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Diffstat (limited to 'docs/reference/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 110 |
1 files changed, 59 insertions, 51 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index e1fb0437..c14740c2 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -25,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -70,8 +72,14 @@ <li> <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -102,54 +110,54 @@ 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 +<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> - <pre><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, + <pre class="usage"><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 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> 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><a href='mkinmod.html'>mkinmod</a></code>, containing the names of + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>parms</th> + <td><p>Parameters of kinetic models as used in the differential equations.</p></td> + </tr> + <tr> + <th>transparms</th> + <td><p>Transformed parameters of kinetic models as used in the fitting procedure.</p></td> + </tr> + <tr> + <th>mkinmod</th> + <td><p>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 + the information if the pathway to sink is included in the model.</p></td> + </tr> + <tr> + <th>transform_rates</th> + <td><p>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 + of the HS model.</p></td> + </tr> + <tr> + <th>transform_fractions</th> + <td><p>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> + transformation.</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -162,10 +170,10 @@ <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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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'><a href='mkinfit.html'>mkinfit</a></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: 3.3.2 -#> Date of fit: Thu Dec 8 07:57:59 2016 -#> Date of summary: Thu Dec 8 07:57:59 2016 +<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: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:46:24 2017 +#> Date of summary: Fri May 5 12:46:24 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -173,7 +181,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.621 s +#> Fitted with method Port using 153 model solutions performed in 0.61 s #> #> Weighting: none #> @@ -207,7 +215,7 @@ #> 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 +#> log_k_m1_sink -0.17006 -0.6253 0.47164 1.0000 #> #> Residual standard error: 3.211 on 36 degrees of freedom #> @@ -239,10 +247,10 @@ #> m1 131.761 437.70</div><div class='input'> <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:58:01 2016 -#> Date of summary: Thu Dec 8 07:58:01 2016 +<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:46:26 2017 +#> Date of summary: Fri May 5 12:46:26 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -250,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 327 model solutions performed in 1.419 s +#> Fitted with method Port using 352 model solutions performed in 1.437 s #> #> Weighting: none #> @@ -329,10 +337,10 @@ <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>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</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.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:58:02 2016 -#> Date of summary: Thu Dec 8 07:58:02 2016 +<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:46:27 2017 +#> Date of summary: Fri May 5 12:46:27 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -340,7 +348,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.814 s +#> Fitted with method Port using 185 model solutions performed in 0.776 s #> #> Weighting: none #> @@ -413,10 +421,10 @@ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</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.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:58:03 2016 -#> Date of summary: Thu Dec 8 07:58:03 2016 +<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:46:28 2017 +#> Date of summary: Fri May 5 12:46:28 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -424,7 +432,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.436 s +#> Fitted with method Port using 104 model solutions performed in 0.433 s #> #> Weighting: none #> @@ -463,7 +471,7 @@ #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper -#> parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000 +#> parent_0 84.79000 28.600 3.938e-27 78.78000 90.80000 #> k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483 #> k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853 #> |