# Kinetic Evaluation of Chemical Degradation Data

## Documentation for package ‘mkin’ version 1.1.0

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

## Help Pages

A B C D E F G H I L M N P R S T U misc

## -- A --

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

## -- B --

backtransform_odeparms | Functions to transform and backtransform kinetic parameters for fitting
BIC.mmkin | Calculate the AIC for a column of an mmkin object

## -- C --

CAKE_export | Export a list of datasets format to a CAKE study file
confint.mkinfit | Confidence intervals for parameters of mkinfit objects
create_deg_func | Create degradation functions for known analytical solutions

## -- D --

D24_2014 | Aerobic soil degradation data on 2,4-D from the EU assessment in 2014
DFOP.solution | Double First-Order in Parallel kinetics
dimethenamid_2018 | Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018

## -- E --

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

## -- F --

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)
focus_soil_moisture | FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
FOMC.solution | First-Order Multi-Compartment kinetics
f_time_norm_focus | Normalisation factors for aerobic soil degradation according to FOCUS guidance
f_time_norm_focus.mkindsg | Normalisation factors for aerobic soil degradation according to FOCUS guidance
f_time_norm_focus.numeric | Normalisation factors for aerobic soil degradation according to FOCUS guidance

## -- G --

get_deg_func | Retrieve a degradation function from the mmkin namespace

## -- H --

HS.solution | Hockey-Stick kinetics

## -- I --

ilr | Function to perform isometric log-ratio transformation
intervals.saem.mmkin | Confidence intervals for parameters in saem.mmkin objects
invilr | Function to perform isometric log-ratio transformation
IORE.solution | Indeterminate order rate equation kinetics

## -- L --

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

## -- M --

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
mean_degparms | Calculate mean degradation parameters for an mmkin row object
mixed | Create a mixed effects model from an mmkin row object
mixed.mmkin | Create a mixed effects model from an mmkin row object
mkinds | A dataset class for mkin
mkindsg | A class for dataset groups 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 model with one or more state variables
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

## -- N --

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
nlme.mmkin | Create an nlme model for an mmkin row object
nlme_data | Helper functions to create nlme models from mmkin row objects
nlme_function | Helper functions to create nlme models from mmkin row objects
nobs.mkinfit | Number of observations on which an mkinfit object was fitted

## -- P --

parms | Extract model parameters from mkinfit models
parms.mkinfit | Extract model parameters from mkinfit models
parms.mmkin | Extract model parameters from mkinfit models
plot.mixed.mmkin | Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
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.mixed.mmkin | Create a mixed effects model from an mmkin row object
print.mkinds | A dataset class for mkin
print.mkindsg | A class for dataset groups for mkin
print.mkinmod | Function to set up a kinetic model with one or more state variables
print.mmkin | Fit one or more kinetic models with one or more state variables to one or more datasets
print.nafta | Evaluate parent kinetics using the NAFTA guidance
print.nlme.mmkin | Create an nlme model for an mmkin row object
print.saem.mmkin | Fit nonlinear mixed models with SAEM
print.summary.mkinfit | Summary method for class "mkinfit"
print.summary.nlme.mmkin | Summary method for class "nlme.mmkin"
print.summary.saem.mmkin | Summary method for class "saem.mmkin"

## -- R --

residuals.mkinfit | Extract residuals from an mkinfit model

## -- S --

saem | Fit nonlinear mixed models with SAEM
saem.mmkin | Fit nonlinear mixed models with SAEM
saemix_data | Fit nonlinear mixed models with SAEM
saemix_model | Fit nonlinear mixed models with SAEM
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"
summary.nlme.mmkin | Summary method for class "nlme.mmkin"
summary.saem.mmkin | Summary method for class "saem.mmkin"
synthetic_data_for_UBA_2014 | Synthetic datasets for one parent compound with two metabolites

## -- T --

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

## -- U --

update.mkinfit | Update an mkinfit model with different arguments
update.nlme.mmkin | Create an nlme model for an mmkin row object

## -- misc --

[.mmkin | Subsetting method for mmkin objects