name"><code>multistart.rmd</code></div> @@ -144,23 +144,21 @@ <p>This confirms that the variance of k2 is the most problematic parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span> -<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## character(0)</span></span></code></pre> -<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span> +<span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> <span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span><span class="op">)</span></span></code></pre></div> <p><img src="multistart_files/figure-html/unnamed-chunk-4-1.png" width="700"></p> <p>The results confirm that all remaining parameters can be determined with sufficient certainty.</p> <p>We can also analyse the log-likelihoods obtained in the multiple runs:</p> -<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/llhist.html">llhist</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span></span></code></pre></div> <p><img src="multistart_files/figure-html/unnamed-chunk-5-1.png" width="700"></p> <p>The parameter histograms can be further improved by excluding the result with the low likelihood.</p> -<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, llmin <span class="op">=</span> <span class="op">-</span><span class="fl">326</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="multistart_files/figure-html/unnamed-chunk-6-1.png" width="700"></p> <p>We can use the <code>anova</code> method to compare the models, including a likelihood ratio test if the models are nested.</p> -<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_full</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span> <span><span class="co">## </span></span> diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 35ae54bd..bc48a6f1 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -112,13 +112,13 @@ <p>Ranke J (2022). <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>. -R package version 1.1.2, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. +R package version 1.2.0, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. </p> <pre>@Manual{, title = {mkin: Kinetic Evaluation of Chemical Degradation Data}, author = {Johannes Ranke}, year = {2022}, - note = {R package version 1.1.2}, + note = {R package version 1.2.0}, url = {https://pkgdown.jrwb.de/mkin/}, }</pre> diff --git a/docs/dev/index.html b/docs/dev/index.html index 5257b590..a64fb633 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -45,7 +45,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index b509aca3..1703be16 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -85,14 +85,15 @@ </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.1.2" id="mkin-112">mkin 1.1.2<a class="anchor" aria-label="anchor" href="#mkin-112"></a></h2> -<ul><li><p>‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with diagnostic plotting functions ‘llhist’ and ‘parplot’.</p></li> -<li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li> -<li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li> -<li><p>‘R/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.</p></li> -<li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’ and ‘mhmkin’ objects.</p></li> +<h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-unreleased">mkin 1.2.0 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-120-unreleased"></a></h2> +<ul><li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li> +<li><p>‘R/mhmkin.R’: ‘anova.mhmkin’ for conveniently comparing the resulting fits.</p></li> <li><p>‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.</p></li> +<li><p>‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with function ‘llhist’ and new generic ‘parplot’ for diagnostics, and new generics ‘which.best’ and ‘best’ for extracting the fit with the highest likelihood</p></li> +<li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li> +<li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li> <li><p>‘R/summary.mmkin.R’: Summary method for mmkin objects.</p></li> +<li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li> </ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.1.1" id="mkin-111-2022-07-12">mkin 1.1.1 (2022-07-12)<a class="anchor" aria-label="anchor" href="#mkin-111-2022-07-12"></a></h2> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 12a9b003..aeea435d 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -12,7 +12,7 @@ articles: compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html -last_built: 2022-10-28T21:37Z +last_built: 2022-11-01T13:09Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 6841f086..17a35806 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 11f6a1cd..f06a860e 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/anova.saem.mmkin.html b/docs/dev/reference/anova.saem.mmkin.html index abe77c65..2c109cc2 100644 --- a/docs/dev/reference/anova.saem.mmkin.html +++ b/docs/dev/reference/anova.saem.mmkin.html @@ -1,6 +1,8 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Anova method for saem.mmkin objects — anova.saem.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Anova method for saem.mmkin objects — anova.saem.mmkin"><meta property="og:description" content="Generate an anova object. The method to calculate the BIC is that from -the saemix package. As in other prominent anova methods, models are sorted"><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Anova method for saem.mmkin objects — anova.saem.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Anova method for saem.mmkin objects — anova.saem.mmkin"><meta property="og:description" content="Generate an anova object. The method to calculate the BIC is that from the +saemix package. As in other prominent anova methods, models are sorted by +number of parameters, and the tests (if requested) are always relative to +the model on the previous line."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -18,7 +20,7 @@ the saemix package. As in other prominent anova methods, models are sorted"><met </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -87,8 +89,10 @@ the saemix package. As in other prominent anova methods, models are sorted"><met </div> <div class="ref-description"> - <p>Generate an anova object. The method to calculate the BIC is that from -the saemix package. As in other prominent anova methods, models are sorted</p> + <p>Generate an anova object. The method to calculate the BIC is that from the +saemix package. As in other prominent anova methods, models are sorted by +number of parameters, and the tests (if requested) are always relative to +the model on the previous line.</p> </div> <div id="ref-usage"> diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index 57dfa06c..e552cc62 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -46,12 +46,15 @@ by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- math <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> diff --git a/docs/dev/reference/illparms.html b/docs/dev/reference/illparms.html index 184299ed..c0de4115 100644 --- a/docs/dev/reference/illparms.html +++ b/docs/dev/reference/illparms.html @@ -21,7 +21,7 @@ without parameter transformations is used."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -48,12 +48,15 @@ without parameter transformations is used."