Kinetic Evaluation of Chemical Degradation Data

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Documentation for package ‘mkin’ version 1.1.0

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A B C D E F G H I L M N P R S T U misc

-- A --

add_err Add normally distributed errors to simulated kinetic degradation data
AIC.mmkin Calculate the AIC for a column of an mmkin object
aw Calculate Akaike weights for model averaging
aw.mkinfit Calculate Akaike weights for model averaging
aw.mmkin Calculate Akaike weights for model averaging

-- B --

backtransform_odeparms Functions to transform and backtransform kinetic parameters for fitting
BIC.mmkin Calculate the AIC for a column of an mmkin object

-- C --

CAKE_export Export a list of datasets format to a CAKE study file
confint.mkinfit Confidence intervals for parameters of mkinfit objects
create_deg_func Create degradation functions for known analytical solutions

-- D --

D24_2014 Aerobic soil degradation data on 2,4-D from the EU assessment in 2014
DFOP.solution Double First-Order in Parallel kinetics
dimethenamid_2018 Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018

-- E --

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

-- F --

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)
focus_soil_moisture FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
FOMC.solution First-Order Multi-Compartment kinetics
f_time_norm_focus Normalisation factors for aerobic soil degradation according to FOCUS guidance
f_time_norm_focus.mkindsg Normalisation factors for aerobic soil degradation according to FOCUS guidance
f_time_norm_focus.numeric Normalisation factors for aerobic soil degradation according to FOCUS guidance

-- G --

get_deg_func Retrieve a degradation function from the mmkin namespace

-- H --

HS.solution Hockey-Stick kinetics

-- I --

ilr Function to perform isometric log-ratio transformation
intervals.saem.mmkin Confidence intervals for parameters in saem.mmkin objects
invilr Function to perform isometric log-ratio transformation
IORE.solution Indeterminate order rate equation kinetics

-- L --

loftest Lack-of-fit test for models fitted to data with replicates
loftest.mkinfit Lack-of-fit test for models fitted to data with replicates
logistic.solution Logistic kinetics
logLik.mkinfit Calculated the log-likelihood of a fitted mkinfit object
lrtest.mkinfit Likelihood ratio test for mkinfit models
lrtest.mmkin Likelihood ratio test for mkinfit models

-- M --

max_twa_dfop Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
max_twa_fomc Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
max_twa_hs Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
max_twa_parent Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
max_twa_sfo 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
mean_degparms Calculate mean degradation parameters for an mmkin row object
mixed Create a mixed effects model from an mmkin row object
mixed.mmkin Create a mixed effects model from an mmkin row object
mkinds A dataset class for mkin
mkindsg A class for dataset groups 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 model with one or more state variables
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

-- N --

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
nlme.mmkin Create an nlme model for an mmkin row object
nlme_data Helper functions to create nlme models from mmkin row objects
nlme_function Helper functions to create nlme models from mmkin row objects
nobs.mkinfit Number of observations on which an mkinfit object was fitted

-- P --

parms Extract model parameters from mkinfit models
parms.mkinfit Extract model parameters from mkinfit models
parms.mmkin Extract model parameters from mkinfit models
plot.mixed.mmkin Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
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.
plot_err Plot the observed data and the fitted model of an mkinfit object
plot_res Plot the observed data and the fitted model of an mkinfit object
plot_sep Plot the observed data and the fitted model of an mkinfit object
print.mixed.mmkin Create a mixed effects model from an mmkin row object
print.mkinds A dataset class for mkin
print.mkindsg A class for dataset groups for mkin
print.mkinmod Function to set up a kinetic model with one or more state variables
print.mmkin Fit one or more kinetic models with one or more state variables to one or more datasets
print.nafta Evaluate parent kinetics using the NAFTA guidance
print.nlme.mmkin Create an nlme model for an mmkin row object
print.saem.mmkin Fit nonlinear mixed models with SAEM
print.summary.mkinfit Summary method for class "mkinfit"
print.summary.nlme.mmkin Summary method for class "nlme.mmkin"
print.summary.saem.mmkin Summary method for class "saem.mmkin"

-- R --

residuals.mkinfit Extract residuals from an mkinfit model

-- S --

saem Fit nonlinear mixed models with SAEM
saem.mmkin Fit nonlinear mixed models with SAEM
saemix_data Fit nonlinear mixed models with SAEM
saemix_model Fit nonlinear mixed models with SAEM
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"
summary.nlme.mmkin Summary method for class "nlme.mmkin"
summary.saem.mmkin Summary method for class "saem.mmkin"
synthetic_data_for_UBA_2014 Synthetic datasets for one parent compound with two metabolites

-- T --

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

-- U --

update.mkinfit Update an mkinfit model with different arguments
update.nlme.mmkin Create an nlme model for an mmkin row object

-- misc --

[.mmkin Subsetting method for mmkin objects