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.

Install the latest version of this package by entering the following in R:
install.packages("mkin")
AuthorJohannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb], René Lehmann [ctb], Eurofins Regulatory AG [cph]
Date of publication2016-12-08 16:56:56
MaintainerJohannes Ranke <jranke@uni-bremen.de>
LicenseGPL
Version0.9.45
http://github.com/jranke/mkin

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...

Functions

add_err Man page
backtransform_odeparms Man page
DFOP.solution Man page
endpoints Man page
FOCUS_2006_A Man page
FOCUS_2006_B Man page
FOCUS_2006_C Man page
FOCUS_2006_D Man page
FOCUS_2006_DFOP_ref_A_to_B Man page
FOCUS_2006_E Man page
FOCUS_2006_F Man page
FOCUS_2006_FOMC_ref_A_to_F Man page
FOCUS_2006_HS_ref_A_to_F Man page
FOCUS_2006_SFO_ref_A_to_F Man page
FOMC.solution Man page
geometric_mean Man page
HS.solution Man page
ilr Man page
invilr Man page
IORE.solution Man page
mccall81_245T Man page
mkinds Man page
mkinerrmin Man page
mkinfit Man page
mkin_long_to_wide Man page
mkinmod Man page
mkinparplot Man page
mkinplot Man page
mkinpredict Man page
mkinresplot Man page
mkinsub Man page
mkin_wide_to_long Man page
mmkin Man page
[.mmkin Man page
plot.mkinfit Man page
plot.mmkin Man page
plot_sep Man page
print.mkinds Man page
print.mkinmod Man page
print.summary.mkinfit Man page
schaefer07_complex_case Man page
schaefer07_complex_results Man page
SFORB.solution Man page
SFO.solution Man page
summary.mkinfit Man page
synthetic_data_for_UBA_2014 Man page
transform_odeparms Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.