diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-11 05:15:19 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-11 05:18:32 +0200 |
| commit | 234c9059a95e104917e488a6ddd2313234a96cdc (patch) | |
| tree | f6e54098f79d94578434ef727b62f7cc5d5e79b7 /docs | |
| parent | d113cd79b178fdc91aecb894707ed356129dfb75 (diff) | |
Avoid merge() and data.frame() in cost function
also for deSolve and eigenvalue based solutions. This noticeably increases
performance for these methods, see test.log and benchmark vignette.
Diffstat (limited to 'docs')
21 files changed, 607 insertions, 535 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" 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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 --- 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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> diff --git a/docs/news/index.html b/docs/news/index.html index bc69fd2d..1e13041d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -145,7 +145,6 @@ <ul> <li><p>Support SFORB with formation fractions</p></li> <li><p>‘mkinmod’: Make ‘use_of_ff’ = “max” the default</p></li> -<li><p>Implement analytical solutions for some coupled models, e.g. SFO-SFO, DFOP-SFO, SFORB-SFO</p></li> </ul> </div> <div id="mkin-0-9-49-11-2020-04-20" class="section level1"> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 32bcaa05..b3cd3d30 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: NAFTA_examples: web_only/NAFTA_examples.html benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html -last_built: 2020-05-07T20:11Z +last_built: 2020-05-11T03:18Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index e14857cc..67016be0 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -167,7 +167,21 @@ <pre class="examples"><div class='input'> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div></pre> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='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'># to avoid warnings</span> +<span class='no'>fit_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='co'># \dontrun{</span> +<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) + <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>( + <span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), + <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), + <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='message'>Lade nötiges Paket: rbenchmark</span></div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child +#> 1 analytical 1 0.198 1.000 0.198 0.000 0 +#> 2 deSolve 1 0.350 1.768 0.348 0.001 0 +#> sys.child +#> 1 0 +#> 2 0</div><div class='input'># } +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"> diff --git a/docs/reference/index.html b/docs/reference/index.html index 75820166..7e7fff29 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -557,6 +557,12 @@ kinetic models fitted with mkinfit</p></td> <p><code><a href="mkinerrplot.html">mkinerrplot()</a></code> </p> </td> <td><p>Function to plot squared residuals and the error model for an mkin object</p></td> + </tr><tr> + + <td> + <p><code><a href="create_deg_func.html">create_deg_func()</a></code> </p> + </td> + <td><p>Create degradation functions for known analytical solutions</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 62823c58..9974b66b 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -78,7 +78,7 @@ likelihood function." /> </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> @@ -174,7 +174,6 @@ likelihood function.</p> <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, - <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"const"</span>, <span class='st'>"obs"</span>, <span class='st'>"tc"</span>), <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), @@ -325,13 +324,6 @@ is 1e-8, lower than in <code>lsoda</code>.</p></td> is 1e-10, much lower than in <code>lsoda</code>.</p></td> </tr> <tr> - <th>n.outtimes</th> - <td><p>The length of the dataseries that is produced by the model -prediction function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy -of the numerical solver if that is used (see <code>solution_type</code> -argument. The default value is 100.</p></td> - </tr> - <tr> <th>error_model</th> <td><p>If the error model is "const", a constant standard deviation is assumed.</p> @@ -422,7 +414,87 @@ estimators.