Function reference • mkin

Main functions

Essential functionality

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- Main functions - Essential functionality -
- `mkinmod()` `print(<mkinmod>)` `mkinsub()` -	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()` `print(<mmkin>)` -	Fit one or more kinetic models with one or more state variables to one or -more datasets
- `mhmkin()` `[`(<mhmkin>) `print(<mhmkin>)` -	Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models
- Generics - Generic functions introduced by the package -
- `parms()` -	Extract model parameters
- `status()` `print(<status.mmkin>)` `print(<status.mhmkin>)` -	Method to get status information for fit array objects
- `illparms()` `print(<illparms.mkinfit>)` `print(<illparms.mmkin>)` `print(<illparms.saem.mmkin>)` `print(<illparms.mhmkin>)` -	Method to get the names of ill-defined parameters
- `endpoints()` -	Function to calculate endpoints for further use from kinetic models fitted -with mkinfit
- `aw()` -	Calculate Akaike weights for model averaging
- 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"
- `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
- `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
- `summary(<mmkin>)` `print(<summary.mmkin>)` -	Summary method for class "mmkin"
- Mixed models - Create and work with nonlinear hierarchical models -
- `hierarchical_kinetics()` -	Hierarchical kinetics template
- `read_spreadsheet()` -	Read datasets and relevant meta information from a spreadsheet file
- `nlme(<mmkin>)` `print(<nlme.mmkin>)` `update(<nlme.mmkin>)` -	Create an nlme model for an mmkin row object
- `saem()` `print(<saem.mmkin>)` `saemix_model()` `saemix_data()` -	Fit nonlinear mixed models with SAEM
- `mhmkin()` `[`(<mhmkin>) `print(<mhmkin>)` -	Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models
- `plot(<mixed.mmkin>)` -	Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
- `summary(<nlme.mmkin>)` `print(<summary.nlme.mmkin>)` -	Summary method for class "nlme.mmkin"
- `summary(<saem.mmkin>)` `print(<summary.saem.mmkin>)` -	Summary method for class "saem.mmkin"
- `anova(<saem.mmkin>)` -	Anova method for saem.mmkin objects
- `logLik(<saem.mmkin>)` -	logLik method for saem.mmkin objects
- `nlme_function()` `nlme_data()` -	Helper functions to create nlme models from mmkin row objects
- `get_deg_func()` -	Retrieve a degradation function from the mmkin namespace
- `mixed()` `print(<mixed.mmkin>)` -	Create a mixed effects model from an mmkin row object
- `reexports` `intervals` `lrtest` `nlme` -	Objects exported from other packages
- `intervals(<saem.mmkin>)` -	Confidence intervals for parameters in saem.mmkin objects
- `multistart()` `print(<multistart>)` `best()` `which.best()` -	Perform a hierarchical model fit with multiple starting values
- `llhist()` -	Plot the distribution of log likelihoods from multistart objects
- `parplot()` -	Plot parameter variability of multistart objects
- Datasets and known results - -
- `ds_mixed` `ds_sfo` `ds_fomc` `ds_dfop` `ds_hs` `ds_dfop_sfo` -	Synthetic data for hierarchical kinetic degradation models
- `D24_2014` -	Aerobic soil degradation data on 2,4-D from the EU assessment in 2014
- `dimethenamid_2018` -	Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018
- `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
- `focus_soil_moisture` -	FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
- `print(<mkinds>)` -	A dataset class for mkin
- `print(<mkindsg>)` -	A class for dataset groups for mkin
- 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.
- Utility functions - -
- `summary_listing()` `tex_listing()` `html_listing()` -	Display the output of a summary function according to the output format
- `f_time_norm_focus()` -	Normalisation factors for aerobic soil degradation according to FOCUS guidance
- `set_nd_nq()` `set_nd_nq_focus()` -	Set non-detects and unquantified values in residue series without replicates
- `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
- `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
- Helper functions mainly used internally - -
- `mkinpredict()` -	Produce predictions from a kinetic model using specific parameters
- `transform_odeparms()` `backtransform_odeparms()` -	Functions to transform and backtransform kinetic parameters for fitting
- `ilr()` `invilr()` -	Function to perform isometric log-ratio transformation
- `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
- `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 -
- `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
- `sigma_twocomp()` -	Two-component error model
- Deprecated functions - Functions that have been superseded -
- `mkinplot()` -	Plot the observed data and the fitted model of an mkinfit object

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+ + mkinmod() print(<mkinmod>) mkinsub() +: 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() print(<mmkin>) +: Fit one or more kinetic models with one or more state variables to one or +more datasets

+ + mhmkin() `[`(<mhmkin>) print(<mhmkin>) +: Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models

+ + + -

Example evaluations with (generalised) nonlinear least squares

Example evaluations with hierarchical models (nonlinear mixed-effects models)

Performance

Miscellaneous

Reference

Main functions

Generics

Show results

Work with mmkin objects

Mixed models

Datasets and known results

NAFTA guidance

Utility functions

Helper functions mainly used internally

Analytical solutions

Generate synthetic datasets

Deprecated functions

Generics