Kinetic Evaluation of Chemical Degradation Data

Documentation for package ‘mkin’ version 1.2.1

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A B C D E F G H I L M N P R S T U W 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
anova.saem.mmkin	Anova method for saem.mmkin objects
aw	Calculate Akaike weights for model averaging
aw.mixed.mmkin	Calculate Akaike weights for model averaging
aw.mkinfit	Calculate Akaike weights for model averaging
aw.mmkin	Calculate Akaike weights for model averaging
aw.multistart	Calculate Akaike weights for model averaging

-- B --

backtransform_odeparms	Functions to transform and backtransform kinetic parameters for fitting
best	Perform a hierarchical model fit with multiple starting values
best.default	Perform a hierarchical model fit with multiple starting values
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
ds_dfop	Synthetic data for hierarchical kinetic degradation models
ds_dfop_sfo	Synthetic data for hierarchical kinetic degradation models
ds_fomc	Synthetic data for hierarchical kinetic degradation models
ds_hs	Synthetic data for hierarchical kinetic degradation models
ds_mixed	Synthetic data for hierarchical kinetic degradation models
ds_sfo	Synthetic data for hierarchical kinetic degradation models

-- 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 --

illparms	Method to get the names of ill-defined parameters
illparms.mhmkin	Method to get the names of ill-defined parameters
illparms.mkinfit	Method to get the names of ill-defined parameters
illparms.mmkin	Method to get the names of ill-defined parameters
illparms.saem.mmkin	Method to get the names of ill-defined parameters
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 --

llhist	Plot the distribution of log likelihoods from multistart objects
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
logLik.saem.mmkin	logLik method for saem.mmkin objects
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
mhmkin	Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
mhmkin.list	Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
mhmkin.mmkin	Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
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
multistart	Perform a hierarchical model fit with multiple starting values
multistart.saem.mmkin	Perform a hierarchical model fit with multiple starting values

-- 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
parms.mkinfit	Extract model parameters
parms.mmkin	Extract model parameters
parms.multistart	Extract model parameters
parms.saem.mmkin	Fit nonlinear mixed models with SAEM
parplot	Plot parameter variability of multistart objects
parplot.multistart.saem.mmkin	Plot parameter variability of multistart objects
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.illparms.mhmkin	Method to get the names of ill-defined parameters
print.illparms.mkinfit	Method to get the names of ill-defined parameters
print.illparms.mmkin	Method to get the names of ill-defined parameters
print.illparms.saem.mmkin	Method to get the names of ill-defined parameters
print.mhmkin	Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
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.multistart	Perform a hierarchical model fit with multiple starting values
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.status.mhmkin	Method to get status information for fit array objects
print.status.mmkin	Method to get status information for fit array objects
print.summary.mkinfit	Summary method for class "mkinfit"
print.summary.mmkin	Summary method for class "mmkin"
print.summary.nlme.mmkin	Summary method for class "nlme.mmkin"
print.summary.saem.mmkin	Summary method for class "saem.mmkin"

-- R --

read_spreadsheet	Read datasets and relevant meta information from a spreadsheet file
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
set_nd_nq	Set non-detects and unquantified values in residue series without replicates
set_nd_nq_focus	Set non-detects and unquantified values in residue series without replicates
SFO.solution	Single First-Order kinetics
SFORB.solution	Single First-Order Reversible Binding kinetics
sigma_twocomp	Two-component error model
status	Method to get status information for fit array objects
status.mhmkin	Method to get status information for fit array objects
status.mmkin	Method to get status information for fit array objects
summary.mkinfit	Summary method for class "mkinfit"
summary.mmkin	Summary method for class "mmkin"
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
tex_listing	Wrap the output of a summary function in tex listing environment
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

-- W --

which.best	Perform a hierarchical model fit with multiple starting values
which.best.default	Perform a hierarchical model fit with multiple starting values

-- misc --

[.mhmkin	Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
[.mmkin	Subsetting method for mmkin objects