Function reference • mkin

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Main functions

Essential functionality

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+ Main functions + Essential functionality
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`mkinmod()` `print(<mkinmod>)` `mkinsub()`	Function to set up a kinetic model with one or more state variables
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`mkinfit()`	Fit a kinetic model to data with one or more state variables
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`mmkin()` `print(<mmkin>)`	Fit one or more kinetic models with one or more state variables to one or more datasets
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`nafta()` `print(<nafta>)`	Evaluate parent kinetics using the NAFTA guidance
- Show results - Functions working with mkinfit objects +
+ Show results + Functions working with mkinfit objects
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`plot(<mkinfit>)` `plot_sep()` `plot_res()` `plot_err()`	Plot the observed data and the fitted model of an mkinfit object
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`summary(<mkinfit>)` `print(<summary.mkinfit>)`	Summary method for class "mkinfit"
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`parms()`	Extract model parameters from mkinfit models
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`confint(<mkinfit>)`	Confidence intervals for parameters of mkinfit objects
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`update(<mkinfit>)`	Update an mkinfit model with different arguments
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`lrtest(<mkinfit>)` `lrtest(<mmkin>)`	Likelihood ratio test for mkinfit models
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`loftest()`	Lack-of-fit test for models fitted to data with replicates
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`mkinerrmin()`	Calculate the minimum error to assume in order to pass the variance test
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`endpoints()`	Function to calculate endpoints for further use from kinetic models fitted with mkinfit
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`aw()`	Calculate Akaike weights for model averaging
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`CAKE_export()`	Export a list of datasets format to a CAKE study file
- Work with mmkin objects - Functions working with aggregated results +
+ Work with mmkin objects + Functions working with aggregated results
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`[`(<mmkin>)	Subsetting method for mmkin objects
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`plot(<mmkin>)`	Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
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`AIC(<mmkin>)` `BIC(<mmkin>)`	Calculate the AIC for a column of an mmkin object
- Mixed models - Create and work with nonlinear mixed effects models +
+ Mixed models + Create and work with nonlinear mixed effects models
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`nlme(<mmkin>)` `print(<nlme.mmkin>)` `update(<nlme.mmkin>)`	Create an nlme model for an mmkin row object
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+ `saem()` `print(<saem.mmkin>)` `saemix_model()` `saemix_data()` +	Fit nonlinear mixed models with SAEM
+ `nlmixr(<mmkin>)` `print(<nlmixr.mmkin>)` `nlmixr_model()` `nlmixr_data()` +	Fit nonlinear mixed models using nlmixr
`plot(<mixed.mmkin>)`	Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
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`summary(<nlme.mmkin>)` `print(<summary.nlme.mmkin>)`	Summary method for class "nlme.mmkin"
- `nlme_function()` `mean_degparms()` `nlme_data()` +
+ `summary(<nlmixr.mmkin>)` `print(<summary.nlmixr.mmkin>)` +	Summary method for class "nlmixr.mmkin"
+ `summary(<saem.mmkin>)` `print(<summary.saem.mmkin>)` +	Summary method for class "saem.mmkin"
+ `nlme_function()` `nlme_data()`	Helper functions to create nlme models from mmkin row objects
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`get_deg_func()`	Retrieve a degradation function from the mmkin namespace
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`mixed()` `print(<mixed.mmkin>)`	Create a mixed effects model from an mmkin row object
- Datasets and known results +
+ `reexports` +	Objects exported from other packages
+ `intervals(<saem.mmkin>)` +	Confidence intervals for parameters in saem.mmkin objects
+ `intervals(<nlmixr.mmkin>)` +	Confidence intervals for parameters in nlmixr.mmkin objects
+ Datasets and known results
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`focus_soil_moisture`	FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
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`D24_2014`	Aerobic soil degradation data on 2,4-D from the EU assessment in 2014
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`dimethenamid_2018`	Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018
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`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
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`FOCUS_2006_SFO_ref_A_to_F`	Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
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`FOCUS_2006_FOMC_ref_A_to_F`	Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
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`FOCUS_2006_HS_ref_A_to_F`	Results of fitting the HS model to Datasets A to F of FOCUS (2006)
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`FOCUS_2006_DFOP_ref_A_to_B`	Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