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Use shorthand notation for parent only degradation</span> -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in (function (t, parent_0, alpha, beta) { parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 1, 1.2020202020202, 2.4040404040404, 3, 3.60606060606061, 4.80808080808081, 6.01010101010101, 7, 7.21212121212121, 8.41414141414141, 9.61616161616162, 10.8181818181818, 12.020202020202, 13.2222222222222, 14, 14.4242424242424, 15.6262626262626, 16.8282828282828, 18.030303030303, 19.2323232323232, 20.4343434343434, 21.6363636363636, 22.8383838383838, 24.040404040404, 25.2424242424242, 26.4444444444444, 27.6464646464646, 28, 28.8484848484848, 30.050505050505, 31.2525252525253, 32.4545454545455, 33.6565656565657, 34.8585858585859, 36.0606060606061, 37.2626262626263, 38.4646464646465, 39.6666666666667, 40.8686868686869, 42.0707070707071, 43.2727272727273, 44.4747474747475, 45.6767676767677, 46.8787878787879, 48.0808080808081, 49.2828282828283, 50.4848484848485, 51.6868686868687, 52.8888888888889, 54.0909090909091, 55.2929292929293, 56.4949494949495, 57.6969696969697, 58.8989898989899, 60.1010101010101, 61.3030303030303, 62.5050505050505, 63, 63.7070707070707, 64.9090909090909, 66.1111111111111, 67.3131313131313, 68.5151515151515, 69.7171717171717, 70.9191919191919, 72.1212121212121, 73.3232323232323, 74.5252525252525, 75.7272727272727, 76.9292929292929, 78.1313131313131, 79.3333333333333, 80.5353535353535, 81.7373737373737, 82.9393939393939, 84.1414141414141, 85.3434343434343, 86.5454545454545, 87.7474747474747, 88.9494949494949, 90.1515151515152, 91, 91.3535353535353, 92.5555555555556, 93.7575757575758, 94.959595959596, 96.1616161616162, 97.3636363636364, 98.5656565656566, 99.7676767676768, 100.969696969697, 102.171717171717, 103.373737373737, 104.575757575758, 105.777777777778, 106.979797979798, 108.181818181818, 109.383838383838, 110.585858585859, 111.787878787879, 112.989898989899, 114.191919191919, 115.393939393939, 116.59595959596, 117.79797979798, 119), parent.0 = c(parent = 85.1), alpha = 1, beta = 10): unbenutztes Argument (parent.0 = 85.1)</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'> +<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50 +#> R version used for fitting: 4.0.0 +#> Date of fit: Mon May 11 05:14:26 2020 +#> Date of summary: Mon May 11 05:14:26 2020 +#> +#> Equations: +#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent +#> +#> Model predictions using solution type analytical +#> +#> Fitted using 222 model solutions performed in 0.043 s +#> +#> Error model: Constant variance +#> +#> Error model algorithm: OLS +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 85.1 state +#> alpha 1.0 deparm +#> beta 10.0 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 85.100000 -Inf Inf +#> log_alpha 0.000000 -Inf Inf +#> log_beta 2.302585 -Inf Inf +#> +#> Fixed parameter values: +#> None +#> +#> Results: +#> +#> AIC BIC logLik +#> 44.68652 45.47542 -18.34326 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 85.87000 1.8070 81.23000 90.5200 +#> log_alpha 0.05192 0.1353 -0.29580 0.3996 +#> log_beta 0.65100 0.2287 0.06315 1.2390 +#> sigma 1.85700 0.4378 0.73200 2.9830 +#> +#> Parameter correlation: +#> parent_0 log_alpha log_beta sigma +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.758e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.007e-07 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.568e-08 +#> sigma 4.758e-08 1.007e-07 8.568e-08 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 85.870 47.530 3.893e-08 81.2300 90.520 +#> alpha 1.053 7.393 3.562e-04 0.7439 1.491 +#> beta 1.917 4.373 3.601e-03 1.0650 3.451 +#> sigma 1.857 4.243 4.074e-03 0.7320 2.983 +#> +#> FOCUS Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.657 3 6 +#> parent 6.657 3 6 +#> +#> Estimated disappearance times: +#> DT50 DT90 DT50back +#> parent 1.785 15.15 4.56 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 85.1 85.875 -0.7749 +#> 1 parent 57.9 55.191 2.7091 +#> 3 parent 29.9 31.845 -1.9452 +#> 7 parent 14.6 17.012 -2.4124 +#> 14 parent 9.7 9.241 0.4590 +#> 28 parent 6.6 4.754 1.8460 +#> 63 parent 4.0 2.102 1.8977 +#> 91 parent 3.9 1.441 2.4590 +#> 119 parent 0.6 1.092 -0.4919</div><div class='input'> <span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( @@ -430,86 +502,105 @@ estimators.</p> <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.526 0.000 1.526 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink sigma -#> 99.598483069 0.047920122 0.050777612 0.005260651 3.125503875 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff -#> parent_sink parent_m1 m1_sink -#> 0.485524 0.514476 1.000000 +#> 0.407 0.002 0.409 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 99.598483222 0.098697734 0.005260651 0.514475962 3.125503875 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> parent_m1 parent_sink +#> 0.514476 0.485524 #> #> $distimes #> DT50 DT90 #> parent 7.022929 23.32967 -#> m1 131.760712 437.69961 +#> m1 131.760715 437.69962 #> </div><div class='input'><span class='co'># \dontrun{</span> <span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 18915.53 -#> Sum of squared residuals at call 2: 18915.53 -#> Sum of squared residuals at call 6: 11424.02 -#> Sum of squared residuals at call 10: 11424 -#> Sum of squared residuals at call 12: 4094.396 -#> Sum of squared residuals at call 16: 4094.396 -#> Sum of squared residuals at call 19: 1340.595 -#> Sum of squared residuals at call 20: 1340.593 -#> Sum of squared residuals at call 25: 1072.239 -#> Sum of squared residuals at call 28: 1072.236 -#> Sum of squared residuals at call 