Package: mkin 1.2.9

mkin: Kinetic Evaluation of Chemical Degradation Data

Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using automatically generated C functions. Heteroscedasticity can be taken into account using variance by variable or two-component error models as described by Ranke and Meinecke (2018) <doi:10.3390/environments6120124>. Hierarchical degradation models can be fitted using nonlinear mixed-effects model packages as a back end as described by Ranke et al. (2021) <doi:10.3390/environments8080071>. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.

Authors:Johannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb], René Lehmann [ctb], Eurofins Regulatory AG [cph]

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mkin.pdf |mkin.html✨
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NEWS

# Install 'mkin' in R:

install.packages('mkin', repos = c('https://jranke.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jranke/mkin/issues

Datasets:

D24_2014 - Aerobic soil degradation data on 2,4-D from the EU assessment in 2014
FOCUS_2006_A - Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_B - Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_C - Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_D - Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_DFOP_ref_A_to_B - Results of fitting the DFOP model to Datasets A to B of FOCUS
FOCUS_2006_E - Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_F - Datasets A to F from the FOCUS Kinetics report from 2006
FOCUS_2006_FOMC_ref_A_to_F - Results of fitting the FOMC model to Datasets A to F of FOCUS
FOCUS_2006_HS_ref_A_to_F - Results of fitting the HS model to Datasets A to F of FOCUS
FOCUS_2006_SFO_ref_A_to_F - Results of fitting the SFO model to Datasets A to F of FOCUS
NAFTA_SOP_Appendix_B - Example datasets from the NAFTA SOP published 2015
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
dimethenamid_2018 - Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018
ds_dfop - Synthetic data for hierarchical kinetic degradation models
ds_dfop_sfo - Synthetic data for hierarchical kinetic degradation models
ds_fomc - Synthetic data for hierarchical kinetic degradation models
ds_hs - Synthetic data for hierarchical kinetic degradation models
ds_sfo - Synthetic data for hierarchical kinetic degradation models
experimental_data_for_UBA_2019 - Experimental datasets used for development and testing of error models
focus_soil_moisture - FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
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
schaefer07_complex_results - 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

On CRAN:

degradation focus-kinetics kinetic-models kinetics ode ode-model

8.04 score 10 stars 1 packages 74 scripts 1.0k downloads 2 mentions 69 exports 42 dependencies

Last updated 1 months agofrom:7b14afbeaa. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 06 2024
R-4.5-win	NOTE	Oct 06 2024
R-4.5-linux	NOTE	Oct 06 2024
R-4.4-win	OK	Oct 06 2024
R-4.4-mac	OK	Oct 06 2024
R-4.3-win	OK	Oct 06 2024
R-4.3-mac	OK	Oct 06 2024

Exports:add_err aw backtransform_odeparms best CAKE_export create_deg_func DFOP.solution endpoints f_time_norm_focus FOMC.solution get_deg_func hierarchical_kinetics HS.solution html_listing illparms ilr intervals invilr IORE.solution llhist loftest logistic.solution lrtest max_twa_dfop max_twa_fomc max_twa_hs max_twa_parent max_twa_sfo mean_degparms mhmkin mixed mkin_long_to_wide mkin_wide_to_long mkinds mkindsg mkinerrmin mkinerrplot mkinfit mkinmod mkinparplot mkinplot mkinpredict mkinresplot mkinsub mmkin multistart nafta nlme nlme_data nlme_function parms parplot plot_err plot_res plot_sep read_spreadsheet saem saemix_data saemix_model set_nd_nq set_nd_nq_focus SFO.solution SFORB.solution sigma_twocomp status summary_listing tex_listing transform_odeparms which.best

Dependencies:callr cli colorspace desc deSolve fansi farver ggplot2 glue gridExtra gtable inline isoband labeling lattice lifecycle lmtest magrittr MASS Matrix mclust mgcv munsell nlme npde numDeriv pillar pkgbuild pkgconfig processx ps R6 RColorBrewer rlang saemix scales tibble utf8 vctrs viridisLite withr zoo

Calculation of time weighted average concentrations with mkin

Johannes Ranke

Rendered fromtwa.rmdusingknitr::rmarkdownon Oct 06 2024.

Last update: 2021-02-15
Started: 2017-03-04

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

Rendered fromFOCUS_D.rmdusingknitr::rmarkdownon Oct 06 2024.