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`NAFTA_SOP_Appendix_B` `NAFTA_SOP_Appendix_D`	Example datasets from the NAFTA SOP published 2015
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`NAFTA_SOP_Attachment`	Example datasets from Attachment 1 to the NAFTA SOP published 2015
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`mccall81_245T`	Datasets on aerobic soil metabolism of 2,4,5-T in six soils
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`schaefer07_complex_case`	Metabolism data set used for checking the software quality of KinGUI
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`synthetic_data_for_UBA_2014`	Synthetic datasets for one parent compound with two metabolites
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`experimental_data_for_UBA_2019`	Experimental datasets used for development and testing of error models
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`test_data_from_UBA_2014`	Three experimental datasets from two water sediment systems and one soil
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`print(<mkinds>)`	A dataset class for mkin
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`print(<mkindsg>)`	A class for dataset groups for mkin
- NAFTA guidance +
+ NAFTA guidance
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`nafta()` `print(<nafta>)`	Evaluate parent kinetics using the NAFTA guidance
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`plot(<nafta>)`	Plot the results of the three models used in the NAFTA scheme.
- Utility functions +
+ Utility functions
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`f_time_norm_focus()`	Normalisation factors for aerobic soil degradation according to FOCUS guidance
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`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
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`mkin_wide_to_long()`	Convert a dataframe with observations over time into long format
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`mkin_long_to_wide()`	Convert a dataframe from long to wide format
- Helper functions mainly used internally +
+ Helper functions mainly used internally
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`mkinpredict()`	Produce predictions from a kinetic model using specific parameters
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`transform_odeparms()` `backtransform_odeparms()`	Functions to transform and backtransform kinetic parameters for fitting
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`ilr()` `invilr()`	Function to perform isometric log-ratio transformation
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+ `tffm0()` `invtffm0()` +	Transform formation fractions as in the first published mkin version
`logLik(<mkinfit>)`	Calculated the log-likelihood of a fitted mkinfit object
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`residuals(<mkinfit>)`	Extract residuals from an mkinfit model
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`nobs(<mkinfit>)`	Number of observations on which an mkinfit object was fitted
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`mkinresplot()`	Function to plot residuals stored in an mkin object
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`mkinparplot()`	Function to plot the confidence intervals obtained using mkinfit
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`mkinerrplot()`	Function to plot squared residuals and the error model for an mkin object
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+ `mean_degparms()` +	Calculate mean degradation parameters for an mmkin row object
`create_deg_func()`	Create degradation functions for known analytical solutions
- Analytical solutions - Parent only model solutions +
+ Analytical solutions + Parent only model solutions
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`SFO.solution()`	Single First-Order kinetics
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`FOMC.solution()`	First-Order Multi-Compartment kinetics
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`DFOP.solution()`	Double First-Order in Parallel kinetics
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`SFORB.solution()`	Single First-Order Reversible Binding kinetics
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`HS.solution()`	Hockey-Stick kinetics
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`IORE.solution()`	Indeterminate order rate equation kinetics
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`logistic.solution()`	Logistic kinetics
- Generate synthetic datasets +
+ Generate synthetic datasets
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`add_err()`	Add normally distributed errors to simulated kinetic degradation data
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`sigma_twocomp()`	Two-component error model
- Deprecated functions - Functions that have been superseded +
+ Deprecated functions + Functions that have been superseded
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`mkinplot()`	Plot the observed data and the fitted model of an mkinfit object

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Reference

Main functions

Main functions

Show results

Show results

Work with mmkin objects

Work with mmkin objects

Mixed models

Mixed models

Datasets and known results

Datasets and known results

NAFTA guidance

NAFTA guidance

Utility functions

Utility functions

Helper functions mainly used internally

Helper functions mainly used internally

Analytical solutions

Analytical solutions

Generate synthetic datasets

Generate synthetic datasets

Deprecated functions

Deprecated functions