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function produces a time series for all the observed variables in a kinetic model as specified by mkinmod, using a specific set of -kinetic parameters and initial values for the state variables."><!-- 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> +kinetic parameters and initial values for the state variables."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-default navbar-expand-lg 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modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" 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class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Produce predictions from a kinetic model using specific parameters</h1> + + <h1>Produce predictions from a kinetic model using specific parameters</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinpredict.R" class="external-link"><code>R/mkinpredict.R</code></a></small> <div class="d-none name"><code>mkinpredict.Rd</code></div> </div> @@ -87,7 +74,7 @@ kinetic parameters and initial values for the state variables.</p> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">x</span>, <span class="va">odeparms</span>, <span class="va">odeini</span>, <span class="va">outtimes</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for mkinmod</span></span> +<span><span class="co"># S3 method for class 'mkinmod'</span></span> <span><span class="fu">mkinpredict</span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> <span> odeparms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent_sink <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> @@ -105,7 +92,7 @@ kinetic parameters and initial values for the state variables.</p> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="co"># S3 method for class 'mkinfit'</span></span> <span><span class="fu">mkinpredict</span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> <span> odeparms <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> @@ -123,35 +110,37 @@ kinetic parameters and initial values for the state variables.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>x</dt> + + +<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>A kinetic model as produced by <a href="mkinmod.html">mkinmod</a>, or a kinetic fit as fitted by <a href="mkinfit.html">mkinfit</a>. In the latter case, the fitted parameters are used for the prediction.</p></dd> -<dt>odeparms</dt> +<dt id="arg-odeparms">odeparms<a class="anchor" aria-label="anchor" href="#arg-odeparms"></a></dt> <dd><p>A numeric vector specifying the parameters used in the kinetic model, which is generally defined as a set of ordinary differential equations.</p></dd> -<dt>odeini</dt> +<dt id="arg-odeini">odeini<a class="anchor" aria-label="anchor" href="#arg-odeini"></a></dt> <dd><p>A numeric vector containing the initial values of the state variables of the model. Note that the state variables can differ from the observed variables, for example in the case of the SFORB model.</p></dd> -<dt>outtimes</dt> +<dt id="arg-outtimes">outtimes<a class="anchor" aria-label="anchor" href="#arg-outtimes"></a></dt> <dd><p>A numeric vector specifying the time points for which model predictions should be generated.</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further arguments passed to the ode solver in case such a solver is used.</p></dd> -<dt>solution_type</dt> +<dt id="arg-solution-type">solution_type<a class="anchor" aria-label="anchor" href="#arg-solution-type"></a></dt> <dd><p>The method that should be used for producing the predictions. This should generally be "analytical" if there is only one observed variable, and usually "deSolve" in the case of several observed @@ -160,50 +149,48 @@ ODE models, but not applicable to some models, e.g. using FOMC for the parent compound.</p></dd> -<dt>use_compiled</dt> +<dt id="arg-use-compiled">use_compiled<a class="anchor" aria-label="anchor" href="#arg-use-compiled"></a></dt> <dd><p>If set to <code>FALSE</code>, no compiled version of the <a href="mkinmod.html">mkinmod</a> model is used, even if is present.</p></dd> -<dt>use_symbols</dt> +<dt id="arg-use-symbols">use_symbols<a class="anchor" aria-label="anchor" href="#arg-use-symbols"></a></dt> <dd><p>If set to <code>TRUE</code> (default), symbol info present in the <a href="mkinmod.html">mkinmod</a> object is used if available for accessing compiled code</p></dd> -<dt>method.ode</dt> -<dd><p>The solution method passed via mkinpredict to ode] in +<dt id="arg-method-ode">method.ode<a class="anchor" aria-label="anchor" href="#arg-method-ode"></a></dt> +<dd><p>The solution method passed via mkinpredict to <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code> in case the solution type is "deSolve" and we are not using compiled code. When using compiled code, only lsoda is supported.</p></dd> -<dt>atol</dt> +<dt id="arg-atol">atol<a class="anchor" aria-label="anchor" href="#arg-atol"></a></dt> <dd><p>Absolute error tolerance, passed to the ode solver.</p></dd> -<dt>rtol</dt> +<dt id="arg-rtol">rtol<a class="anchor" aria-label="anchor" href="#arg-rtol"></a></dt> <dd><p>Absolute error tolerance, passed to the ode solver.</p></dd> -<dt>maxsteps</dt> +<dt id="arg-maxsteps">maxsteps<a class="anchor" aria-label="anchor" href="#arg-maxsteps"></a></dt> <dd><p>Maximum number of steps, passed to the ode solver.