30: 874.2615 -#> Sum of squared residuals at call 33: 874.2611 -#> Sum of squared residuals at call 35: 616.2375 -#> Sum of squared residuals at call 37: 616.237 -#> Sum of squared residuals at call 40: 467.4386 -#> Sum of squared residuals at call 42: 467.438 -#> Sum of squared residuals at call 46: 398.2913 -#> Sum of squared residuals at call 48: 398.2913 -#> Sum of squared residuals at call 49: 398.2912 -#> Sum of squared residuals at call 51: 395.0711 -#> Sum of squared residuals at call 54: 395.071 -#> Sum of squared residuals at call 56: 378.3298 -#> Sum of squared residuals at call 59: 378.3298 -#> Sum of squared residuals at call 62: 376.9812 -#> Sum of squared residuals at call 64: 376.9811 -#> Sum of squared residuals at call 67: 375.2085 -#> Sum of squared residuals at call 69: 375.2085 -#> Sum of squared residuals at call 70: 375.2085 -#> Sum of squared residuals at call 71: 375.2085 -#> Sum of squared residuals at call 72: 374.5723 -#> Sum of squared residuals at call 74: 374.5723 -#> Sum of squared residuals at call 77: 374.0075 -#> Sum of squared residuals at call 79: 374.0075 -#> Sum of squared residuals at call 80: 374.0075 -#> Sum of squared residuals at call 82: 373.1711 -#> Sum of squared residuals at call 84: 373.1711 -#> Sum of squared residuals at call 87: 372.6445 -#> Sum of squared residuals at call 88: 372.1614 -#> Sum of squared residuals at call 90: 372.1614 -#> Sum of squared residuals at call 91: 372.1614 -#> Sum of squared residuals at call 94: 371.6464 -#> Sum of squared residuals at call 99: 371.4299 -#> Sum of squared residuals at call 101: 371.4299 -#> Sum of squared residuals at call 104: 371.4071 -#> Sum of squared residuals at call 106: 371.4071 -#> Sum of squared residuals at call 107: 371.4071 -#> Sum of squared residuals at call 109: 371.2524 -#> Sum of squared residuals at call 113: 371.2524 -#> Sum of squared residuals at call 114: 371.2136 -#> Sum of squared residuals at call 115: 371.2136 -#> Sum of squared residuals at call 116: 371.2136 -#> Sum of squared residuals at call 119: 371.2134 -#> Sum of squared residuals at call 120: 371.2134 -#> Sum of squared residuals at call 122: 371.2134 -#> Sum of squared residuals at call 123: 371.2134 -#> Sum of squared residuals at call 125: 371.2134 -#> Sum of squared residuals at call 126: 371.2134 -#> Sum of squared residuals at call 135: 371.2134 -#> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 1.084 0.000 1.085 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink sigma -#> 99.598483072 0.047920122 0.050777612 0.005260651 3.125503874 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff -#> parent_sink parent_m1 m1_sink -#> 0.485524 0.514476 1.000000 + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 15156.12 +#> Sum of squared residuals at call 2: 15156.12 +#> Sum of squared residuals at call 6: 8243.645 +#> Sum of squared residuals at call 12: 6290.712 +#> Sum of squared residuals at call 13: 6290.683 +#> Sum of squared residuals at call 15: 6290.452 +#> Sum of squared residuals at call 18: 1700.749 +#> Sum of squared residuals at call 20: 1700.611 +#> Sum of squared residuals at call 24: 1190.923 +#> Sum of squared residuals at call 26: 1190.922 +#> Sum of squared residuals at call 29: 1017.417 +#> Sum of squared residuals at call 31: 1017.417 +#> Sum of squared residuals at call 33: 1017.416 +#> Sum of squared residuals at call 34: 644.0471 +#> Sum of squared residuals at call 36: 644.0469 +#> Sum of squared residuals at call 38: 644.0469 +#> Sum of squared residuals at call 39: 590.5025 +#> Sum of squared residuals at call 41: 590.5022 +#> Sum of squared residuals at call 43: 590.5016 +#> Sum of squared residuals at call 44: 543.219 +#> Sum of squared residuals at call 45: 543.2187 +#> Sum of squared residuals at call 46: 543.2186 +#> Sum of squared residuals at call 50: 391.348 +#> Sum of squared residuals at call 51: 391.3479 +#> Sum of squared residuals at call 56: 386.4789 +#> Sum of squared residuals at call 58: 386.4789 +#> Sum of squared residuals at call 60: 386.4779 +#> Sum of squared residuals at call 61: 384.0686 +#> Sum of squared residuals at call 63: 384.0686 +#> Sum of squared residuals at call 66: 382.7813 +#> Sum of squared residuals at call 68: 382.7813 +#> Sum of squared residuals at call 70: 382.7813 +#> Sum of squared residuals at call 71: 378.9273 +#> Sum of squared residuals at call 73: 378.9273 +#> Sum of squared residuals at call 75: 378.9272 +#> Sum of squared residuals at call 76: 377.4847 +#> Sum of squared residuals at call 78: 377.4846 +#> Sum of squared residuals at call 81: 375.9738 +#> Sum of squared residuals at call 83: 375.9738 +#> Sum of squared residuals at call 86: 375.3387 +#> Sum of squared residuals at call 88: 375.3387 +#> Sum of squared residuals at call 91: 374.5774 +#> Sum of squared residuals at call 93: 374.5774 +#> Sum of squared residuals at call 95: 374.5774 +#> Sum of squared residuals at call 96: 373.5433 +#> Sum of squared residuals at call 100: 