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mkin (version 0.9-31)

Routines for fitting kinetic models with one or more state variables to chemical degradation data

Description

Calculation routines based on the FOCUS Kinetics Report (2006). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers and a choice of the optimisation methods made available by the FME package (default is a Levenberg-Marquardt variant). Please note that no warranty is implied for correctness of results or fitness for a particular purpose.

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Version

Install

install.packages('mkin')

Monthly Downloads

429

Version

0.9-31

License

GPL

Issues

2

Pull Requests

0

Stars

11

Forks

4

Maintainer

Johannes Ranke

Last Published

July 14th, 2014

Functions in mkin (0.9-31)

DFOP.solution

Dual First-Order in Parallel kinetics
FOCUS_2006_DFOP_ref_A_to_B

Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
HS.solution

Hockey-Stick kinetics
mkinplot

Plot the observed data and the fitted model of an mkinfit.
FOCUS_2006_FOMC_ref_A_to_F

Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
mkinresplot

Function to plot residuals stored in an mkin object
mkinerrmin

Calculate the minimum error to assume in order to pass the variance test
mkinpredict

Produce predictions from a kinetic model using specifc parameters
mkin_long_to_wide

Convert a dataframe from long to wide format.
plot.mkinfit

Plot the observed data and the fitted model of an mkinfit object.
geometric_mean

Calculate the geometric mean
FOCUS_2006_datasets

Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_HS_ref_A_to_F

Results of fitting the HS model to Datasets A to F of FOCUS (2006)
endpoints

Function to calculate endpoints for further use from kinetic models fitted with mkinfit
schaefer07_complex_case

Metabolism data set used for checking the software quality of KinGUI
SFORB.solution

Single First-Order Reversible Binding kinetics
mkinparplot

Function to plot the confidence intervals obtained using mkinfit
mkinfit

Fit a kinetic model to data with one or more state variables.
SFO.solution

Single First-Order kinetics
summary.mkinfit

Summary method for class "mkinfit".
transform_odeparms

Functions to transform and backtransform kinetic parameters for fitting
mccall81_245T

Datasets on aerobic soil metabolism of 2,4,5-T in six soils
FOCUS_2006_SFO_ref_A_to_F

Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
mkinmod

Function to set up a kinetic model with one or more state variables.
ilr

Function to perform isometric log-ratio transformation
FOMC.solution

First-Order Multi-Compartment kinetics
mkin_wide_to_long

Convert a dataframe with observations over time into long format.