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diff --git a/docs/transform_odeparms.html b/docs/transform_odeparms.html new file mode 100644 index 00000000..6f48b1fa --- /dev/null +++ b/docs/transform_odeparms.html @@ -0,0 +1,281 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>transform_odeparms. mkin 0.9.44.9000</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=" + Johannes Ranke +"> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="index.html">mkin 0.9.44.9000</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html">Home</a></li> + <li><a href="reference.html">Reference</a></li> + </ul> + </div> + </div> + </div> +</div> + + + <div class="container"> + <header> + + </header> + + <h1> + Functions to transform and backtransform kinetic parameters for fitting +</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><span class="functioncall"><a href='transform_odeparms.html'>transform_odeparms</a></span><span class="keyword">(</span><span class="symbol">parms</span><span class="keyword">,</span> <span class="symbol">mkinmod</span><span class="keyword">,</span> + <span class="argument">transform_rates</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">transform_fractions</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span> +<span class="functioncall"><a href='transform_odeparms.html'>backtransform_odeparms</a></span><span class="keyword">(</span><span class="symbol">transparms</span><span class="keyword">,</span> <span class="symbol">mkinmod</span><span class="keyword">,</span> + <span class="argument">transform_rates</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">transform_fractions</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></pre> + + <h2>Arguments</h2> + <dl> + <dt>parms</dt> + <dd> + Parameters of kinetic models as used in the differential equations. + </dd> + <dt>transparms</dt> + <dd> + Transformed parameters of kinetic models as used in the fitting procedure. + </dd> + <dt>mkinmod</dt> + <dd> + The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of + the model variables that are needed for grouping the formation fractions + before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and + the information if the pathway to sink is included in the model. + </dd> + <dt>transform_rates</dt> + <dd> + Boolean specifying if kinetic rate constants should be transformed in the + model specification used in the fitting for better compliance with the + assumption of normal distribution of the estimator. If TRUE, also + alpha and beta parameters of the FOMC model are log-transformed, as well + as k1 and k2 rate constants for the DFOP and HS models and the break point tb + of the HS model. + </dd> + <dt>transform_fractions</dt> + <dd> + Boolean specifying if formation fractions constants should be transformed in the + model specification used in the fitting for better compliance with the + assumption of normal distribution of the estimator. The default (TRUE) is + to do transformations. The g parameter of the DFOP and HS models are also + transformed, as they can also be seen as compositional data. The + transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> + transformation. + </dd> + </dl> + + <div class="Description"> + <h2>Description</h2> + + <p>The transformations are intended to map parameters that should only take + on restricted values to the full scale of real numbers. For kinetic rate + constants and other paramters that can only take on positive values, a + simple log transformation is used. For compositional parameters, such as + the formations fractions that should always sum up to 1 and can not be + negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> + + <p>The transformation of sets of formation fractions is fragile, as it supposes + the same ordering of the components in forward and backward transformation. + This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p> + + </div> + + <div class="Value"> + <h2>Value</h2> + + <p><dl> + A vector of transformed or backtransformed parameters with the same names + as the original parameters. +</dl></p> + + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class="symbol">SFO_SFO</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span> + <span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">to</span> <span class="argument">=</span> <span class="string">"m1"</span><span class="keyword">,</span> <span class="argument">sink</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span></div> +<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> +<div class='input'><span class="comment"># Fit the model to the FOCUS example dataset D using defaults</span> +<span class="symbol">fit</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO</span><span class="keyword">,</span> <span class="symbol">FOCUS_2006_D</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">data</span><span class="argument">=</span><span class="number">FALSE</span><span class="keyword">)</span> <span class="comment"># See transformed and backtransformed parameters</span></div> +<div class='output'>mkin version: 0.9.44.9000 +R version: 3.3.1 +Date of fit: Sat Sep 10 05:53:13 2016 +Date of summary: Sat Sep 10 05:53:13 2016 + +Equations: +d_parent = - k_parent_sink * parent - k_parent_m1 * parent +d_m1 = + k_parent_m1 * parent - k_m1_sink * m1 + +Model