Function reference • mkin

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

Reference

Main functions

Show results

Work with mmkin objects

Mixed models

Datasets and known results

NAFTA guidance

Helper functions mainly used internally

Analytical solutions

Generate synthetic datasets

Deprecated functions