# Kinetic Evaluation of Chemical Degradation Data

## Documentation for package ‘mkin’ version 0.9.49.5

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

## Help Pages

add_err | Add normally distributed errors to simulated kinetic degradation data
AIC.mmkin | Calculated the AIC for a column of an mmkin object
backtransform_odeparms | Functions to transform and backtransform kinetic parameters for fitting
CAKE_export | Export a list of datasets format to a CAKE study file
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
geometric_mean | Calculate the geometric mean
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
logistic.solution | Logistic kinetics
logLik.mkinfit | Calculated the log-likelihood of a fitted mkinfit object
max_twa_parent | 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
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. The plots are ordered with increasing complexity of the model in this function (SFO, then IORE, then DFOP).
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 | Print nafta objects
print.summary.mkinfit | Summary method for class "mkinfit"
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
[.mmkin | Subsetting method for mmkin objects