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 and a choice of the optimisation methods made available by the 'FME' package. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using compiled C functions. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.

Author
Johannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb], René Lehmann [ctb], Eurofins Regulatory AG [cph]
Date of publication
2016-06-29 02:40:33
Maintainer
Johannes Ranke <jranke@uni-bremen.de>
License
GPL
Version
0.9.44
URLs

View on CRAN

Man pages

add_err
Add normally distributed errors to simulated kinetic...
DFOP.solution
Double First-Order in Parallel kinetics
endpoints
Function to calculate endpoints for further use from kinetic...
Extract.mmkin
Subsetting method for mmkin objects
FOCUS_2006_datasets
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_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...
FOMC.solution
First-Order Multi-Compartment kinetics
geometric_mean
Calculate the geometric mean
HS.solution
Hockey-Stick kinetics
ilr
Function to perform isometric log-ratio transformation
IORE.solution
Indeterminate order rate equation kinetics
mccall81_245T
Datasets on aerobic soil metabolism of 2,4,5-T in six soils
mkinds
A dataset class for mkin
mkinerrmin
Calculate the minimum error to assume in order to pass the...
mkinfit
Fit a kinetic model to data with one or more state variables
mkin_long_to_wide
Convert a dataframe from long to wide format
mkinmod
Function to set up a kinetic model with one or more state...
mkinparplot
Function to plot the confidence intervals obtained using...
mkinplot
Plot the observed data and the fitted model of an mkinfit...
mkinpredict
Produce predictions from a kinetic model using specific...
mkinresplot
Function to plot residuals stored in an mkin object
mkinsub
Function to set up a kinetic submodel for one state variable
mkin_wide_to_long
Convert a dataframe with observations over time into long...
mmkin
Fit one or more kinetic models with one or more state...
plot.mkinfit
Plot the observed data and the fitted model of an mkinfit...
plot.mmkin
Plot model fits (observed and fitted) and the residuals for a...
print.mkinds
Print mkinds objects
print.mkinmod
Print mkinmod objects
schaefer07_complex_case
Metabolism data set used for checking the software quality of...
SFORB.solution
Single First-Order Reversible Binding kinetics
SFO.solution
Single First-Order kinetics
summary.mkinfit
Summary method for class "mkinfit"
synthetic_data_for_UBA
Synthetic datasets for one parent compound with two...
transform_odeparms
Functions to transform and backtransform kinetic parameters...

