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authorJohannes Ranke <johannes.ranke@jrwb.de>2025-02-13 12:43:29 +0100
committerJohannes Ranke <johannes.ranke@jrwb.de>2025-02-13 13:48:57 +0100
commit328d1173db2395c1a5705b5f0980e2956db8be1f (patch)
treece7eb2d2476230c0b8935eeb2d42b5234479e670 /docs/reference/mkinpredict.html
parentba3eaa0d61d4980a61ebbcd105f07d21dd2aabb6 (diff)
Update wordlist, bump date and simplify DESCRIPTION
Also, the R-Universe URL that the badge points to is updated
Diffstat (limited to 'docs/reference/mkinpredict.html')
-rw-r--r--docs/reference/mkinpredict.html158
1 files changed, 73 insertions, 85 deletions
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 860c7cfc..13f42da0 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -1,78 +1,65 @@
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kinetic model as specified by mkinmod, using a specific set of
-kinetic parameters and initial values for the state variables."><title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict"><meta property="og:description" content="This function produces a time series for all the observed variables in a
+kinetic parameters and initial values for the state variables."><meta property="og:description" content="This function produces a time series for all the observed variables in a
kinetic model as specified by mkinmod, using a specific set of
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- <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">#&gt;</span> Loading required package: rbenchmark</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> test relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4 analytical 1 0.001</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled 2 0.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 eigen 8 0.008</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3 deSolve 64 0.064</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled 1.0 0.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 eigen 3.5 0.007</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 analytical 4.0 0.008</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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>
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