diff options
Diffstat (limited to 'docs/articles')
| -rw-r--r-- | docs/articles/FOCUS_D.html | 110 | ||||
| -rw-r--r-- | docs/articles/FOCUS_D_files/figure-html/plot-1.png | bin | 101585 -> 101350 bytes | |||
| -rw-r--r-- | docs/articles/FOCUS_D_files/figure-html/plot_2-1.png | bin | 14220 -> 15733 bytes | |||
| -rw-r--r-- | docs/articles/mkin.html | 113 | ||||
| -rw-r--r-- | docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png | bin | 113818 -> 116140 bytes | |||
| -rw-r--r-- | docs/articles/web_only/benchmarks.html | 248 |
6 files changed, 208 insertions, 263 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index e9c6b005..0a9ddf4a 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> </span> </div> @@ -97,7 +97,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-07</h4> + <h4 class="date">2020-05-11</h4> <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -159,10 +159,10 @@ <div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></div> -<pre><code>## parent -## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" -## m1 -## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre> +<pre><code>## parent +## "d_parent = - k_parent * parent" +## m1 +## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> <div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">fit</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value @@ -175,85 +175,83 @@ <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.49.11 +<pre><code>## mkin version used for fitting: 0.9.50 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 7 08:59:27 2020 -## Date of summary: Thu May 7 08:59:27 2020 +## Date of fit: Mon May 11 05:14:41 2020 +## Date of summary: Mon May 11 05:14:41 2020 ## ## Equations: -## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent -## d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +## d_parent/dt = - k_parent * parent +## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 ## -## Model predictions using solution type deSolve +## Model predictions using solution type analytical ## -## Fitted using 389 model solutions performed in 1.031 s +## Fitted using 421 model solutions performed in 0.167 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 100.7500 state -## k_parent_sink 0.1000 deparm -## k_parent_m1 0.1001 deparm -## k_m1_sink 0.1002 deparm +## value type +## parent_0 100.7500 state +## k_parent 0.1000 deparm +## k_m1 0.1001 deparm +## f_parent_to_m1 0.5000 deparm ## ## Starting values for the transformed parameters actually optimised: -## value lower upper -## parent_0 100.750000 -Inf Inf -## log_k_parent_sink -2.302585 -Inf Inf -## log_k_parent_m1 -2.301586 -Inf Inf -## log_k_m1_sink -2.300587 -Inf Inf +## value lower upper +## parent_0 100.750000 -Inf Inf +## log_k_parent -2.302585 -Inf Inf +## log_k_m1 -2.301586 -Inf Inf +## f_parent_ilr_1 0.000000 -Inf Inf ## ## Fixed parameter values: ## value type ## m1_0 0 state ## +## Results: +## +## AIC BIC logLik +## 204.4486 212.6365 -97.22429 +## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 99.600 1.57000 96.400 102.800 -## log_k_parent_sink -3.038 0.07626 -3.193 -2.883 -## log_k_parent_m1 -2.980 0.04033 -3.062 -2.898 -## log_k_m1_sink -5.248 0.13320 -5.518 -4.977 -## sigma 3.126 0.35850 2.396 3.855 +## Estimate Std. Error Lower Upper +## parent_0 99.60000 1.57000 96.40000 102.8000 +## log_k_parent -2.31600 0.04087 -2.39900 -2.2330 +## log_k_m1 -5.24800 0.13320 -5.51800 -4.9770 +## f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694 +## sigma 3.12600 0.35850 2.39600 3.8550 ## ## Parameter correlation: -## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -## parent_0 1.000e+00 6.067e-01 -6.372e-02 -1.688e-01 -## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 -6.252e-01 -## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 4.731e-01 -## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 1.000e+00 -## sigma 5.287e-10 3.306e-09 4.421e-08 -3.319e-10 -## sigma -## parent_0 5.287e-10 -## log_k_parent_sink 3.306e-09 -## log_k_parent_m1 4.421e-08 -## log_k_m1_sink -3.319e-10 -## sigma 1.000e+00 +## parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma +## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.214e-07 +## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07 +## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.410e-07 +## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 5.093e-10 +## sigma -3.214e-07 3.168e-07 -1.410e-07 5.093e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. -## Estimate t value Pr(>t) Lower Upper -## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02 -## k_parent_sink 0.047920 13.110 6.126e-15 0.041030 5.596e-02 -## k_parent_m1 0.050780 24.800 3.269e-23 0.046780 5.512e-02 -## k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03 -## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 +## Estimate t value Pr(>t) Lower Upper +## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02 +## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01 +## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03 +## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01 +## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 6.398 4 15 -## parent 6.827 3 6 -## m1 4.490 1 9 +## parent 6.459 2 7 +## m1 4.690 2 8 ## ## Resulting formation fractions: ## ff -## parent_sink 0.4855 ## parent_m1 0.5145 -## m1_sink 1.0000 +## parent_sink 0.4855 ## ## Estimated disappearance