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
mkin/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

degradationfocus-kineticskinetic-modelskineticsodeode-model

69 exports 10 stars 2.14 score 42 dependencies 1 dependents 2 mentions 926 downloads

Last updated 3 months agofrom:e18c8da322

Exports:add_errawbacktransform_odeparmsbestCAKE_exportcreate_deg_funcDFOP.solutionendpointsf_time_norm_focusFOMC.solutionget_deg_funchierarchical_kineticsHS.solutionhtml_listingillparmsilrintervalsinvilrIORE.solutionllhistloftestlogistic.solutionlrtestmax_twa_dfopmax_twa_fomcmax_twa_hsmax_twa_parentmax_twa_sfomean_degparmsmhmkinmixedmkin_long_to_widemkin_wide_to_longmkindsmkindsgmkinerrminmkinerrplotmkinfitmkinmodmkinparplotmkinplotmkinpredictmkinresplotmkinsubmmkinmultistartnaftanlmenlme_datanlme_functionparmsparplotplot_errplot_resplot_sepread_spreadsheetsaemsaemix_datasaemix_modelset_nd_nqset_nd_nq_focusSFO.solutionSFORB.solutionsigma_twocompstatussummary_listingtex_listingtransform_odeparmswhich.best

Dependencies:callrclicolorspacedescdeSolvefansifarverggplot2gluegridExtragtableinlineisobandlabelinglatticelifecyclelmtestmagrittrMASSMatrixmclustmgcvmunsellnlmenpdenumDerivpillarpkgbuildpkgconfigprocessxpsR6RColorBrewerrlangsaemixscalestibbleutf8vctrsviridisLitewithrzoo

Calculation of time weighted average concentrations with mkin

Rendered fromtwa.rmdusingknitr::rmarkdownon Jun 26 2024.

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

Example evaluation of FOCUS Example Dataset D

Rendered fromFOCUS_D.rmdusingknitr::rmarkdownon Jun 26 2024.

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

Example evaluation of FOCUS Laboratory Data L1 to L3

Rendered fromFOCUS_L.rmdusingknitr::rmarkdownon Jun 26 2024.

