# Kinetic Evaluation of Chemical Degradation Data

## Documentation for package ‘mkin’ version 1.2.9

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

## Help Pages

A B C D E F G H I L M N P R S T U W 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
anova.saem.mmkin | Anova method for saem.mmkin objects
aw | Calculate Akaike weights for model averaging
aw.mixed.mmkin | Calculate Akaike weights for model averaging
aw.mkinfit | Calculate Akaike weights for model averaging
aw.mmkin | Calculate Akaike weights for model averaging
aw.multistart | Calculate Akaike weights for model averaging

## -- B --

backtransform_odeparms | Functions to transform and backtransform kinetic parameters for fitting
best | Perform a hierarchical model fit with multiple starting values
best.default | Perform a hierarchical model fit with multiple starting values
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
check_failed | Check if fit within an mhmkin object failed
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
ds_dfop | Synthetic data for hierarchical kinetic degradation models
ds_dfop_sfo | Synthetic data for hierarchical kinetic degradation models
ds_fomc | Synthetic data for hierarchical kinetic degradation models
ds_hs | Synthetic data for hierarchical kinetic degradation models
ds_mixed | Synthetic data for hierarchical kinetic degradation models
ds_sfo | Synthetic data for hierarchical kinetic degradation models

## -- 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 --

hierarchical_kinetics | Hierarchical kinetics template
HS.solution | Hockey-Stick kinetics
html_listing | Display the output of a summary function according to the output format

## -- I --

illparms | Method to get the names of ill-defined parameters
illparms.mhmkin | Method to get the names of ill-defined parameters
illparms.mkinfit | Method to get the names of ill-defined parameters
illparms.mmkin | Method to get the names of ill-defined parameters
illparms.saem.mmkin | Method to get the names of ill-defined parameters
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 --

llhist | Plot the distribution of log likelihoods from multistart objects
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
logLik.saem.mmkin | logLik method for saem.mmkin objects
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
mhmkin | Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
mhmkin.list | Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
mhmkin.mmkin | Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
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
multistart | Perform a hierarchical model fit with multiple starting values
multistart.saem.mmkin | Perform a hierarchical model fit with multiple starting values

## -- 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
parms.mkinfit | Extract model parameters
parms.mmkin | Extract model parameters
parms.multistart | Extract model parameters
parms.saem.mmkin | Extract model parameters
parplot | Plot parameter variability of multistart objects
parplot.multistart.saem.mmkin | Plot parameter variability of multistart objects
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.illparms.mhmkin | Method to get the names of ill-defined parameters
print.illparms.mkinfit | Method to get the names of ill-defined parameters
print.illparms.mmkin | Method to get the names of ill-defined parameters
print.illparms.saem.mmkin | Method to get the names of ill-defined parameters
print.mhmkin | Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
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.multistart | Perform a hierarchical model fit with multiple starting values
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.status.mhmkin | Method to get status information for fit array objects
print.status.mmkin | Method to get status information for fit array objects
print.summary.mkinfit | Summary method for class "mkinfit"
print.summary.mmkin | Summary method for class "mmkin"
print.summary.nlme.mmkin | Summary method for class "nlme.mmkin"
print.summary.saem.mmkin | Summary method for class "saem.mmkin"

## -- R --

read_spreadsheet | Read datasets and relevant meta information from a spreadsheet file
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
set_nd_nq | Set non-detects and unquantified values in residue series without replicates
set_nd_nq_focus | Set non-detects and unquantified values in residue series without replicates
SFO.solution | Single First-Order kinetics
SFORB.solution | Single First-Order Reversible Binding kinetics
sigma_twocomp | Two-component error model
status | Method to get status information for fit array objects
status.mhmkin | Method to get status information for fit array objects
status.mmkin | Method to get status information for fit array objects
summary.mkinfit | Summary method for class "mkinfit"
summary.mmkin | Summary method for class "mmkin"
summary.nlme.mmkin | Summary method for class "nlme.mmkin"
summary.saem.mmkin | Summary method for class "saem.mmkin"
summary_listing | Display the output of a summary function according to the output format
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
tex_listing | Display the output of a summary function according to the output format
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

## -- W --

which.best | Perform a hierarchical model fit with multiple starting values
which.best.default | Perform a hierarchical model fit with multiple starting values

## -- misc --

[.mhmkin | Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
[.mmkin | Subsetting method for mmkin objects