Static documentation rebuilt with current staticdocs

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author: Johannes Ranke <jranke@uni-bremen.de> 2016-09-10 05:21:52 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2016-09-10 05:55:25 +0200
commit: a350a16bb2c11986faf5883a2804d46b03bd7c8f (patch)
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+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8">
+<title>Function reference. mkin 0.9.44.9000</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<meta name="author" content="">
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+  <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>
+      
+      <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>
+</div>
+      
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+\ No newline at end of file
author	Johannes Ranke <jranke@uni-bremen.de>	2016-09-10 05:21:52 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2016-09-10 05:55:25 +0200
commit	a350a16bb2c11986faf5883a2804d46b03bd7c8f (patch)
tree	00ca40222b1f4c9bcffca081982e006763e697d8 /docs/reference.html
parent	3b399df5231576880fd9e0ae7253064d82edfe86 (diff)