# Kinetic Evaluation of Chemical Degradation Data

## Documentation for package ‘mkin’ version 0.9.49.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_err | Add normally distributed errors to simulated kinetic degradation data
AIC.mmkin | Calculate the AIC for a column of an mmkin object
aw | Calculate Akaike weights for model averaging
aw.mkinfit | Calculate Akaike weights for model averaging
aw.mmkin | Calculate Akaike weights for model averaging
backtransform_odeparms | Functions to transform and backtransform kinetic parameters for fitting
BIC.mmkin | Calculate the AIC for a column of an mmkin object
CAKE_export | Export a list of datasets format to a CAKE study file
confint.mkinfit | Confidence intervals for parameters of mkinfit objects
DFOP.solution | Double First-Order in Parallel kinetics
endpoints | Function to calculate endpoints for further use from kinetic models fitted with mkinfit
experimental_data_for_UBA_2019 | Experimental datasets used for development and testing of error models
FOCUS_2006_A | Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_B | Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_C | Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_D | Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_DFOP_ref_A_to_B | Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
FOCUS_2006_E | Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_F | Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_FOMC_ref_A_to_F | Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
FOCUS_2006_HS_ref_A_to_F | Results of fitting the HS model to Datasets A to F of FOCUS (2006)
FOCUS_2006_SFO_ref_A_to_F | Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
FOMC.solution | First-Order Multi-Compartment kinetics
HS.solution | Hockey-Stick kinetics
ilr | Function to perform isometric log-ratio transformation
invilr | Function to perform isometric log-ratio transformation
IORE.solution | Indeterminate order rate equation kinetics
loftest | Lack-of-fit test for models fitted to data with replicates
loftest.mkinfit | Lack-of-fit test for models fitted to data with replicates
logistic.solution | Logistic kinetics
logLik.mkinfit | Calculated the log-likelihood of a fitted mkinfit object
lrtest.mkinfit | Likelihood ratio test for mkinfit models
lrtest.mmkin | Likelihood ratio test for mkinfit models
max_twa_dfop | Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
max_twa_fomc | Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
max_twa_hs | Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
max_twa_parent | Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
max_twa_sfo | Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
mccall81_245T | Datasets on aerobic soil metabolism of 2,4,5-T in six soils
mkinds | A dataset class for mkin
mkinerrmin | Calculate the minimum error to assume in order to pass the variance test
mkinerrplot | Function to plot squared residuals and the error model for an mkin object
mkinfit | Fit a kinetic model to data with one or more state variables
mkinmod | Function to set up a kinetic model with one or more state variables
mkinparplot | Function to plot the confidence intervals obtained using mkinfit
mkinplot | Plot the observed data and the fitted model of an mkinfit object
mkinpredict | Produce predictions from a kinetic model using specific parameters
mkinpredict.mkinfit | Produce predictions from a kinetic model using specific parameters
mkinpredict.mkinmod | Produce predictions from a kinetic model using specific parameters
mkinresplot | Function to plot residuals stored in an mkin object
mkinsub | Function to set up a kinetic submodel for one state variable
mkin_long_to_wide | Convert a dataframe from long to wide format
mkin_wide_to_long | Convert a dataframe with observations over time into long format
mmkin | Fit one or more kinetic models with one or more state variables to one or more datasets
nafta | Evaluate parent kinetics using the NAFTA guidance
NAFTA_SOP_Appendix_B | Example datasets from the NAFTA SOP published 2015
NAFTA_SOP_Appendix_D | Example datasets from the NAFTA SOP published 2015
NAFTA_SOP_Attachment | Example datasets from Attachment 1 to the NAFTA SOP published 2015
nobs.mkinfit | Number of observations on which an mkinfit object was fitted
parms | Extract model parameters from mkinfit models
parms.mkinfit | Extract model parameters from mkinfit models
plot.mkinfit | Plot the observed data and the fitted model of an mkinfit object
plot.mmkin | Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
plot.nafta | Plot the results of the three models used in the NAFTA scheme.
plot_err | Plot the observed data and the fitted model of an mkinfit object
plot_res | Plot the observed data and the fitted model of an mkinfit object
plot_sep | Plot the observed data and the fitted model of an mkinfit object
print.mkinds | Print mkinds objects
print.mkinmod | Print mkinmod objects
print.nafta | Evaluate parent kinetics using the NAFTA guidance
print.summary.mkinfit | Summary method for class "mkinfit"
residuals.mkinfit | Extract residuals from an mkinfit model
schaefer07_complex_case | Metabolism data set used for checking the software quality of KinGUI
schaefer07_complex_results | Metabolism data set used for checking the software quality of KinGUI
SFO.solution | Single First-Order kinetics
SFORB.solution | Single First-Order Reversible Binding kinetics
sigma_twocomp | Two-component error model
summary.mkinfit | Summary method for class "mkinfit"
synthetic_data_for_UBA_2014 | Synthetic datasets for one parent compound with two metabolites
test_data_from_UBA_2014 | Three experimental datasets from two water sediment systems and one soil
transform_odeparms | Functions to transform and backtransform kinetic parameters for fitting
update.mkinfit | Update an mkinfit model with different arguments
[.mmkin | Subsetting method for mmkin objects