times: ## DT50 DT90 @@ -266,10 +264,10 @@ ## 0 parent 102.04 99.59848 2.442e+00 ## 1 parent 93.50 90.23787 3.262e+00 ## 1 parent 92.50 90.23787 2.262e+00 -## 3 parent 63.23 74.07320 -1.084e+01 -## 3 parent 68.99 74.07320 -5.083e+00 -## 7 parent 52.32 49.91207 2.408e+00 -## 7 parent 55.13 49.91207 5.218e+00 +## 3 parent 63.23 74.07319 -1.084e+01 +## 3 parent 68.99 74.07319 -5.083e+00 +## 7 parent 52.32 49.91206 2.408e+00 +## 7 parent 55.13 49.91206 5.218e+00 ## 14 parent 27.27 25.01257 2.257e+00 ## 14 parent 26.64 25.01257 1.627e+00 ## 21 parent 11.50 12.53462 -1.035e+00 @@ -279,7 +277,7 @@ ## 50 parent 0.69 0.71624 -2.624e-02 ## 50 parent 0.63 0.71624 -8.624e-02 ## 75 parent 0.05 0.06074 -1.074e-02 -## 75 parent 0.06 0.06074 -7.382e-04 +## 75 parent 0.06 0.06074 -7.381e-04 ## 1 m1 4.84 4.80296 3.704e-02 ## 1 m1 5.64 4.80296 8.370e-01 ## 3 m1 12.91 13.02400 -1.140e-01 diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex a7944b84..306244b3 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex 97c61a16..158e3c50 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 42eb6c0a..b828b7dc 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -6,19 +6,19 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Introduction to mkin • mkin</title> -<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous"> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous"> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<!-- 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="Introduction to mkin"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> +<meta property="og:description" content="mkin"> <!-- 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> +<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"> @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> </span> </div> @@ -74,7 +74,14 @@ <a href="../news/index.html">News</a> </li> </ul> -<ul class="nav navbar-nav navbar-right"></ul> +<ul class="nav navbar-nav navbar-right"> +<li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> </div> <!--/.nav-collapse --> </div> @@ -87,12 +94,12 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1>Introduction to mkin</h1> + <h1 data-toc-skip>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-11-01</h4> - + <h4 class="date">2020-05-11</h4> + <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/mkin.Rmd"><code>vignettes/mkin.Rmd</code></a></small> <div class="hidden name"><code>mkin.Rmd</code></div> </div> @@ -104,34 +111,34 @@ <h1 class="hasAnchor"> <a href="#abstract" class="anchor"></a>Abstract</h1> <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The <code>R</code> add-on package <code>mkin</code> implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-2" title="2"><span class="co"># Define the kinetic model</span></a> -<a class="sourceLine" id="cb1-3" title="3">m_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> -<a class="sourceLine" id="cb1-4" title="4"> <span class="dt">M1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> -<a class="sourceLine" id="cb1-5" title="5"> <span class="dt">M2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-7" title="7"></a> -<a class="sourceLine" id="cb1-8" title="8"></a> -<a class="sourceLine" id="cb1-9" title="9"><span class="co"># Produce model predictions using some arbitrary parameters</span></a> -<a class="sourceLine" id="cb1-10" title="10">sampling_times =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>, <span class="dv">60</span>, <span class="dv">90</span>, <span class="dv">120</span>)</a> -<a class="sourceLine" id="cb1-11" title="11">d_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinpredict.html">mkinpredict</a></span>(m_SFO_SFO_SFO,</a> -<a class="sourceLine" id="cb1-12" title="12"> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dt">k_parent =</span> <span class="fl">0.03</span>,</a> -<a class="sourceLine" id="cb1-13" title="13"> <span class="dt">f_parent_to_M1 =</span> <span class="fl">0.5</span>, <span class="dt">k_M1 =</span> <span class="kw"><a href="https://rdrr.io/r/base/Log.html">log</a></span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">100</span>,</a> -<a class="sourceLine" id="cb1-14" title="14"> <span class="dt">f_M1_to_M2 =</span> <span class="fl">0.9</span>, <span class="dt">k_M2 =</span> <span class="kw"><a href="https://rdrr.io/r/base/Log.html">log</a></span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">50</span>),</a> -<a class="sourceLine" id="cb1-15" title="15"> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dt">parent =</span> <span class="dv">100</span>, <span class="dt">M1 =</span> <span class="dv">0</span>, <span class="dt">M2 =</span> <span class="dv">0</span>),</a> -<a class="sourceLine" id="cb1-16" title="16"> sampling_times)</a> -<a class="sourceLine" id="cb1-17" title="17"></a> -<a class="sourceLine" id="cb1-18" title="18"><span class="co"># Generate a dataset by adding normally distributed errors with</span></a> -<a class="sourceLine" id="cb1-19" title="19"><span class="co"># standard deviation 3, for two replicates at each sampling time</span></a> -<a class="sourceLine" id="cb1-20" title="20">d_SFO_SFO_SFO_err <-<span class="st"> </span><span class="kw"><a href="../reference/add_err.html">add_err</a></span>(d_SFO_SFO_SFO, <span class="dt">reps =</span> <span class="dv">2</span>,</a> -<a class="sourceLine" id="cb1-21" title="21"> <span class="dt">sdfunc =</span> <span