</p></dd> -<dt>map_output</dt> +<dt id="arg-map-output">map_output<a class="anchor" aria-label="anchor" href="#arg-map-output"></a></dt> <dd><p>Boolean to specify if the output should list values for the observed variables (default) or for all state variables (if set to FALSE). Setting this to FALSE has no effect for analytical solutions, as these always return mapped output.</p></dd> -<dt>na_stop</dt> -<dd><p>Should it be an error if ode returns NaN values</p></dd> +<dt id="arg-na-stop">na_stop<a class="anchor" aria-label="anchor" href="#arg-na-stop"></a></dt> +<dd><p>Should it be an error if <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code> returns NaN values</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A matrix with the numeric solution in wide format</p> + <p>A matrix with the numeric solution in wide format</p> </div> <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> @@ -365,11 +352,12 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1 0.001</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 2 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 8 0.008</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 64 0.064</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 3.5 0.007</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 4.0 0.008</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 31.5 0.063</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> @@ -381,23 +369,23 @@ as these always return mapped output.</p></dd> <span class="r-in"><span></span></span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 9583da2a..ecb71d6c 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex 02aa0573..e3a6e226 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index d94e4bbe..0eaba377 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -1,80 +1,67 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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They are used internally by the nlme.mmkin() method."><meta property="og:description" content="These functions facilitate setting up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of -datasets. They are used internally by the nlme.mmkin() method."><!-- 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> +datasets. They are used internally by the nlme.mmkin() method."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.6</small> + <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - 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+ </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Helper functions to create nlme models from mmkin row objects</h1> + + <h1>Helper functions to create nlme models from mmkin row objects</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.R" class="external-link"><code>R/nlme.R</code></a></small> <div class="d-none name"><code>nlme.Rd</code></div> </div> @@ -95,18 +82,16 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>object</dt> + + +<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt> <dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A function that can be used with nlme</p> - - -<p>A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> + <p>A function that can be used with nlme</p> +<p>A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">nlme::groupedData</a></code> object</p> </div> <div class="section level2"> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> @@ -156,28 +141,28 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m <span class="r-out co"><span class="r-pr">#></span> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) </span> <span class="r-out co"><span class="r-pr">#></span> Data: grouped_data </span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 266.6428 275.8935 -128.3214</span> +<span class="r-out co"><span class="r-pr">#></span> 298.2781 307.7372 -144.1391</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)</span> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 0.0003775775 0.7058039 3.065183</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 0.9376498 0.7098079 3.835419</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects: parent_0 + log_k_parent_sink ~ 1 </span> -<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 101.18323 0.7900461 43 128.07257 0</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.08708 0.4171755 43 -7.39995 0</span> +<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.76810 1.1445941 45 88.91196 0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.05445 0.4195607 45 -7.28011 0</span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> prnt_0</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.031 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.034 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Standardized Within-Group Residuals:</span> <span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> -<span class="r-out co"><span class="r-pr">#></span> -2.38427070 -0.52059848 0.03593021 0.39987268 2.73188969 </span> +<span class="r-out co"><span class="r-pr">#></span> -2.61695902 -0.21869858 0.05745687 0.57209490 3.04575223 </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 47</span> +<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 49</span> <span class="r-out co"><span class="r-pr">#></span> Number of Groups: 3 </span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme-1.png" alt="" width="700" height="433"></span> @@ -190,23 +175,23 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m <span class="r-plt img"><img src="nlme-2.png" alt="" width="700" height="433"></span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> </footer></div> - - + + </body></html> |
