diff options
Diffstat (limited to 'docs/reference/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 276 |
1 files changed, 276 insertions, 0 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html new file mode 100644 index 00000000..3b8be856 --- /dev/null +++ b/docs/reference/transform_odeparms.html @@ -0,0 +1,276 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>transform_odeparms. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <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>ilr</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>mkinfit</code>.</p> + + + <pre><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <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>mkinmod</code>, containing the names of + the model variables that are needed for grouping the formation fractions + before <code>ilr</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>ilr</code> + transformation. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A vector of transformed or backtransformed parameters with the same names + as the original parameters.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><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'>list</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'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.1 +#> Date of fit: Thu Oct 6 09:18:08 2016 +#> Date of summary: Thu Oct 6 09:18:08 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 0.636 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='co'>## Not run: ------------------------------------</span> +<span class='co'># fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span> +<span class='co'># summary(fit.2, data=FALSE) </span> +<span class='co'>## ---------------------------------------------</span> + +<span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> +<span class='fu'>names</span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start</span>) +<span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> +<span class='fu'>names</span>(<span class='no'>transformed</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>) +<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> 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='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> 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='co'>## Not run: ------------------------------------</span> +<span class='co'># # The case of formation fractions</span> +<span class='co'># SFO_SFO.ff <- mkinmod(</span> +<span class='co'># parent = list(type = "SFO", to = "m1", sink = TRUE),</span> +<span class='co'># m1 = list(type = "SFO"),</span> +<span class='co'># use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span> +<span class='co'># summary(fit.ff, data = FALSE)</span> +<span class='co'># initials <- c("f_parent_to_m1" = 0.5)</span> +<span class='co'># transformed <- transform_odeparms(initials, SFO_SFO.ff)</span> +<span class='co'># backtransform_odeparms(transformed, SFO_SFO.ff)</span> +<span class='co'># </span> +<span class='co'># # And without sink</span> +<span class='co'># SFO_SFO.ff.2 <- mkinmod(</span> +<span class='co'># parent = list(type = "SFO", to = "m1", sink = FALSE),</span> +<span class='co'># m1 = list(type = "SFO"),</span> +<span class='co'># use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># </span> +<span class='co'># fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)</span> +<span class='co'># summary(fit.ff.2, data = FALSE)</span> +<span class='co'>## ---------------------------------------------</span></div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> |