class="cf">function</span>(x) <span class="dv">3</span>,</a> -<a class="sourceLine" id="cb1-22" title="22"> <span class="dt">n =</span> <span class="dv">1</span>, <span class="dt">seed =</span> <span class="dv">123456789</span> )</a> -<a class="sourceLine" id="cb1-23" title="23"></a> -<a class="sourceLine" id="cb1-24" title="24"><span class="co"># Fit the model to the dataset</span></a> -<a class="sourceLine" id="cb1-25" title="25">f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-26" title="26"></a> -<a class="sourceLine" id="cb1-27" title="27"><span class="co"># Plot the results separately for parent and metabolites</span></a> -<a class="sourceLine" id="cb1-28" title="28"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"mkin"</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +<span class="co"># Define the kinetic model</span> +<span class="no">m_SFO_SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>), + <span class="kw">M1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>), + <span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), + <span class="kw">use_of_ff</span> <span class="kw">=</span> <span class="st">"max"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) + + +<span class="co"># Produce model predictions using some arbitrary parameters</span> +<span class="no">sampling_times</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span>) +<span class="no">d_SFO_SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span>(<span class="no">m_SFO_SFO_SFO</span>, + <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">k_parent</span> <span class="kw">=</span> <span class="fl">0.03</span>, + <span class="kw">f_parent_to_M1</span> <span class="kw">=</span> <span class="fl">0.5</span>, <span class="kw">k_M1</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html">log</a></span>(<span class="fl">2</span>)/<span class="fl">100</span>, + <span class="kw">f_M1_to_M2</span> <span class="kw">=</span> <span class="fl">0.9</span>, <span class="kw">k_M2</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html">log</a></span>(<span class="fl">2</span>)/<span class="fl">50</span>), + <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fl">100</span>, <span class="kw">M1</span> <span class="kw">=</span> <span class="fl">0</span>, <span class="kw">M2</span> <span class="kw">=</span> <span class="fl">0</span>), + <span class="no">sampling_times</span>) + +<span class="co"># Generate a dataset by adding normally distributed errors with</span> +<span class="co"># standard deviation 3, for two replicates at each sampling time</span> +<span class="no">d_SFO_SFO_SFO_err</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span>(<span class="no">d_SFO_SFO_SFO</span>, <span class="kw">reps</span> <span class="kw">=</span> <span class="fl">2</span>, + <span class="kw">sdfunc</span> <span class="kw">=</span> <span class="kw">function</span>(<span class="no">x</span>) <span class="fl">3</span>, + <span class="kw">n</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">seed</span> <span class="kw">=</span> <span class="fl">123456789</span> ) + +<span class="co"># Fit the model to the dataset</span> +<span class="no">f_SFO_SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">m_SFO_SFO_SFO</span>, <span class="no">d_SFO_SFO_SFO_err</span><span class="kw">[[</span><span class="fl">1</span>]], <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) + +<span class="co"># Plot the results separately for parent and metabolites</span> +<span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">f_SFO_SFO_SFO</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> @@ -222,29 +229,11 @@ </div> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <div id="tocnav"> - <h2 class="hasAnchor"> -<a href="#tocnav" class="anchor"></a>Contents</h2> - <ul class="nav nav-pills nav-stacked"> -<li><a href="#abstract">Abstract</a></li> - <li> -<a href="#background">Background</a><ul class="nav nav-pills nav-stacked"> -<li><a href="#derived-software-tools">Derived software tools</a></li> - <li><a href="#recent-developments">Recent developments</a></li> - </ul> -</li> - <li> -<a href="#internal-parameter-transformations">Internal parameter transformations</a><ul class="nav nav-pills nav-stacked"> -<li><a href="#confidence-intervals-based-on-transformed-parameters">Confidence intervals based on transformed parameters</a></li> - <li><a href="#parameter-t-test-based-on-untransformed-parameters">Parameter t-test based on untransformed parameters</a></li> - </ul> -</li> - <li><a href="#references">References</a></li> - </ul> + <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> + </nav> </div> - </div> </div> @@ -255,7 +244,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex e21b4233..bdc067c1 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 4fb76fa2..ad7cf62c 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -6,19 +6,19 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Benchmark timings for mkin on various systems • mkin</title> -<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous"> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous"> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../../pkgdown.css" rel="stylesheet"> +<!-- 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="Benchmark timings for mkin on various systems"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> +<meta property="og:description" content="mkin"> <!