Files in this package

mkin
mkin/TODO
mkin/inst
mkin/inst/examples
mkin/inst/examples/mkinds.R
mkin/inst/doc
mkin/inst/doc/FOCUS_Z.pdf
mkin/inst/doc/FOCUS_D.R
mkin/inst/doc/FOCUS_L.R
mkin/inst/doc/FOCUS_Z.Rnw
mkin/inst/doc/mkin.html
mkin/inst/doc/compiled_models.Rmd
mkin/inst/doc/FOCUS_D.Rmd
mkin/inst/doc/FOCUS_D.html
mkin/inst/doc/mkin.R
mkin/inst/doc/FOCUS_L.html
mkin/inst/doc/compiled_models.html
mkin/inst/doc/compiled_models.R
mkin/inst/doc/mkin.Rmd
mkin/inst/doc/FOCUS_Z.R
mkin/inst/doc/FOCUS_L.Rmd
mkin/tests
mkin/tests/testthat.R
mkin/tests/testthat
mkin/tests/testthat/test_mkinpredict_SFO_SFO.R
mkin/tests/testthat/test_FOMC_ill-defined.R
mkin/tests/testthat/test_schaefer07_complex_case.R
mkin/tests/testthat/test_FOCUS_D_UBA_expertise.R
mkin/tests/testthat/test_FOCUS_chi2_error_level.R
mkin/tests/testthat/test_parent_only.R
mkin/tests/testthat/test_synthetic_data_for_UBA_2014.R
mkin/NAMESPACE
mkin/NEWS.md
mkin/data
mkin/data/schaefer07_complex_case.RData
mkin/data/synthetic_data_for_UBA_2014.RData
mkin/data/FOCUS_2006_datasets.RData
mkin/data/FOCUS_2006_HS_ref_A_to_F.rda
mkin/data/mccall81_245T.RData
mkin/data/FOCUS_2006_FOMC_ref_A_to_F.rda
mkin/data/FOCUS_2006_DFOP_ref_A_to_B.rda
mkin/data/FOCUS_2006_SFO_ref_A_to_F.rda
mkin/R
mkin/R/mkinsub.R
mkin/R/SFO.solution.R
mkin/R/plot.mmkin.R
mkin/R/transform_odeparms.R
mkin/R/SFORB.solution.R
mkin/R/mkinparplot.R
mkin/R/mkinresplot.R
mkin/R/mmkin.R
mkin/R/plot.mkinfit.R
mkin/R/mkinmod.R
mkin/R/mkinplot.R
mkin/R/mkinds.R
mkin/R/add_err.R
mkin/R/geometric_mean.R
mkin/R/FOMC.solution.R
mkin/R/mkinfit.R
mkin/R/endpoints.R
mkin/R/HS.solution.R
mkin/R/mkinpredict.R
mkin/R/ilr.R
mkin/R/mkin_wide_to_long.R
mkin/R/IORE.solution.R
mkin/R/DFOP.solution.R
mkin/R/mkin_long_to_wide.R
mkin/R/mkinerrmin.R
mkin/vignettes
mkin/vignettes/FOCUS_Z.Rnw
mkin/vignettes/mkin_vignettes.css
mkin/vignettes/compiled_models.Rmd
mkin/vignettes/FOCUS_D.Rmd
mkin/vignettes/references.bib
mkin/vignettes/mkin.Rmd
mkin/vignettes/header.tex
mkin/vignettes/FOCUS_L.Rmd
mkin/README.md
mkin/MD5
mkin/build
mkin/build/vignette.rds
mkin/DESCRIPTION
mkin/man
mkin/man/SFO.solution.Rd
mkin/man/print.mkinds.Rd
mkin/man/add_err.Rd
mkin/man/SFORB.solution.Rd
mkin/man/HS.solution.Rd
mkin/man/geometric_mean.Rd
mkin/man/summary.mkinfit.Rd
mkin/man/Extract.mmkin.Rd
mkin/man/ilr.Rd
mkin/man/mkinerrmin.Rd
mkin/man/FOCUS_2006_HS_ref_A_to_F.Rd
mkin/man/mkin_wide_to_long.Rd
mkin/man/mkinparplot.Rd
mkin/man/plot.mmkin.Rd
mkin/man/mccall81_245T.Rd
mkin/man/FOCUS_2006_SFO_ref_A_to_F.Rd
mkin/man/mkinmod.Rd
mkin/man/synthetic_data_for_UBA.Rd
mkin/man/schaefer07_complex_case.Rd
mkin/man/mkin_long_to_wide.Rd
mkin/man/mkinresplot.Rd
mkin/man/transform_odeparms.Rd
mkin/man/DFOP.solution.Rd
mkin/man/mkinds.Rd
mkin/man/mkinfit.Rd
mkin/man/plot.mkinfit.Rd
mkin/man/mmkin.Rd
mkin/man/endpoints.Rd
mkin/man/mkinsub.Rd
mkin/man/FOMC.solution.Rd
mkin/man/FOCUS_2006_FOMC_ref_A_to_F.Rd
mkin/man/IORE.solution.Rd
mkin/man/print.mkinmod.Rd
mkin/man/FOCUS_2006_DFOP_ref_A_to_B.Rd
mkin/man/mkinplot.Rd
mkin/man/FOCUS_2006_datasets.Rd
mkin/man/mkinpredict.Rd