predictions using solution type deSolve + +Fitted with method Port using 153 model solutions performed in 0.634 s + +Weighting: none + +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 + +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 + +Fixed parameter values: + value type +m1_0 0 state + +Optimised, transformed parameters with symmetric confidence intervals: + Estimate Std. Error Lower Upper +parent_0 99.600 1.61400 96.330 102.900 +log_k_parent_sink -3.038 0.07826 -3.197 -2.879 +log_k_parent_m1 -2.980 0.04124 -3.064 -2.897 +log_k_m1_sink -5.248 0.13610 -5.523 -4.972 + +Parameter correlation: + parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +parent_0 1.00000 0.6075 -0.06625 -0.1701 +log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +log_k_m1_sink -0.17006 -0.6253 0.47163 1.0000 + +Residual standard error: 3.211 on 36 degrees of freedom + +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 61.720 2.024e-38 96.330000 1.029e+02 +k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02 +k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02 +k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03 + +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 + +Resulting formation fractions: + ff +parent_sink 0.4855 +parent_m1 0.5145 +m1_sink 1.0000 + +Estimated disappearance times: + DT50 DT90 +parent 7.023 23.33 +m1 131.761 437.70 +</div> +<div class='input'> +<span class="comment">## Not run: ------------------------------------</span> +<span class="comment"># fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span> +<span class="comment"># summary(fit.2, data=FALSE) </span> +<span class="comment">## ---------------------------------------------</span> + +<span class="symbol">initials</span> <span class="assignement"><-</span> <span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">start</span><span class="keyword">$</span><span class="symbol">value</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/names'>names</a></span><span class="keyword">(</span><span class="symbol">initials</span><span class="keyword">)</span> <span class="assignement"><-</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">start</span><span class="keyword">)</span> +<span class="symbol">transformed</span> <span class="assignement"><-</span> <span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">start_transformed</span><span class="keyword">$</span><span class="symbol">value</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/names'>names</a></span><span class="keyword">(</span><span class="symbol">transformed</span><span class="keyword">)</span> <span class="assignement"><-</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">start_transformed</span><span class="keyword">)</span> +<span class="functioncall"><a href='transform_odeparms.html'>transform_odeparms</a></span><span class="keyword">(</span><span class="symbol">initials</span><span class="keyword">,</span> <span class="symbol">SFO_SFO</span><span class="keyword">)</span></div> +<div class='output'> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink + 100.750000 -2.302585 -2.301586 -2.300587 +</div> +<div class='input'><span class="functioncall"><a href='transform_odeparms.html'>backtransform_odeparms</a></span><span class="keyword">(</span><span class="symbol">transformed</span><span class="keyword">,</span> <span class="symbol">SFO_SFO</span><span class="keyword">)</span></div> +<div class='output'> parent_0 k_parent_sink k_parent_m1 k_m1_sink + 100.7500 0.1000 0.1001 0.1002 +</div> +<div class='input'> +<span class="comment">## Not run: ------------------------------------</span> +<span class="comment"># # The case of formation fractions</span> +<span class="comment"># SFO_SFO.ff <- mkinmod(</span> +<span class="comment"># parent = list(type = "SFO", to = "m1", sink = TRUE),</span> +<span class="comment"># m1 = list(type = "SFO"),</span> +<span class="comment"># use_of_ff = "max")</span> +<span class="comment"># </span> +<span class="comment"># fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span> +<span class="comment"># summary(fit.ff, data = FALSE)</span> +<span class="comment"># initials <- c("f_parent_to_m1" = 0.5)</span> +<span class="comment"># transformed <- transform_odeparms(initials, SFO_SFO.ff)</span> +<span class="comment"># backtransform_odeparms(transformed, SFO_SFO.ff)</span> +<span class="comment"># </span> +<span class="comment"># # And without sink</span> +<span class="comment"># SFO_SFO.ff.2 <- mkinmod(</span> +<span class="comment"># parent = list(type = "SFO", to = "m1", sink = FALSE),</span> +<span class="comment"># m1 = list(type = "SFO"),</span> +<span class="comment"># use_of_ff = "max")</span> +<span class="comment"># </span> +<span class="comment"># </span> +<span class="comment"># fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)</span> +<span class="comment"># summary(fit.ff.2, data = FALSE)</span> +<span class="comment">## ---------------------------------------------</span></div></pre> + </div> + <div class="span4 sidebar"> + <!-- <ul> + <li>transform_odeparms</li><li>backtransform_odeparms</li> + </ul> + <ul> + <li> manip </li> + </ul> --> + + + + <h2>Author</h2> + + Johannes Ranke + + + </div> +</div> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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