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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
| commit | a77a10ea6c607346778ba0700b3b66ac393101a2 (patch) | |
| tree | e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/summary.mkinfit.html | |
| parent | 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff) | |
Create up to date pkgdown docs in development mode
Diffstat (limited to 'docs/dev/reference/summary.mkinfit.html')
| -rw-r--r-- | docs/dev/reference/summary.mkinfit.html | 337 |
1 files changed, 337 insertions, 0 deletions
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class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/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> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Summary method for class "mkinfit"</h1> + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/summary.mkinfit.R'><code>R/summary.mkinfit.R</code></a></small> + <div class="hidden name"><code>summary.mkinfit.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Lists model equations, initial parameter values, optimised parameters with +some uncertainty statistics, the chi2 error levels calculated according to +FOCUS guidance (2006) as defined therein, formation fractions, DT50 values +and optionally the data, consisting of observed, predicted and residual +values.</p> + </div> + + <pre class="usage"><span class='co'># S3 method for mkinfit</span> +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for summary.mkinfit</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + </tr> + <tr> + <th>data</th> + <td><p>logical, indicating whether the data should be included in the +summary.</p></td> + </tr> + <tr> + <th>distimes</th> + <td><p>logical, indicating whether DT50 and DT90 values should be +included.</p></td> + </tr> + <tr> + <th>alpha</th> + <td><p>error level for confidence interval estimation from t +distribution</p></td> + </tr> + <tr> + <th>...</th> + <td><p>optional arguments passed to methods like <code>print</code>.</p></td> + </tr> + <tr> + <th>x</th> + <td><p>an object of class <code>summary.mkinfit</code>.</p></td> + </tr> + <tr> + <th>digits</th> + <td><p>Number of digits to use for printing</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The summary function returns a list with components, among others</p> +<dt>version, Rversion</dt><dd><p>The mkin and R versions used</p></dd> +<dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were +produced</p></dd> +<dt>diffs</dt><dd><p>The differential equations used in the model</p></dd> +<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd> +<dt>bpar</dt><dd><p>Optimised and backtransformed +parameters</p></dd> +<dt>data</dt><dd><p>The data (see Description above).</p></dd> +<dt>start</dt><dd><p>The starting values and bounds, if applicable, for optimised +parameters.</p></dd> +<dt>fixed</dt><dd><p>The values of fixed parameters.</p></dd> +<dt>errmin </dt><dd><p>The chi2 error levels for +each observed variable.</p></dd> +<dt>bparms.ode</dt><dd><p>All backtransformed ODE +parameters, for use as starting parameters for related models.</p></dd> +<dt>errparms</dt><dd><p>Error model parameters.</p></dd> +<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted +model.</p></dd> +<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> +<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> +The print method is called for its side effect, i.e. printing the summary. + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.50.3 +#> R version used for fitting: 4.0.0 +#> Date of fit: Wed May 27 06:02:05 2020 +#> Date of summary: Wed May 27 06:02:05 2020 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> +#> Model predictions using solution type analytical +#> +#> Fitted using 131 model solutions performed in 0.027 s +#> +#> Error model: Constant variance +#> +#> Error model algorithm: OLS +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 101.24 state +#> k_parent 0.10 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 101.240000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> +#> Fixed parameter values: +#> None +#> +#> Results: +#> +#> AIC BIC logLik +#> 55.28197 55.5203 -24.64099 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 109.200 3.70400 99.630 118.700 +#> log_k_parent -3.291 0.09176 -3.527 -3.055 +#> sigma 5.266 1.31600 1.882 8.649 +#> +#> Parameter correlation: +#> parent_0 log_k_parent sigma +#> parent_0 1.000e+00 5.428e-01 1.648e-07 +#> log_k_parent 5.428e-01 1.000e+00 2.513e-07 +#> sigma 1.648e-07 2.513e-07 1.000e+00 +#> +#> 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_0 109.20000 29.47 4.218e-07 99.6300 118.70000 +#> k_parent 0.03722 10.90 5.650e-05 0.0294 0.04712 +#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 +#> +#> FOCUS Chi2 error levels in percent: +#> err.min n.optim df +#> All data 8.385 2 6 +#> parent 8.385 2 6 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 18.62 61.87 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 101.24 109.153 -7.9132 +#> 3 parent 99.27 97.622 1.6484 +#> 7 parent 90.11 84.119 5.9913 +#> 14 parent 72.19 64.826 7.3641 +#> 30 parent 29.71 35.738 -6.0283 +#> 62 parent 5.98 10.862 -4.8818 +#> 90 parent 1.54 3.831 -2.2911 +#> 118 parent 0.39 1.351 -0.9613</div><div class='input'> +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |