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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
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-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>Function reference. mkin 0.9.44.9000</title>
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- <div class="container">
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- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
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-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <div class="row">
- <div class="span8">
- <h2>Function reference</h2>
-
- <h3>Main functions</h3>
- <p>Essential functionality</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="mkinmod.html">mkinmod</a></code><br />
- Function to set up a kinetic model with one or more state variables
-</li>
-
- <li>
- <code><a href="mkinfit.html">mkinfit</a></code><br />
- Fit a kinetic model to data with one or more state variables
-</li>
-
- <li>
- <code><a href="mmkin.html">mmkin</a></code><br />
- Fit one or more kinetic models with one or more state variables to one or more datasets
-</li>
-
- </ul>
- <h3>Show results</h3>
- <p>Functions working on mkinfit objects</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>(plot_sep)<br />
- Plot the observed data and the fitted model of an mkinfit object
-</li>
-
- <li>
- <code><a href="summary.mkinfit.html">summary.mkinfit</a></code>(print.summary.mkinfit)<br />
- Summary method for class &quot;mkinfit&quot;
-</li>
-
- <li>
- <code><a href="mkinresplot.html">mkinresplot</a></code><br />
- Function to plot residuals stored in an mkin object
-</li>
-
- <li>
- <code><a href="mkinparplot.html">mkinparplot</a></code><br />
- Function to plot the confidence intervals obtained using
- <code><a href='mkinfit.html'>mkinfit</a></code>
-</li>
-
- <li>
- <code><a href="endpoints.html">endpoints</a></code><br />
-Function to calculate endpoints for further use from kinetic models fitted with mkinfit
-</li>
-
- <li>
- <code><a href="mkinerrmin.html">mkinerrmin</a></code><br />
-Calculate the minimum error to assume in order to pass the variance test
-</li>
-
- </ul>
- <h3>Work with mmkin objects</h3>
- <p>Functions working with aggregated results</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="Extract.mmkin.html">[.mmkin</a></code><br />Subsetting method for mmkin objects</li>
-
- <li>
- <code><a href="plot.mmkin.html">plot.mmkin</a></code><br />
- Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
-</li>
-
- </ul>
- <h3>Datasets and known results</h3>
-
-
- <ul class="index">
-
- <li>
- <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_datasets</a></code>(FOCUS_2006_A, FOCUS_2006_B, FOCUS_2006_C, FOCUS_2006_D, FOCUS_2006_E, FOCUS_2006_F)<br />
-Datasets A to F from the FOCUS Kinetics report from 2006
-</li>
-
- <li>
- <code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code><br />
-Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
-</li>
-
- <li>
- <code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code><br />
-Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
-</li>
-
- <li>
- <code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code><br />
-Results of fitting the HS model to Datasets A to F of FOCUS (2006)
-</li>
-
- <li>
- <code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code><br />
-Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
-</li>
-
- <li>
- <code><a href="mccall81_245T.html">mccall81_245T</a></code><br />
- Datasets on aerobic soil metabolism of 2,4,5-T in six soils
-</li>
-
- <li>
- <code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code>(schaefer07_complex_results)<br />
- Metabolism data set used for checking the software quality of KinGUI
-</li>
-
- <li>
- <code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code><br />
- Synthetic datasets for one parent compound with two metabolites
-</li>
-
- </ul>
- <h3>Helper functions</h3>
-
-
- <ul class="index">
-
- <li>
- <code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code><br />
- Convert a dataframe with observations over time into long format
-</li>
-
- <li>
- <code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code><br />
- Convert a dataframe from long to wide format
-</li>
-
- <li>
- <code><a href="mkinsub.html">mkinsub</a></code><br />
- Function to set up a kinetic submodel for one state variable
-</li>
-
- <li>
- <code><a href="mkinds.html">mkinds</a></code><br />A dataset class for mkin</li>
-
- <li>
- <code><a href="print.mkinds.html">print.mkinds</a></code><br />
- Print mkinds objects
-</li>
-
- <li>
- <code><a href="print.mkinmod.html">print.mkinmod</a></code><br />
- Print mkinmod objects
-</li>
-
- <li>
- <code><a href="mkinpredict.html">mkinpredict</a></code><br />
- Produce predictions from a kinetic model using specific parameters
-</li>
-
- <li>
- <code><a href="transform_odeparms.html">transform_odeparms</a></code>(backtransform_odeparms)<br />
- Functions to transform and backtransform kinetic parameters for fitting
-</li>
-
- <li>
- <code><a href="ilr.html">ilr</a></code>(invilr)<br />
- Function to perform isometric log-ratio transformation
-</li>
-
- <li>
- <code><a href="geometric_mean.html">geometric_mean</a></code><br /> Calculate the geometric mean </li>
-
- </ul>
- <h3>Analytical solutions</h3>
- <p>Parent only model solutions</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="SFO.solution.html">SFO.solution</a></code><br /> Single First-Order kinetics </li>
-
- <li>
- <code><a href="FOMC.solution.html">FOMC.solution</a></code><br /> First-Order Multi-Compartment kinetics </li>
-
- <li>
- <code><a href="DFOP.solution.html">DFOP.solution</a></code><br />
-Double First-Order in Parallel kinetics
-</li>
-
- <li>
- <code><a href="SFORB.solution.html">SFORB.solution</a></code><br /> Single First-Order Reversible Binding kinetics </li>
-
- <li>
- <code><a href="HS.solution.html">HS.solution</a></code><br /> Hockey-Stick kinetics </li>
-
- <li>
- <code><a href="IORE.solution.html">IORE.solution</a></code><br /> Indeterminate order rate equation kinetics </li>
-
- </ul>
- <h3>Deprecated functions</h3>
- <p>Functions that have been superseeded</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="mkinplot.html">mkinplot</a></code><br />
- Plot the observed data and the fitted model of an mkinfit object
-</li>
-
- </ul>
- <h3>Other</h3>
-
-
- <ul class="index">
-
- <li>
- <code><a href="add_err.html">add_err</a></code><br />
- Add normally distributed errors to simulated kinetic degradation data
-</li>
-
- </ul>
- </div>
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