><meta name="robots" content="noindex <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -100,6 +103,9 @@ without parameter transformations is used.</p> <span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> +<span><span class="co"># S3 method for illparms.mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> <span><span class="co"># S3 method for mmkin</span></span> <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> @@ -109,6 +115,9 @@ without parameter transformations is used.</p> <span><span class="co"># S3 method for saem.mmkin</span></span> <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> +<span><span class="co"># S3 method for illparms.saem.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> <span><span class="co"># S3 method for mhmkin</span></span> <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> @@ -149,8 +158,7 @@ tested?</p></dd> <p>For <a href="mkinfit.html">mkinfit</a> or <a href="saem.html">saem</a> objects, a character vector of parameter names. For <a href="mmkin.html">mmkin</a> or <a href="mhmkin.html">mhmkin</a> objects, a matrix like object of class -'illparms.mmkin' or 'illparms.mhmkin'. The latter objects have a suitable -printing method.</p> +'illparms.mmkin' or 'illparms.mhmkin'.</p> </div> <div id="details"> <h2>Details</h2> @@ -161,6 +169,11 @@ effects expressed as standard deviations include zero, and if the confidence intervals for the error model parameters include zero.</p> </div> + <div id="note"> + <h2>Note</h2> + <p>All return objects have printing methods. For the single fits, printing +does not output anything in the case no ill-defined parameters are found.</p> + </div> <div id="ref-examples"> <h2>Examples</h2> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 0fac6842..0b127b57 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -118,7 +118,7 @@ degradation models and one or more error models</p></td> </td> <td><p>Method to get status information for fit array objects</p></td> </tr><tr><td> - <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> </p> + <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mkinfit></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.saem.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> </p> </td> <td><p>Method to get the names of ill-defined parameters</p></td> </tr><tr><td> diff --git a/docs/dev/reference/llhist.html b/docs/dev/reference/llhist.html index e110416e..314cb923 100644 --- a/docs/dev/reference/llhist.html +++ b/docs/dev/reference/llhist.html @@ -18,7 +18,7 @@ original fit is shown as a red vertical line."><meta name="robots" content="noin </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html index 99b3b906..b1ea22ef 100644 --- a/docs/dev/reference/logLik.saem.mmkin.html +++ b/docs/dev/reference/logLik.saem.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> diff --git a/docs/dev/reference/mhmkin.html b/docs/dev/reference/mhmkin.html index e77aace3..cbfeae60 100644 --- a/docs/dev/reference/mhmkin.html +++ b/docs/dev/reference/mhmkin.html @@ -22,7 +22,7 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -49,12 +49,15 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -98,6 +101,9 @@ mixed-effects model fitting functions.</p> <div id="ref-usage"> <div class="sourceCode"><pre><code>mhmkin(objects, backend = "saemix", algorithm = "saem", ...) +# S3 method for mmkin +mhmkin(objects, ...) + # S3 method for list mhmkin( objects, @@ -118,7 +124,9 @@ print(x, ...)</code></pre></div> <h2>Arguments</h2> <dl><dt>objects</dt> <dd><p>A list of <a href="mmkin.html">mmkin</a> objects containing fits of the same -degradation models to the same data, but using different error models.</p></dd> +degradation models to the same data, but using different error models. +Alternatively, a single <a href="mmkin.html">mmkin</a> object containing fits of several +degradation models to the same data</p></dd> <dt>backend</dt> diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index bcc86ded..17da44cb 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><meta name="robots" content="noindex"><!-- mathjax --><scr </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -52,12 +52,15 @@ likelihood function."><meta name="robots" content="noindex"><!-- mathjax --><scr <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -378,17 +381,17 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:29:10 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:29:10 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:09:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:09:26 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.045 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.049 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -530,9 +533,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.577</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.537 0.887</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.551 1.472</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.559</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.556 0.870</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.603 1.455</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -559,10 +562,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:29:21 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:29:21 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:09:37 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:09:37 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -571,7 +574,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.48 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.43 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html index 176d40c0..3f5c4b35 100644 --- a/docs/dev/reference/multistart.html +++ b/docs/dev/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."><meta name="robots" content="noi </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -202,7 +202,6 @@ doi: 10.1186/s12859-021-04373-4.</p> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> character(0)</span> <span class="r-in"><span><span class="co"># On Windows, we need to create a cluster first. When working with</span></span></span> <span class="r-in"><span><span class="co"># such a cluster, we need to export the mmkin object to the cluster</span></span></span> <span class="r-in"><span><span class="co"># nodes, as it is referred to when updating the saem object on the nodes.</span></span></span> diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index 949bb2f9..95db0593 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."><meta nam </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html index 38a93e27..ffe93e6c 100644 --- a/docs/dev/reference/parplot.html +++ b/docs/dev/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> diff --git a/docs/dev/reference/plot.mixed.mmkin-4.png b/docs/dev/reference/plot.mixed.mmkin-4.png Binary files differindex d2fa1ae1..a849aaee 100644 --- a/docs/dev/reference/plot.mixed.mmkin-4.png +++ b/docs/dev/reference/plot.mixed.mmkin-4.png diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 83017908..b1c62721 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -44,12 +44,15 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -96,6 +99,7 @@ <span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> <span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>,</span> <span> resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"predicted"</span>, <span class="st">"time"</span><span class="op">)</span>,</span> +<span> pop_curve <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> pred_over <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> @@ -149,6 +153,12 @@ variables in the model.</p></dd> predicted values?</p></dd> +<dt>pop_curve</dt> +<dd><p>Per default, a population curve is drawn in case +population parameters are fitted by the model, e.g. for saem objects. +In case there is a covariate model, no population curve is currently shown.</p></dd> + + <dt>pred_over</dt> <dd><p>Named list of alternative predictions as obtained from <a href="mkinpredict.html">mkinpredict</a> with a compatible <a href="mkinmod.html">mkinmod</a>.</p></dd> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index c8a7504f..8ea0ef6e 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -100,6 +100,7 @@ Expectation Maximisation algorithm (SAEM).</p> <span><span class="fu">saem</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span> <span> test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> @@ -124,6 +125,7 @@ Expectation Maximisation algorithm (SAEM).</p> <span> <span class="va">object</span>,</span> <span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span> <span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> @@ -160,6 +162,10 @@ SFO, FOMC, DFOP and HS without fixing <code>parent_0</code>, and SFO or DFOP wit one SFO metabolite.</p></dd> +<dt>error_model</dt> +<dd><p>Possibility to override the error model used in the mmkin object</p></dd> + + <dt>degparms_start</dt> <dd><p>Parameter values given as a named numeric vector will be used to override the starting values obtained from the 'mmkin' object.</p></dd> @@ -409,10 +415,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Oct 26 09:20:37 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Oct 26 09:20:37 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:12:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:12:07 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -427,7 +433,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.902 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.45 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html index 26a28339..6c6a5d46 100644 --- a/docs/dev/reference/set_nd_nq.html +++ b/docs/dev/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."><meta name="robots" content= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> diff --git a/docs/dev/reference/status.html b/docs/dev/reference/status.html index 778446b3..4c856100 100644 --- a/docs/dev/reference/status.html +++ b/docs/dev/reference/status.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index c58fffbb..993544c7 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."><meta name="robots" content="noindex"><!-- mathjax --><script src="http </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -48,12 +48,15 @@ values."><meta name="robots" content="noindex"><!-- mathjax --><script src="http <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -207,10 +210,10 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:30:48 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:30:48 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:12:09 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:12:09 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html index 145e3ba1..96c2d0e5 100644 --- a/docs/dev/reference/summary.mmkin.html +++ b/docs/dev/reference/summary.mmkin.html @@ -18,7 +18,7 @@ and gives an overview of ill-defined parameters calculated by illparms."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -93,7 +93,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for summary.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> @@ -130,9 +130,9 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span> <span class="r-in"><span> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span> <span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 1.032 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.767 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 1a6da753..d8a41356 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> </span> </div> @@ -48,12 +48,15 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -262,7 +265,6 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)" "sd(g_qlogis)"</span> <span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> character(0)</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Approximate 95% confidence intervals</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -286,11 +288,11 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> a.1 0.70273100 0.88750764 1.07228428</span> <span class="r-out co"><span class="r-pr">#></span> b.1 0.06781347 0.08328016 0.09874685</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:31:33 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:31:33 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:12:50 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:12:50 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -305,7 +307,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 27.615 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 25.006 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -326,13 +328,18 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> 825.6 821.3 -401.8</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.4624 97.5484 103.3763</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.0576 -4.1504 -3.9647</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9136 -1.3240 -0.5031</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.8822 -3.6302 -2.1341</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.6307 -4.3226 -2.9388</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.0519 -0.7783 0.8821</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.46239 97.54845 103.37634</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.05756 -4.15040 -3.96472</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.91358 -1.32403 -0.50312</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.88215 -3.63019 -2.13412</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63069 -4.32261 -2.93876</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.05190 -0.77834 0.88213</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.88751 0.70273 1.07228</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.08328 0.06781 0.09875</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44712 0.16584 0.72840</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.79292 0.27688 1.30896</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75661 0.26936 1.24386</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 </span> diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda Binary files differindex 06d62afd..ea9abf65 100644 --- a/vignettes/web_only/mkin_benchmarks.rda +++ b/vignettes/web_only/mkin_benchmarks.rda |