Last update: 2021-02-15
Started: 2020-05-13

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

Rendered fromFOCUS_L.rmdusingknitr::rmarkdownon Oct 06 2024.

Last update: 2023-05-19
Started: 2020-05-13

Short introduction to mkin

Johannes Ranke

Rendered frommkin.rmdusingknitr::rmarkdownon Oct 06 2024.

Last update: 2023-05-19
Started: 2020-05-13

Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione

Rendered frommesotrione_parent_2023_prebuilt.rnwusingutils::Sweaveon Oct 06 2024.

Last update: 2023-08-04
Started: 2023-08-04

Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P

Rendered fromdmta_parent_2022_prebuilt.rnwusingutils::Sweaveon Oct 06 2024.

Last update: 2023-02-17
Started: 2023-02-13

Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P

Rendered fromdmta_pathway_2022_prebuilt.rnwusingutils::Sweaveon Oct 06 2024.

Last update: 2023-02-17
Started: 2023-02-13

Help page	Topics
Subsetting method for mmkin objects	[.mmkin
Add normally distributed errors to simulated kinetic degradation data	add_err
Calculate the AIC for a column of an mmkin object	AIC.mmkin BIC.mmkin
Anova method for saem.mmkin objects	anova.saem.mmkin
Calculate Akaike weights for model averaging	aw aw.mixed.mmkin aw.mkinfit aw.mmkin aw.multistart
Export a list of datasets format to a CAKE study file	CAKE_export
Check if fit within an mhmkin object failed	check_failed
Confidence intervals for parameters of mkinfit objects	confint.mkinfit
Create degradation functions for known analytical solutions	create_deg_func
Aerobic soil degradation data on 2,4-D from the EU assessment in 2014	D24_2014
Double First-Order in Parallel kinetics	DFOP.solution
Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018	dimethenamid_2018
Synthetic data for hierarchical kinetic degradation models	ds_dfop ds_dfop_sfo ds_fomc ds_hs ds_mixed ds_sfo
Function to calculate endpoints for further use from kinetic models fitted with mkinfit	endpoints
Experimental datasets used for development and testing of error models	experimental_data_for_UBA_2019
Normalisation factors for aerobic soil degradation according to FOCUS guidance	f_time_norm_focus f_time_norm_focus.mkindsg f_time_norm_focus.numeric
Datasets A to F from the FOCUS Kinetics report from 2006	FOCUS_2006_A FOCUS_2006_B FOCUS_2006_C FOCUS_2006_D FOCUS_2006_E FOCUS_2006_F
Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)	FOCUS_2006_DFOP_ref_A_to_B
Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)	FOCUS_2006_FOMC_ref_A_to_F
Results of fitting the HS model to Datasets A to F of FOCUS (2006)	FOCUS_2006_HS_ref_A_to_F
Results of fitting the SFO model to Datasets A to F of FOCUS (2006)	FOCUS_2006_SFO_ref_A_to_F
FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar	focus_soil_moisture
First-Order Multi-Compartment kinetics	FOMC.solution
Retrieve a degradation function from the mmkin namespace	get_deg_func
Hierarchical kinetics template	hierarchical_kinetics
Hockey-Stick kinetics	HS.solution
Method to get the names of ill-defined parameters	illparms illparms.mhmkin illparms.mkinfit illparms.mmkin illparms.saem.mmkin print.illparms.mhmkin print.illparms.mkinfit print.illparms.mmkin print.illparms.saem.mmkin
Function to perform isometric log-ratio transformation	ilr invilr
Confidence intervals for parameters in saem.mmkin objects	intervals.saem.mmkin
Indeterminate order rate equation kinetics	IORE.solution
Plot the distribution of log likelihoods from multistart objects	llhist
Lack-of-fit test for models fitted to data with replicates	loftest loftest.mkinfit
Logistic kinetics	logistic.solution
Calculated the log-likelihood of a fitted mkinfit object	logLik.mkinfit
logLik method for saem.mmkin objects	logLik.saem.mmkin
Likelihood ratio test for mkinfit models	lrtest.mkinfit lrtest.mmkin
Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit	max_twa_dfop max_twa_fomc max_twa_hs max_twa_parent max_twa_sfo
Datasets on aerobic soil metabolism of 2,4,5-T in six soils	mccall81_245T
Calculate mean degradation parameters for an mmkin row object	mean_degparms
Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models	mhmkin mhmkin.list mhmkin.mmkin print.mhmkin [.mhmkin
