Function reference • mkin

- 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

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

Main functions

- -

Essential functionality

- -

- - - +

Essential functionality

+ + +

- - mkinmod() print(<mkinmod>) mkinsub() + + mkinmod() print(<mkinmod>) mkinsub() +: Function to set up a kinetic model with one or more state variables

- - mkinfit() + + mkinfit() +: Fit a kinetic model to data with one or more state variables

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

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

- -

- - - +

Generic functions introduced by the package

+ + +

- - parms() + + parms() +: Extract model parameters

- - status() print(<status.mmkin>) print(<status.mhmkin>) + + 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>) + + illparms() print(<illparms.mkinfit>) print(<illparms.mmkin>) print(<illparms.saem.mmkin>) print(<illparms.mhmkin>) +: Method to get the names of ill-defined parameters

- - endpoints() + + endpoints() +: Function to calculate endpoints for further use from kinetic models fitted -with mkinfit; Function to calculate endpoints for further use from kinetic models fitted with mkinfit

- - aw() + + aw() +: Calculate Akaike weights for model averaging

Show results

- -

Functions working with mkinfit objects

- -

- - - +

Functions working with mkinfit objects

+ + +

- - plot(<mkinfit>) plot_sep() plot_res() plot_err() + + 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(<mkinfit>) print(<summary.mkinfit>) +: Summary method for class "mkinfit"

- - confint(<mkinfit>) + + confint(<mkinfit>) +: Confidence intervals for parameters of mkinfit objects

- - update(<mkinfit>) + + update(<mkinfit>) +: Update an mkinfit model with different arguments

- - lrtest(<mkinfit>) lrtest(<mmkin>) + + lrtest(<mkinfit>) lrtest(<mmkin>) +: Likelihood ratio test for mkinfit models

- - loftest() + + loftest() +: Lack-of-fit test for models fitted to data with replicates

- - mkinerrmin() + + mkinerrmin() +: Calculate the minimum error to assume in order to pass the variance test

- - CAKE_export() + + CAKE_export() +: Export a list of datasets format to a CAKE study file

Work with mmkin objects

- -

Functions working with aggregated results

- -

- - - +

Functions working with aggregated results

+ + +

- - `[`(<mmkin>) + + `[`(<mmkin>) +: Subsetting method for mmkin objects

- - plot(<mmkin>) + + plot(<mmkin>) +: Plot model fits (observed and fitted) and the residuals for a row or column -of an mmkin object; Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object

- - AIC(<mmkin>) BIC(<mmkin>) + + AIC(<mmkin>) BIC(<mmkin>) +: Calculate the AIC for a column of an mmkin object

- - summary(<mmkin>) print(<summary.mmkin>) + + summary(<mmkin>) print(<summary.mmkin>) +: Summary method for class "mmkin"

Mixed models

- -

Create and work with nonlinear hierarchical models

- -

- - - +

Create and work with nonlinear hierarchical models

+ + +

- - hierarchical_kinetics() + + hierarchical_kinetics() +: Hierarchical kinetics template

- - read_spreadsheet() + + read_spreadsheet() +: Read datasets and relevant meta information from a spreadsheet file

- - nlme(<mmkin>) print(<nlme.mmkin>) update(<nlme.mmkin>) + + 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() + + saem() print(<saem.mmkin>) saemix_model() saemix_data() +: Fit nonlinear mixed models with SAEM

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

- - plot(<mixed.mmkin>) + + 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(<nlme.mmkin>) print(<summary.nlme.mmkin>) +: Summary method for class "nlme.mmkin"

- - summary(<saem.mmkin>) print(<summary.saem.mmkin>) + + summary(<saem.mmkin>) print(<summary.saem.mmkin>) +: Summary method for class "saem.mmkin"

- - anova(<saem.mmkin>) + + anova(<saem.mmkin>) +: Anova method for saem.mmkin objects

- - logLik(<saem.mmkin>) + + logLik(<saem.mmkin>) +: logLik method for saem.mmkin objects

- - nlme_function() nlme_data() + + nlme_function() nlme_data() +: Helper functions to create nlme models from mmkin row objects

- - get_deg_func() + + get_deg_func() +: Retrieve a degradation function from the mmkin namespace

- - mixed() print(<mixed.mmkin>) + + mixed() print(<mixed.mmkin>) +: Create a mixed effects model from an mmkin row object

- - reexports intervals lrtest nlme + + reexports intervals lrtest nlme +: Objects exported from other packages

- - intervals(<saem.mmkin>) + + intervals(<saem.mmkin>) +: Confidence intervals for parameters in saem.mmkin objects

- - multistart() print(<multistart>) best() which.best() + + multistart() print(<multistart>) best() which.best() +: Perform a hierarchical model fit with multiple starting values

- - llhist() + + llhist() +: Plot the distribution of log likelihoods from multistart objects