373.5433 +#> Sum of squared residuals at call 102: 373.2654 +#> Sum of squared residuals at call 104: 373.2654 +#> Sum of squared residuals at call 107: 372.6841 +#> Sum of squared residuals at call 111: 372.684 +#> Sum of squared residuals at call 114: 372.6374 +#> Sum of squared residuals at call 116: 372.6374 +#> Sum of squared residuals at call 119: 372.6223 +#> Sum of squared residuals at call 121: 372.6223 +#> Sum of squared residuals at call 123: 372.6223 +#> Sum of squared residuals at call 124: 372.5903 +#> Sum of squared residuals at call 126: 372.5903 +#> Sum of squared residuals at call 129: 372.5445 +#> Sum of squared residuals at call 130: 372.4921 +#> Sum of squared residuals at call 131: 372.2377 +#> Sum of squared residuals at call 132: 371.5434 +#> Sum of squared residuals at call 134: 371.5434 +#> Sum of squared residuals at call 137: 371.2857 +#> Sum of squared residuals at call 139: 371.2857 +#> Sum of squared residuals at call 143: 371.2247 +#> Sum of squared residuals at call 144: 371.2247 +#> Sum of squared residuals at call 149: 371.2189 +#> Sum of squared residuals at call 150: 371.2145 +#> Sum of squared residuals at call 153: 371.2145 +#> Sum of squared residuals at call 155: 371.2138 +#> Sum of squared residuals at call 156: 371.2138 +#> Sum of squared residuals at call 157: 371.2138 +#> Sum of squared residuals at call 161: 371.2134 +#> Sum of squared residuals at call 162: 371.2134 +#> Sum of squared residuals at call 165: 371.2134 +#> Sum of squared residuals at call 166: 371.2134 +#> Sum of squared residuals at call 168: 371.2134 +#> Negative log-likelihood at call 178: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen +#> 0.349 0.000 0.350 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 99.598480759 0.098697739 0.005260651 0.514475958 3.125503874 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff +#> parent_m1 parent_sink +#> 0.514476 0.485524 #> #> $distimes #> DT50 DT90 -#> parent 7.022929 23.32967 -#> m1 131.760712 437.69961 +#> parent 7.022929 23.32966 +#> m1 131.760731 437.69967 #> </div><div class='input'><span class='co'># }</span> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span> @@ -518,31 +609,33 @@ estimators.</p> <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='co'># Use starting parameters from parent only FOMC fit</span> -<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in (function (t, parent_0, alpha, beta) { parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 0.757575757575758, 1, 1.51515151515152, 2.27272727272727, 3, 3.03030303030303, 3.78787878787879, 4.54545454545454, 5.3030303030303, 6.06060606060606, 6.81818181818182, 7, 7.57575757575758, 8.33333333333333, 9.09090909090909, 9.84848484848485, 10.6060606060606, 11.3636363636364, 12.1212121212121, 12.8787878787879, 13.6363636363636, 14, 14.3939393939394, 15.1515151515152, 15.9090909090909, 16.6666666666667, 17.4242424242424, 18.1818181818182, 18.9393939393939, 19.6969696969697, 20.4545454545455, 21, 21.2121212121212, 21.969696969697, 22.7272727272727, 23.4848484848485, 24.2424242424242, 25, 25.7575757575758, 26.5151515151515, 27.2727272727273, 28.030303030303, 28.7878787878788, 29.5454545454545, 30.3030303030303, 31.0606060606061, 31.8181818181818, 32.5757575757576, 33.3333333333333, 34.0909090909091, 34.8484848484849, 35, 35.6060606060606, 36.3636363636364, 37.1212121212121, 37.8787878787879, 38.6363636363636, 39.3939393939394, 40.1515151515151, 40.9090909090909, 41.6666666666667, 42.4242424242424, 43.1818181818182, 43.9393939393939, 44.6969696969697, 45.4545454545455, 46.2121212121212, 46.969696969697, 47.7272727272727, 48.4848484848485, 49.2424242424242, 50, 50.7575757575758, 51.5151515151515, 52.2727272727273, 53.030303030303, 53.7878787878788, 54.5454545454545, 55.3030303030303, 56.0606060606061, 56.8181818181818, 57.5757575757576, 58.3333333333333, 59.0909090909091, 59.8484848484849, 60.6060606060606, 61.3636363636364, 62.1212121212121, 62.8787878787879, 63.6363636363636, 64.3939393939394, 65.1515151515152, 65.9090909090909, 66.6666666666667, 67.4242424242424, 68.1818181818182, 68.9393939393939, 69.6969696969697, 70.4545454545455, 71.2121212121212, 71.969696969697, 72.7272727272727, 73.4848484848485, 74.2424242424242, 75), parent.0 = c(parent = 100.75), alpha = 1, beta = 10): unbenutztes Argument (parent.0 = 100.75)</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'><span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode): Objekt 'fit.FOMC' nicht gefunden</span></div><div class='input'> +<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span> <span class='no'>SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFORB"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span> -<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in (function (t, parent_0, k_12, k_21, k_1output) { sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21) b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp parent = parent_0 * (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) + ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))})(t = c(0, 0.757575757575758, 1, 1.51515151515152, 2.27272727272727, 3, 3.03030303030303, 3.78787878787879, 4.54545454545454, 5.3030303030303, 6.06060606060606, 6.81818181818182, 7, 7.57575757575758, 8.33333333333333, 9.09090909090909, 9.84848484848485, 10.6060606060606, 11.3636363636364, 12.1212121212121, 12.8787878787879, 13.6363636363636, 14, 14.3939393939394, 15.1515151515152, 15.9090909090909, 16.6666666666667, 17.4242424242424, 18.1818181818182, 18.9393939393939, 19.6969696969697, 20.4545454545455, 21, 21.2121212121212, 21.969696969697, 22.7272727272727, 23.4848484848485, 24.2424242424242, 25, 25.7575757575758, 26.5151515151515, 27.2727272727273, 28.030303030303, 28.7878787878788, 29.5454545454545, 30.3030303030303, 31.0606060606061, 31.8181818181818, 32.5757575757576, 33.3333333333333, 34.0909090909091, 34.8484848484849, 35, 35.6060606060606, 36.3636363636364, 37.1212121212121, 37.8787878787879, 38.6363636363636, 39.3939393939394, 40.1515151515151, 40.9090909090909, 41.6666666666667, 42.4242424242424, 43.1818181818182, 43.9393939393939, 44.6969696969697, 45.4545454545455, 46.2121212121212, 46.969696969697, 47.7272727272727, 48.4848484848485, 49.2424242424242, 50, 50.7575757575758, 51.5151515151515, 52.2727272727273, 53.030303030303, 53.7878787878788, 54.5454545454545, 55.3030303030303, 56.0606060606061, 56.8181818181818, 57.5757575757576, 58.3333333333333, 59.0909090909091, 59.8484848484849, 60.6060606060606, 61.3636363636364, 62.1212121212121, 62.8787878787879, 63.6363636363636, 64.3939393939394, 65.1515151515152, 65.9090909090909, 66.6666666666667, 67.4242424242424, 68.1818181818182, 68.9393939393939, 69.6969696969697, 70.4545454545455, 71.2121212121212, 71.969696969697, 72.7272727272727, 73.4848484848485, 74.2424242424242, 75), parent.0 = c(parent_free = 100.75), k_1output = 0.1, k_12 = 0.1, k_21 = 0.02): unbenutztes Argument (parent.0 = 100.75)</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.001 0 0.001</span></div><div class='input'><span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE): Objekt 'fit.SFORB' nicht gefunden</span></div><div class='input'><span class='co'># }</span> +<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Initial parameter(s) k_parent_free_sink not used in the model</span></div><div class='input'><span class='co'># }</span> <span class='co'># \dontrun{</span> <span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.11 + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50 #> R version used for fitting: 4.0.0 -#> Date of fit: Thu May 7 08:59:03 2020 -#> Date of summary: Thu May 7 08:59:03 2020 +#> Date of fit: Mon May 11 05:14:31 2020 +#> Date of summary: Mon May 11 05:14:31 2020 #> #> Equations: #> 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 422 model solutions performed in 1.106 s +#> Fitted using 421 model solutions performed in 0.124 s #> #> Error model: Constant variance #> @@ -566,6 +659,11 @@ estimators.</p> #> 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 99.60000 1.57000 96.40000 102.8000 @@ -576,11 +674,11 @@ estimators.</p> #> #> Parameter correlation: #> 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 -2.443e-07 -#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.181e-07 -#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.369e-07 -#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -2.287e-08 -#> sigma -2.443e-07 3.181e-07 -1.369e-07 -2.287e-08 1.000e+00 +#> 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. @@ -648,18 +746,18 @@ estimators.</p> #> 100 m1 31.04 31.98163 -9.416e-01 #> 100 m1 33.13 31.98163 1.148e+00 #> 120 m1 25.15 28.78984 -3.640e+00 -#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.11 +#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50 #> R version used for fitting: 4.0.0 -#> Date of fit: Thu May 7 08:59:06 2020 -#> Date of summary: Thu May 7 08:59:06 2020 +#> Date of fit: Mon May 11 05:14:32 2020 +#> Date of summary: Mon May 11 05:14:32 2020 #> #> Equations: #> 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 979 model solutions performed in 2.604 s +#> Fitted using 978 model solutions performed in 0.336 s #> #> Error model: Variance unique to each observed variable #> @@ -688,6 +786,11 @@ estimators.</p> #> value type #> m1_0 0 state #> +#> Results: +#> +#> AIC BIC logLik +#> 205.8727 215.6982 -96.93634 +#> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> parent_0 99.65000 1.70200 96.19000 103.1000 @@ -780,23 +883,23 @@ estimators.</p> #> 100 m1 31.04 31.98773 -9.477e-01 #> 100 m1 33.13 31.98773 1.142e+00 #> 120 m1 25.15 28.80429 -3.654e+00 -#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.11 +#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50 #> R version used for fitting: 4.0.0 -#> Date of fit: Thu May 7 08:59:16 2020 -#> Date of summary: Thu May 7 08:59:16 2020 +#> Date of fit: Mon May 11 05:14:32 2020 +#> Date of summary: Mon May 11 05:14:32 2020 #> #> Equations: #> 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 2552 model solutions performed in 10.544 s +#> Fitted using 1875 model solutions performed in 0.642 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Three-step fitting yielded a higher likelihood than direct fitting +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type @@ -820,6 +923,11 @@ estimators.