Reference

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()	Evaluate parent kinetics using the NAFTA guidance
Show results Functions working with mkinfit objects
plot(<mkinfit>) plot_sep()	Plot the observed data and the fitted model of an mkinfit object
summary(<mkinfit>) print(<summary.mkinfit>)	Summary method for class "mkinfit"
mkinresplot()	Function to plot residuals stored in an mkin object
mkinparplot()	Function to plot the confidence intervals obtained using mkinfit
endpoints()	Function to calculate endpoints for further use from kinetic models fitted with mkinfit
mkinerrmin()	Calculate the minimum error to assume in order to pass the variance test
logLik(<mkinfit>)	Calculated the log-likelihood of a fitted mkinfit object
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>)	Calculated the AIC for a column of an mmkin object
Datasets and known results
FOCUS_2006_datasets	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_2015	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
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()	Evaluate parent kinetics using the NAFTA guidance
print(<nafta>)	Print nafta objects
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).
Helper functions
geometric_mean()	Calculate the geometric mean
mkinsub()	Function to set up a kinetic submodel for one state variable
max_twa_parent()	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
CAKE_export()	Export a list of datasets format to a CAKE study file
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 superseeded
mkinplot()	Plot the observed data and the fitted model of an mkinfit object