Create a mixed effects model from an mmkin row object	mixed mixed.mmkin print.mixed.mmkin
Convert a dataframe from long to wide format	mkin_long_to_wide
Convert a dataframe with observations over time into long format	mkin_wide_to_long
A dataset class for mkin	mkinds print.mkinds
A class for dataset groups for mkin	mkindsg print.mkindsg
Calculate the minimum error to assume in order to pass the variance test	mkinerrmin
Function to plot squared residuals and the error model for an mkin object	mkinerrplot
Fit a kinetic model to data with one or more state variables	mkinfit
Function to set up a kinetic model with one or more state variables	mkinmod mkinsub print.mkinmod
Function to plot the confidence intervals obtained using mkinfit	mkinparplot
Plot the observed data and the fitted model of an mkinfit object	mkinplot
Produce predictions from a kinetic model using specific parameters	mkinpredict mkinpredict.mkinfit mkinpredict.mkinmod
Function to plot residuals stored in an mkin object	mkinresplot
Fit one or more kinetic models with one or more state variables to one or more datasets	mmkin print.mmkin
Perform a hierarchical model fit with multiple starting values	best best.default multistart multistart.saem.mmkin print.multistart which.best which.best.default
Evaluate parent kinetics using the NAFTA guidance	nafta print.nafta
Example datasets from the NAFTA SOP published 2015	NAFTA_SOP_Appendix_B NAFTA_SOP_Appendix_D
Example datasets from Attachment 1 to the NAFTA SOP published 2015	NAFTA_SOP_Attachment
Helper functions to create nlme models from mmkin row objects	nlme_data nlme_function
Create an nlme model for an mmkin row object	nlme.mmkin print.nlme.mmkin update.nlme.mmkin
Number of observations on which an mkinfit object was fitted	nobs.mkinfit
Extract model parameters	parms parms.mkinfit parms.mmkin parms.multistart parms.saem.mmkin
Plot parameter variability of multistart objects	parplot parplot.multistart.saem.mmkin
Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object	plot.mixed.mmkin
Plot the observed data and the fitted model of an mkinfit object	plot.mkinfit plot_err plot_res plot_sep
Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object	plot.mmkin
Plot the results of the three models used in the NAFTA scheme.	plot.nafta
Read datasets and relevant meta information from a spreadsheet file	read_spreadsheet
Extract residuals from an mkinfit model	residuals.mkinfit
Fit nonlinear mixed models with SAEM	print.saem.mmkin saem saem.mmkin saemix_data saemix_model
Metabolism data set used for checking the software quality of KinGUI	schaefer07_complex_case schaefer07_complex_results
Set non-detects and unquantified values in residue series without replicates	set_nd_nq set_nd_nq_focus
Single First-Order kinetics	SFO.solution
Single First-Order Reversible Binding kinetics	SFORB.solution
Two-component error model	sigma_twocomp
Method to get status information for fit array objects	print.status.mhmkin print.status.mmkin status status.mhmkin status.mmkin
Display the output of a summary function according to the output format	html_listing summary_listing tex_listing
Summary method for class "mkinfit"	print.summary.mkinfit summary.mkinfit
Summary method for class "mmkin"	print.summary.mmkin summary.mmkin
Summary method for class "nlme.mmkin"	print.summary.nlme.mmkin summary.nlme.mmkin
Summary method for class "saem.mmkin"	print.summary.saem.mmkin summary.saem.mmkin
Synthetic datasets for one parent compound with two metabolites	synthetic_data_for_UBA_2014
Three experimental datasets from two water sediment systems and one soil	test_data_from_UBA_2014
Functions to transform and backtransform kinetic parameters for fitting	backtransform_odeparms transform_odeparms
Update an mkinfit model with different arguments	update.mkinfit

Package: mkin 1.2.9

mkin: Kinetic Evaluation of Chemical Degradation Data

Calculation of time weighted average concentrations with mkin

Example evaluation of FOCUS Example Dataset D

Example evaluation of FOCUS Laboratory Data L1 to L3

Short introduction to mkin

Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione

Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P

Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)