- - parplot() + + parplot() +: Plot parameter variability of multistart objects

+ + check_failed() + +: Check if fit within an mhmkin object failed

Datasets and known results

- - - -

- - - + + + +

+ + +

- - ds_mixed ds_sfo ds_fomc ds_dfop ds_hs ds_dfop_sfo + + ds_mixed ds_sfo ds_fomc ds_dfop ds_hs ds_dfop_sfo +: Synthetic data for hierarchical kinetic degradation models

- - D24_2014 + + D24_2014 +: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014

- - dimethenamid_2018 + + 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 + + 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 + + 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 + + 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 + + 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 + + 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 + + NAFTA_SOP_Appendix_B NAFTA_SOP_Appendix_D +: Example datasets from the NAFTA SOP published 2015

- - NAFTA_SOP_Attachment + + NAFTA_SOP_Attachment +: Example datasets from Attachment 1 to the NAFTA SOP published 2015

- - mccall81_245T + + mccall81_245T +: Datasets on aerobic soil metabolism of 2,4,5-T in six soils

- - schaefer07_complex_case + + schaefer07_complex_case +: Metabolism data set used for checking the software quality of KinGUI

- - synthetic_data_for_UBA_2014 + + synthetic_data_for_UBA_2014 +: Synthetic datasets for one parent compound with two metabolites

- - experimental_data_for_UBA_2019 + + experimental_data_for_UBA_2019 +: Experimental datasets used for development and testing of error models

- - test_data_from_UBA_2014 + + test_data_from_UBA_2014 +: Three experimental datasets from two water sediment systems and one soil

- - focus_soil_moisture + + focus_soil_moisture +: FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar

- - print(<mkinds>) + + print(<mkinds>) +: A dataset class for mkin

- - print(<mkindsg>) + + print(<mkindsg>) +: A class for dataset groups for mkin

NAFTA guidance

- - - -

- - - + + + +

+ + +

- - nafta() print(<nafta>) + + nafta() print(<nafta>) +: Evaluate parent kinetics using the NAFTA guidance

- - plot(<nafta>) + + plot(<nafta>) +: Plot the results of the three models used in the NAFTA scheme.

Utility functions

- - - -

- - - + + + +

+ + +

- - summary_listing() tex_listing() html_listing() + + summary_listing() tex_listing() html_listing() +: Display the output of a summary function according to the output format

- - f_time_norm_focus() + + f_time_norm_focus() +: Normalisation factors for aerobic soil degradation according to FOCUS guidance

- - set_nd_nq() set_nd_nq_focus() + + 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() + + 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; Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit

- - mkin_wide_to_long() + + mkin_wide_to_long() +: Convert a dataframe with observations over time into long format

- - mkin_long_to_wide() + + mkin_long_to_wide() +: Convert a dataframe from long to wide format

Helper functions mainly used internally

- - - -

- - - + + + +

+ + +

- - mkinpredict() + + mkinpredict() +: Produce predictions from a kinetic model using specific parameters

- - transform_odeparms() backtransform_odeparms() + + transform_odeparms() backtransform_odeparms() +: Functions to transform and backtransform kinetic parameters for fitting

- - ilr() invilr() + + ilr() invilr() +: Function to perform isometric log-ratio transformation

- - logLik(<mkinfit>) + + logLik(<mkinfit>) +: Calculated the log-likelihood of a fitted mkinfit object

- - residuals(<mkinfit>) + + residuals(<mkinfit>) +: Extract residuals from an mkinfit model

- - nobs(<mkinfit>) + + nobs(<mkinfit>) +: Number of observations on which an mkinfit object was fitted

- - mkinresplot() + + mkinresplot() +: Function to plot residuals stored in an mkin object

- - mkinparplot() + + mkinparplot() +: Function to plot the confidence intervals obtained using mkinfit

- - mkinerrplot() + + mkinerrplot() +: Function to plot squared residuals and the error model for an mkin object

- - mean_degparms() + + mean_degparms() +: Calculate mean degradation parameters for an mmkin row object

- - create_deg_func() + + create_deg_func() +: Create degradation functions for known analytical solutions

Analytical solutions

- -

Parent only model solutions

- -

- - - +

Parent only model solutions

+ + +

- - SFO.solution() + + SFO.solution() +: Single First-Order kinetics

- - FOMC.solution() + + FOMC.solution() +: First-Order Multi-Compartment kinetics

- - DFOP.solution() + + DFOP.solution() +: Double First-Order in Parallel kinetics

- - SFORB.solution() + + SFORB.solution() +: Single First-Order Reversible Binding kinetics

- - HS.solution() + + HS.solution() +: Hockey-Stick kinetics

- - IORE.solution() + + IORE.solution() +: Indeterminate order rate equation kinetics

- - logistic.solution() + + logistic.solution() +: Logistic kinetics

Generate synthetic datasets

- - - -

- - - + + + +

+ + +

- - add_err() + + add_err() +: Add normally distributed errors to simulated kinetic degradation data

- - sigma_twocomp() + + sigma_twocomp() +: Two-component error model

Deprecated functions

- -

Functions that have been superseded

- -

- - - +

Functions that have been superseded

+ + +

- - mkinplot() + + mkinplot() +: Plot the observed data and the fitted model of an mkinfit object

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