-- 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> +<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"> @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> </span> </div> @@ -74,7 +74,14 @@ <a href="../../news/index.html">News</a> </li> </ul> -<ul class="nav navbar-nav navbar-right"></ul> +<ul class="nav navbar-nav navbar-right"> +<li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> </div> <!--/.nav-collapse --> </div> @@ -87,12 +94,12 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1>Benchmark timings for mkin on various systems</h1> + <h1 data-toc-skip>Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-11-01</h4> - + <h4 class="date">2020-05-11</h4> + <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.Rmd"><code>vignettes/web_only/benchmarks.Rmd</code></a></small> <div class="hidden name"><code>benchmarks.Rmd</code></div> </div> @@ -103,192 +110,143 @@ <h2 class="hasAnchor"> <a href="#systems" class="anchor"></a>Systems</h2> <p>Each system is characterized by its CPU type, the operating system type and the mkin version.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">cpu_model <-<span class="st"> </span>benchmarkme<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/benchmarkme/man/get_cpu.html">get_cpu</a></span>()<span class="op">$</span>model_name</a> -<a class="sourceLine" id="cb1-2" title="2">operating_system <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/Sys.info.html">Sys.info</a></span>()[[<span class="st">"sysname"</span>]]</a> -<a class="sourceLine" id="cb1-3" title="3">mkin_version <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/character.html">as.character</a></span>(<span class="kw"><a href="https://rdrr.io/r/utils/packageDescription.html">packageVersion</a></span>(<span class="st">"mkin"</span>))</a> -<a class="sourceLine" id="cb1-4" title="4">system_string <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(operating_system, <span class="st">", "</span>, cpu_model, <span class="st">", mkin version "</span>, mkin_version)</a> -<a class="sourceLine" id="cb1-5" title="5"><span class="kw"><a href="https://rdrr.io/r/base/load.html">load</a></span>(<span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>)</a> -<a class="sourceLine" id="cb1-6" title="6">mkin_benchmarks[system_string, <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"CPU"</span>, <span class="st">"OS"</span>, <span class="st">"mkin"</span>)] <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(cpu_model, operating_system, mkin_version)</a> -<a class="sourceLine" id="cb1-7" title="7"></a> -<a class="sourceLine" id="cb1-8" title="8"><span class="cf">if</span> (mkin_version <span class="op">></span><span class="st"> "0.9.48.1"</span>) {</a> -<a class="sourceLine" id="cb1-9" title="9"> mmkin_bench <-<span class="st"> </span><span class="cf">function</span>(models, datasets, <span class="dt">error_model =</span> <span class="st">"const"</span>) <span class="kw"><a href="../../reference/mmkin.html">mmkin</a></span>(models, datasets, <span class="dt">error_model =</span> error_model, <span class="dt">cores =</span> <span class="dv">1</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-10" title="10">} <span class="cf">else</span> {</a> -<a class="sourceLine" id="cb1-11" title="11"> mmkin_bench <-<span class="st"> </span><span class="cf">function</span>(models, datasets, <span class="dt">error_model =</span> <span class="ot">NULL</span>) <span class="kw"><a href="../../reference/mmkin.html">mmkin</a></span>(models, datasets, <span class="dt">reweight.method =</span> error_model, <span class="dt">cores =</span> <span class="dv">1</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-12" title="12">}</a></code></pre></div> -<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># Parent only</span></a> -<a class="sourceLine" id="cb2-2" title="2">t1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb2-3" title="3">t2 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">cpu_model</span> <span class="kw"><-</span> <span class="kw pkg">benchmarkme</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/benchmarkme/man/get_cpu.html">get_cpu</a></span>()$<span class="no">model_name</span> +<span class="no">operating_system</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html">Sys.info</a></span>()<span class="kw">[[</span><span class="st">"sysname"</span>]] +<span class="no">mkin_version</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html">as.character</a></span>(<span class="fu"><a href="https://rdrr.io/r/utils/packageDescription.html">packageVersion</a></span>(<span class="st">"mkin"</span>)) +<span class="no">system_string</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="no">operating_system</span>, <span class="st">", "</span>, <span class="no">cpu_model</span>, <span class="st">", mkin version "</span>, <span class="no">mkin_version</span>) +<span class="fu"><a href="https://rdrr.io/r/base/load.html">load</a></span>(<span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>) +<span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"CPU"</span>, <span class="st">"OS"</span>, <span class="st">"mkin"</span>)] <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">cpu_model</span>, <span class="no">operating_system</span>, <span class="no">mkin_version</span>) + +<span class="kw">if</span> (<span