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], RenĂ© Lehmann [ctb], Eurofins Regulatory AG [cph] |

Date of publication | 2016-12-08 16:56:56 |

Maintainer | Johannes Ranke <jranke@uni-bremen.de> |

License | GPL |

Version | 0.9.45 |

http://github.com/jranke/mkin |

**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...

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
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