</p> #> value type #> m1_0 0 state #> +#> Results: +#> +#> AIC BIC logLik +#> 141.9656 151.7911 -64.98278 +#> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> parent_0 100.70000 2.621000 95.400000 106.10000 @@ -868,14 +976,14 @@ estimators.</p> #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 100.73434 -1.274339 -#> 0 parent 102.04 100.73434 1.305661 +#> 0 parent 99.46 100.73434 -1.274340 +#> 0 parent 102.04 100.73434 1.305660 #> 1 parent 93.50 91.09751 2.402486 #> 1 parent 92.50 91.09751 1.402486 #> 3 parent 63.23 74.50141 -11.271410 #> 3 parent 68.99 74.50141 -5.511410 -#> 7 parent 52.32 49.82880 2.491201 -#> 7 parent 55.13 49.82880 5.301201 +#> 7 parent 52.32 49.82880 2.491200 +#> 7 parent 55.13 49.82880 5.301200 #> 14 parent 27.27 24.64809 2.621908 #> 14 parent 26.64 24.64809 1.991908 #> 21 parent 11.50 12.19232 -0.692315 @@ -902,8 +1010,8 @@ estimators.</p> #> 50 m1 40.01 41.34199 -1.331985 #> 75 m1 40.09 36.61471 3.475295 #> 75 m1 33.85 36.61471 -2.764705 -#> 100 m1 31.04 32.20082 -1.160824 -#> 100 m1 33.13 32.20082 0.929176 +#> 100 m1 31.04 32.20082 -1.160823 +#> 100 m1 33.13 32.20082 0.929177 #> 120 m1 25.15 29.04130 -3.891304 #> 120 m1 33.31 29.04130 4.268696</div><div class='input'># } diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 2f2e89d9..81b62ae1 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -237,7 +237,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> -<span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) +<span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)) <span class='co'># One parent compound, one metabolite, both single first order</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( @@ -252,7 +252,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB fileb6a4eaab60.c 2> fileb6a4eaab60.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file1a1abf38df.c 2> file1a1abf38df.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 21c13156..e48a0cdb 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -251,7 +251,8 @@ is 1e-10, much lower than in <code>lsoda</code>.</p></td> <th>map_output</th> <td><p>Boolean to specify if the output should list values for the observed variables (default) or for all state variables (if set to -FALSE).</p></td> +FALSE). Setting this to FALSE has no effect for analytical solutions, +as these always return mapped output.</p></td> </tr> <tr> <th>...</th> @@ -262,7 +263,7 @@ solver is used.</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A matrix in the same format as the output of <code>ode</code>.</p> + <p>A matrix with the numeric solution in wide format</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -270,149 +271,147 @@ solver is used.</p></td> <span class='co'># Compare solution types</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#> time degradinol -#> 1 0 100.0000000 -#> 2 1 74.0818221 -#> 3 2 54.8811636 -#> 4 3 40.6569660 -#> 5 4 30.1194212 -#> 6 5 22.3130160 -#> 7 6 16.5298888 -#> 8 7 12.2456428 -#> 9 8 9.0717953 -#> 10 9 6.7205513 -#> 11 10 4.9787068 -#> 12 11 3.6883167 -#> 13 12 2.7323722 -#> 14 13 2.0241911 -#> 15 14 1.4995577 -#> 16 15 1.1108997 -#> 17 16 0.8229747 -#> 18 17 0.6096747 -#> 19 18 0.4516581 -#> 20 19 0.3345965 -#> 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 0 0 100.0000000 +#> 1 1 74.0818221 +#> 2 2 54.8811636 +#> 3 3 40.6569660 +#> 4 4 30.1194212 +#> 5 5 22.3130160 +#> 6 6 16.5298888 +#> 7 7 12.2456428 +#> 8 8 9.0717953 +#> 9 9 6.7205513 +#> 10 10 4.9787068 +#> 11 11 3.6883167 +#> 12 12 2.7323722 +#> 13 13 2.0241911 +#> 14 14 1.4995577 +#> 15 15 1.1108997 +#> 16 16 0.8229747 +#> 17 17 0.6096747 +#> 18 18 0.4516581 +#> 19 19 0.3345965 +#> 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#> time degradinol -#> 1 0 100.0000000 -#> 2 1 74.0818221 -#> 3 2 54.8811636 -#> 4 3 40.6569660 -#> 5 4 30.1194212 -#> 6 5 22.3130160 -#> 7 6 16.5298888 -#> 8 7 12.2456428 -#> 9 8 9.0717953 -#> 10 9 6.7205513 -#> 11 10 4.9787068 -#> 12 11 3.6883167 -#> 13 12 2.7323722 -#> 14 13 2.0241911 -#> 15 14 1.4995577 -#> 16 15 1.1108996 -#> 17 16 0.8229747 -#> 18 17 0.6096747 -#> 19 18 0.4516581 -#> 20 19 0.3345965 -#> 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 0 0 100.0000000 +#> 1 1 74.0818221 +#> 2 2 54.8811636 +#> 3 3 40.6569660 +#> 4 4 30.1194212 +#> 5 5 22.3130160 +#> 6 6 16.5298888 +#> 7 7 12.2456428 +#> 8 8 9.0717953 +#> 9 9 6.7205513 +#> 10 10 4.9787068 +#> 11 11 3.6883167 +#> 12 12 2.7323722 +#> 13 13 2.0241911 +#> 14 14 1.4995577 +#> 15 15 1.1108996 +#> 16 16 0.8229747 +#> 17 17 0.6096747 +#> 18 18 0.4516581 +#> 19 19 0.3345965 +#> 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> time degradinol -#> 1 0 