class="no">mkin_version</span> <span class="kw">></span> <span class="st">"0.9.48.1"</span>) { + <span class="no">mmkin_bench</span> <span class="kw"><-</span> <span class="kw">function</span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="no">error_model</span> <span class="kw">=</span> <span class="st">"const"</span>) <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="kw">error_model</span> <span class="kw">=</span> <span class="no">error_model</span>, <span class="kw">cores</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +} <span class="kw">else</span> { + <span class="no">mmkin_bench</span> <span class="kw"><-</span> <span class="kw">function</span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="no">error_model</span> <span class="kw">=</span> <span class="kw">NULL</span>) <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="kw">reweight.method</span> <span class="kw">=</span> <span class="no">error_model</span>, <span class="kw">cores</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +}</pre></body></html></div> +<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">FOCUS_C</span> <span class="kw"><-</span> <span class="no">FOCUS_2006_C</span> +<span class="no">FOCUS_D</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html">subset</a></span>(<span class="no">FOCUS_2006_D</span>, <span class="no">value</span> <span class="kw">!=</span> <span class="fl">0</span>) +<span class="co"># Parent only</span> +<span class="no">t1</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_C</span>, <span class="no">FOCUS_D</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]] +<span class="no">t2</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_C</span>, <span class="no">FOCUS_D</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: +## iteration limit reached without convergence (10) + +## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: ## iteration limit reached without convergence (10)</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># One metabolite</span></a> -<a class="sourceLine" id="cb4-2" title="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb4-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb4-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># One metabolite</span> +<span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( + <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), + <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb6-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb6-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">FOMC_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( + <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), + <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">DFOP_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="no">DFOP_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( + <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), + <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t3 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data +<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">t3</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]] +<span class="no">t4</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] +<span class="no">t5</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] + +<span class="co"># Two metabolites, synthetic data</span> +<span class="no">m_synth_SFO_lin</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>), + <span class="kw">M1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>), + <span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), + <span class="kw">use_of_ff</span> <span class="kw">=</span> <span class="st">"max"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) + +<span class="no">m_synth_DFOP_par</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)), + <span class="kw">M1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), + <span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), + <span class="kw">use_of_ff</span> <span class="kw">=</span> <span class="st">"max"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) + +<span class="no">SFO_lin_a</span> <span class="kw"><-</span> <span class="no">synthetic_data_for_UBA_2014</span><span class="kw">[[</span><span class="fl">1</span>]]$<span class="no">data</span> -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">t4 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/subset.html">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb13-2" title="2">t5 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data +<span class="no">DFOP_par_c</span> <span class="kw"><-</span> <span class="no">synthetic_data_for_UBA_2014</span><span class="kw">[[</span><span class="fl">12</span>]]$<span class="no">data</span> -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data +<span class="no">t6</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>)))[<span class="st">"elapsed"</span>] +<span class="no">t7</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>)))[<span class="st">"elapsed"</span>] -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a> -<a class="sourceLine" id="cb15-2" title="2">m_synth_SFO_lin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> -<a class="sourceLine" id="cb15-3" title="3"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> -<a