Function reference • mkin

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+ 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