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diff --git a/docs/transform_odeparms.html b/docs/transform_odeparms.html deleted file mode 100644 index 6f48b1fa..00000000 --- a/docs/transform_odeparms.html +++ /dev/null @@ -1,281 +0,0 @@ -<!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> - 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