class="sourceLine" id="cb15-4" title="4"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb15-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb15-6" title="6"></a> -<a class="sourceLine" id="cb15-7" title="7">m_synth_DFOP_par <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a> -<a class="sourceLine" id="cb15-8" title="8"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb15-9" title="9"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb15-10" title="10"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb15-11" title="11"></a> -<a class="sourceLine" id="cb15-12" title="12">SFO_lin_a <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a> -<a class="sourceLine" id="cb15-13" title="13"></a> -<a class="sourceLine" id="cb15-14" title="14">DFOP_par_c <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a> -<a class="sourceLine" id="cb15-15" title="15"></a> -<a class="sourceLine" id="cb15-16" title="16">t6 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb15-17" title="17">t7 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb15-18" title="18"></a> -<a class="sourceLine" id="cb15-19" title="19">t8 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb15-20" title="20">t9 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb15-21" title="21"></a> -<a class="sourceLine" id="cb15-22" title="22">t10 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb15-23" title="23">t11 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb15-24" title="24"></a> -<a class="sourceLine" id="cb15-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a> -<a class="sourceLine" id="cb15-26" title="26">mkin_benchmarks</a></code></pre></div> -<pre><code>## CPU -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 AMD Ryzen 7 1700 Eight-Core Processor -## OS -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 Linux -## mkin -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 0.9.49.6 -## t1 +<span class="no">t8</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>] +<span class="no">t9</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>] + +<span class="no">t10</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>] +<span class="no">t11</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>] + +<span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">1</span>:<span class="fl">11</span>)] <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">t1</span>, <span class="no">t2</span>, <span class="no">t3</span>, <span class="no">t4</span>, <span class="no">t5</span>, <span class="no">t6</span>, <span class="no">t7</span>, <span class="no">t8</span>, <span class="no">t9</span>, <span class="no">t10</span>, <span class="no">t11</span>) +<span class="no">mkin_benchmarks</span>[, -<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">1</span>:<span class="fl">3</span>)]</pre></body></html></div> +<pre><code>## t1 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.901 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 1.683 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.164 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 3.862 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.510 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 1.369 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 30.849 -## t5 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.545 -## t6 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.563 -## t7 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.252 -## t8 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 7.865 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 6.104 +## t5 t6 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 2.623 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 2.542 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 2.723 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 2.643 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 2.635 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 2.718 0.752 +## t7 t8 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 7.525 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 4.632 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 4.862 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 7.02 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 4.737 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 1.214 1.276 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.195 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 2.858 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 7.729 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 2.032 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.787</code></pre> -<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/save.html">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 2.973</code></pre> +<div class="sourceCode" id="cb12"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span>(<span class="no">mkin_benchmarks</span>, <span class="kw">file</span> <span class="kw">=</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</pre></body></html></div> </div> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <div id="tocnav"> - <h2 class="hasAnchor"> -<a href="#tocnav" class="anchor"></a>Contents</h2> - <ul class="nav nav-pills nav-stacked"> -<li><a href="#systems">Systems</a></li> - </ul> + <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> + </nav> </div> - </div> </div> @@ -299,7 +257,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> |