100.0000000 -#> 2 1 74.0818221 -#> 3 2 54.8811636 -#> 4 3 40.6569660 -#> 5 4 30.1194212 -#> 6 5 22.3130160 -#> 7 6 16.5298888 -#> 8 7 12.2456428 -#> 9 8 9.0717953 -#> 10 9 6.7205513 -#> 11 10 4.9787068 -#> 12 11 3.6883167 -#> 13 12 2.7323722 -#> 14 13 2.0241911 -#> 15 14 1.4995577 -#> 16 15 1.1108996 -#> 17 16 0.8229747 -#> 18 17 0.6096747 -#> 19 18 0.4516581 -#> 20 19 0.3345965 -#> 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 0 0 100.0000000 +#> 1 1 74.0818221 +#> 2 2 54.8811636 +#> 3 3 40.6569660 +#> 4 4 30.1194212 +#> 5 5 22.3130160 +#> 6 6 16.5298888 +#> 7 7 12.2456428 +#> 8 8 9.0717953 +#> 9 9 6.7205513 +#> 10 10 4.9787068 +#> 11 11 3.6883167 +#> 12 12 2.7323722 +#> 13 13 2.0241911 +#> 14 14 1.4995577 +#> 15 15 1.1108996 +#> 16 16 0.8229747 +#> 17 17 0.6096747 +#> 18 18 0.4516581 +#> 19 19 0.3345965 +#> 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#> time degradinol -#> 1 0 100.0000000 -#> 2 1 74.0818221 -#> 3 2 54.8811636 -#> 4 3 40.6569660 -#> 5 4 30.1194212 -#> 6 5 22.3130160 -#> 7 6 16.5298888 -#> 8 7 12.2456428 -#> 9 8 9.0717953 -#> 10 9 6.7205513 -#> 11 10 4.9787068 -#> 12 11 3.6883167 -#> 13 12 2.7323722 -#> 14 13 2.0241911 -#> 15 14 1.4995577 -#> 16 15 1.1108997 -#> 17 16 0.8229747 -#> 18 17 0.6096747 -#> 19 18 0.4516581 -#> 20 19 0.3345965 -#> 21 20 0.2478752</div><div class='input'> +#> 0 0 100.0000000 +#> 1 1 74.0818221 +#> 2 2 54.8811636 +#> 3 3 40.6569660 +#> 4 4 30.1194212 +#> 5 5 22.3130160 +#> 6 6 16.5298888 +#> 7 7 12.2456428 +#> 8 8 9.0717953 +#> 9 9 6.7205513 +#> 10 10 4.9787068 +#> 11 11 3.6883167 +#> 12 12 2.7323722 +#> 13 13 2.0241911 +#> 14 14 1.4995577 +#> 15 15 1.1108997 +#> 16 16 0.8229747 +#> 17 17 0.6096747 +#> 18 18 0.4516581 +#> 19 19 0.3345965 +#> 20 20 0.2478752</div><div class='input'> <span class='co'># Compare integration methods to analytical solution</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, - <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, - <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, - <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2480043</div><div class='input'><span class='co'># rk4 is not as precise here</span> + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol +#> 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol +#> 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol +#> 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol +#> 20.0000000 0.2480043 </div><div class='input'><span class='co'># rk4 is not as precise here</span> <span class='co'># The number of output times used to make a lot of difference until the</span> <span class='co'># default for atol was adjusted</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), - <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#> time degradinol -#> 201 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), - <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#> time degradinol -#> 2001 20 0.2478752</div><div class='input'> -<span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span> + <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#> time degradinol +#> 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), + <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#> time degradinol +#> 20.0000000 0.2478752 </div><div class='input'> +<span class='co'># Comparison of the performance of solution types</span> <span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) { - <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>( - <span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) { + <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(<span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>order</span> <span class='kw'>=</span> <span class='st'>"relative"</span>, <span class='kw'>columns</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"test"</span>, <span class='st'>"relative"</span>, <span class='st'>"elapsed"</span>), + <span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>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'>0.15</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='fl'>0.01</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='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,], <span class='kw'>deSolve_compiled</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</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='fl'>0.01</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='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,], - <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), - <span class='fu'><a href='https://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='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,], - <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>10</span>) -}</div><div class='output co'>#> <span class='message'>Lade nötiges Paket: rbenchmark</span></div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child -#> 3 deSolve 10 0.229 28.625 0.229 0 0 -#> 2 deSolve_compiled 10 0.008 1.000 0.008 0 0 -#> 1 eigen 10 0.026 