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

Short introduction to mkin

Rendered frommkin.rmdusingknitr::rmarkdownon Jun 26 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 Jun 26 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 Jun 26 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 Jun 26 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Subsetting method for mmkin objects[.mmkin
Add normally distributed errors to simulated kinetic degradation dataadd_err
Calculate the AIC for a column of an mmkin objectAIC.mmkin BIC.mmkin
Anova method for saem.mmkin objectsanova.saem.mmkin
Calculate Akaike weights for model averagingaw aw.mixed.mmkin aw.mkinfit aw.mmkin aw.multistart
Export a list of datasets format to a CAKE study fileCAKE_export
Check if fit within an mhmkin object failedcheck_failed
Confidence intervals for parameters of mkinfit objectsconfint.mkinfit
Create degradation functions for known analytical solutionscreate_deg_func
Aerobic soil degradation data on 2,4-D from the EU assessment in 2014D24_2014
Double First-Order in Parallel kineticsDFOP.solution
Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018dimethenamid_2018
Synthetic data for hierarchical kinetic degradation modelsds_dfop ds_dfop_sfo ds_fomc ds_hs ds_mixed ds_sfo
Function to calculate endpoints for further use from kinetic models fitted with mkinfitendpoints
Experimental datasets used for development and testing of error modelsexperimental_data_for_UBA_2019
Normalisation factors for aerobic soil degradation according to FOCUS guidancef_time_norm_focus f_time_norm_focus.mkindsg f_time_norm_focus.numeric
Datasets A to F from the FOCUS Kinetics report from 2006FOCUS_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 barfocus_soil_moisture
First-Order Multi-Compartment kineticsFOMC.solution
Retrieve a degradation function from the mmkin namespaceget_deg_func
Hierarchical kinetics templatehierarchical_kinetics
Hockey-Stick kineticsHS.solution
Method to get the names of ill-defined parametersillparms 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 transformationilr invilr
Confidence intervals for parameters in saem.mmkin objectsintervals.saem.mmkin
Indeterminate order rate equation kineticsIORE.solution
Plot the distribution of log likelihoods from multistart objectsllhist
Lack-of-fit test for models fitted to data with replicatesloftest loftest.mkinfit
Logistic kineticslogistic.solution
Calculated the log-likelihood of a fitted mkinfit objectlogLik.mkinfit
logLik method for saem.mmkin objectslogLik.saem.mmkin
Likelihood ratio test for mkinfit modelslrtest.mkinfit lrtest.mmkin
Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfitmax_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 soilsmccall81_245T
Calculate mean degradation parameters for an mmkin row objectmean_degparms
Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error modelsmhmkin mhmkin.list mhmkin.mmkin print.mhmkin [.mhmkin
Create a mixed effects model from an mmkin row objectmixed mixed.mmkin print.mixed.mmkin
Convert a dataframe from long to wide formatmkin_long_to_wide
Convert a dataframe with observations over time into long formatmkin_wide_to_long
A dataset class for mkinmkinds print.mkinds
A class for dataset groups for mkinmkindsg print.mkindsg
Calculate the minimum error to assume in order to pass the variance testmkinerrmin
Function to plot squared residuals and the error model for an mkin objectmkinerrplot
Fit a kinetic model to data with one or more state variablesmkinfit
Function to set up a kinetic model with one or more state variablesmkinmod mkinsub print.mkinmod
Function to plot the confidence intervals obtained using mkinfitmkinparplot
Plot the observed data and the fitted model of an mkinfit objectmkinplot
Produce predictions from a kinetic model using specific parametersmkinpredict mkinpredict.mkinfit mkinpredict.mkinmod
Function to plot residuals stored in an mkin objectmkinresplot
Fit one or more kinetic models with one or more state variables to one or more datasetsmmkin print.mmkin
Perform a hierarchical model fit with multiple starting valuesbest best.default multistart multistart.saem.mmkin print.multistart which.best which.best.default
Evaluate parent kinetics using the NAFTA guidancenafta print.nafta
Example datasets from the NAFTA SOP published 2015NAFTA_SOP_Appendix_B NAFTA_SOP_Appendix_D
Example datasets from Attachment 1 to the NAFTA SOP published 2015NAFTA_SOP_Attachment
Helper functions to create nlme models from mmkin row objectsnlme_data nlme_function
Create an nlme model for an mmkin row objectnlme.mmkin print.nlme.mmkin update.nlme.mmkin
Number of observations on which an mkinfit object was fittednobs.mkinfit
Extract model parametersparms parms.mkinfit parms.mmkin parms.multistart parms.saem.mmkin
Plot parameter variability of multistart objectsparplot parplot.multistart.saem.mmkin
Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row objectplot.mixed.mmkin
Plot the observed data and the fitted model of an mkinfit objectplot.mkinfit plot_err plot_res plot_sep
Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin objectplot.mmkin
Plot the results of the three models used in the NAFTA scheme.plot.nafta
Read datasets and relevant meta information from a spreadsheet fileread_spreadsheet
Extract residuals from an mkinfit modelresiduals.mkinfit
Fit nonlinear mixed models with SAEMprint.saem.mmkin saem saem.mmkin saemix_data saemix_model
Metabolism data set used for checking the software quality of KinGUIschaefer07_complex_case schaefer07_complex_results
Set non-detects and unquantified values in residue series without replicatesset_nd_nq set_nd_nq_focus
Single First-Order kineticsSFO.solution
Single First-Order Reversible Binding kineticsSFORB.solution
Two-component error modelsigma_twocomp
Method to get status information for fit array objectsprint.status.mhmkin print.status.mmkin status status.mhmkin status.mmkin
Display the output of a summary function according to the output formathtml_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 metabolitessynthetic_data_for_UBA_2014
Three experimental datasets from two water sediment systems and one soiltest_data_from_UBA_2014
Functions to transform and backtransform kinetic parameters for fittingbacktransform_odeparms transform_odeparms
Update an mkinfit model with different argumentsupdate.mkinfit