Kinetic Evaluation of Chemical Degradation Data


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Documentation for package ‘mkin’ version 0.9.49.5

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add_err Add normally distributed errors to simulated kinetic degradation data
AIC.mmkin Calculated the AIC for a column of an mmkin object
backtransform_odeparms Functions to transform and backtransform kinetic parameters for fitting
CAKE_export Export a list of datasets format to a CAKE study file
DFOP.solution Double First-Order in Parallel kinetics
endpoints Function to calculate endpoints for further use from kinetic models fitted with mkinfit
experimental_data_for_UBA_2019 Experimental datasets used for development and testing of error models
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 (2006)
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 (2006)
FOCUS_2006_HS_ref_A_to_F Results of fitting the HS model to Datasets A to F of FOCUS (2006)
FOCUS_2006_SFO_ref_A_to_F Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
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
invilr Function to perform isometric log-ratio transformation
IORE.solution Indeterminate order rate equation kinetics
logistic.solution Logistic kinetics
logLik.mkinfit Calculated the log-likelihood of a fitted mkinfit object
max_twa_parent Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
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 variance test
mkinerrplot Function to plot squared residuals and the error model for an mkin object
mkinfit Fit a kinetic model to data with one or more state variables
mkinmod Function to set up a kinetic model with one or more state variables
mkinparplot Function to plot the confidence intervals obtained using mkinfit
mkinplot Plot the observed data and the fitted model of an mkinfit object
mkinpredict Produce predictions from a kinetic model using specific parameters
mkinpredict.mkinfit Produce predictions from a kinetic model using specific parameters
mkinpredict.mkinmod Produce predictions from a kinetic model using specific parameters
mkinresplot Function to plot residuals stored in an mkin object
mkinsub Function to set up a kinetic submodel for one state variable
mkin_long_to_wide Convert a dataframe from long to wide format
mkin_wide_to_long Convert a dataframe with observations over time into long format
mmkin Fit one or more kinetic models with one or more state variables to one or more datasets
nafta Evaluate parent kinetics using the NAFTA guidance
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
plot.mkinfit Plot the observed data and the fitted model of an mkinfit object
plot.mmkin Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
plot.nafta Plot the results of the three models used in the NAFTA scheme. The plots are ordered with increasing complexity of the model in this function (SFO, then IORE, then DFOP).
plot_sep Plot the observed data and the fitted model of an mkinfit object
print.mkinds Print mkinds objects
print.mkinmod Print mkinmod objects
print.nafta Print nafta objects
print.summary.mkinfit Summary method for class "mkinfit"
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
SFO.solution Single First-Order kinetics
SFORB.solution Single First-Order Reversible Binding kinetics
sigma_twocomp Two component error model
summary.mkinfit Summary method for class "mkinfit"
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
transform_odeparms Functions to transform and backtransform kinetic parameters for fitting
[.mmkin Subsetting method for mmkin objects