3.250 0.025 0 0 -#> sys.child -#> 3 0 -#> 2 0 -#> 1 0</div><div class='input'> -<span class='co'># Since mkin 0.9.49.11 we also have analytical solutions for some models, including SFO-SFO</span> -<span class='co'># deSolve = mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),</span> -<span class='co'># c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),</span> -<span class='co'># solution_type = "analytical", use_compiled = FALSE)[201,],</span> - + <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>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'>0.15</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='fl'>0.01</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='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,], + <span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>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'>0.15</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='fl'>0.01</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='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]) +}</div><div class='output co'>#> test relative elapsed +#> 4 analytical 1.00 0.004 +#> 2 deSolve_compiled 1.25 0.005 +#> 1 eigen 5.00 0.020 +#> 3 deSolve 54.25 0.217</div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#> time parent m1 -#> 1 0.0 82.49216 0.000000 -#> 2 0.1 80.00563 1.179963 -#> 3 0.2 77.59404 2.312596 -#> 4 0.3 75.25515 3.399443 -#> 5 0.4 72.98675 4.442000 -#> 6 0.5 70.78673 5.441717</div><div class='input'># } + <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>) + <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#> time parent m1 +#> 0 0.0 82.49216 0.000000 +#> 0.1 0.1 80.00562 1.236198 +#> 0.2 0.2 77.59404 2.422818 +#> 0.3 0.3 75.25514 3.561476 +#> 0.4 0.4 72.98675 4.653740 +#> 0.5 0.5 70.78673 5.701130</div><div class='input'># } </div></pre> </div> diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png Binary files differindex 0fe3c263..c6a415d7 100644 --- a/docs/reference/plot.mkinfit-1.png +++ b/docs/reference/plot.mkinfit-1.png diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 72bc331e..5dd3731e 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 6910ae47..59cf8f8d 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 8d399598..d9867952 100644 --- 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src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<script 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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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -39,7 +43,6 @@ <meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters from a previous successful call to mkinfit and plots the observed data together with the solution of the fitted model." /> -<meta name="twitter:card" content="summary" /> @@ -57,7 +60,7 @@ observed data together with the solution of the fitted model." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -71,7 +74,7 @@ observed data together with the solution of the fitted model." /> </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">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> </span> </div> @@ -115,7 +118,12 @@ observed data together with the solution of the fitted model." /> </li> </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 --> @@ -130,7 +138,7 @@ observed data together with the solution of the fitted model." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the observed data and the fitted model of an mkinfit object</h1> - + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><code>R/plot.mkinfit.R</code></a></small> <div class="hidden name"><code>plot.mkinfit.Rd</code></div> </div> @@ -141,7 +149,7 @@ observed data together with the solution of the fitted model.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>( <span class='no'>x</span>, <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), @@ -303,7 +311,7 @@ chi2 error percentage.</p></td> </tr> <tr> <th>...</th> - <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></code>.</p></td> + <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/base/plot.html'>plot</a></code>.</p></td> </tr> <tr> <th>standardized</th> @@ -327,29 +335,22 @@ latex is being used for the formatting of the chi2 error level, if <span class='co'># parent to sink included</span> <span class='co'># \dontrun{</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately, with residuals</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span> <span class='fu'>plot_sep</span>(<span class='no'>fit</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>))</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately, with the error model</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-7.png' alt='' width='700' height='433' /></div><div class='input'># } </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> </div> </div> @@ -360,7 +361,7 @@ latex is being used for the formatting of the chi2 error level, if </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> |
