Reference

Main functions

Essential functionality

mkinmod() print(<mkinmod>) mkinsub()

Function to set up a kinetic model with one or more state variables

mkinfit()

Fit a kinetic model to data with one or more state variables

mmkin() print(<mmkin>)

Fit one or more kinetic models with one or more state variables to one or more datasets

mhmkin() `[`(<mhmkin>) print(<mhmkin>)

Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models

Generics

Generic functions introduced by the package

parms()

Extract model parameters

status() print(<status.mmkin>) print(<status.mhmkin>)

Method to get status information for fit array objects

illparms() print(<illparms.mkinfit>) print(<illparms.mmkin>) print(<illparms.saem.mmkin>) print(<illparms.mhmkin>)

Method to get the names of ill-defined parameters

endpoints()

Function to calculate endpoints for further use from kinetic models fitted with mkinfit

aw()

Calculate Akaike weights for model averaging

Show results

Functions working with mkinfit objects

plot(<mkinfit>) plot_sep() plot_res() plot_err()

Plot the observed data and the fitted model of an mkinfit object

summary(<mkinfit>) print(<summary.mkinfit>)

Summary method for class "mkinfit"

confint(<mkinfit>)

Confidence intervals for parameters of mkinfit objects

update(<mkinfit>)

Update an mkinfit model with different arguments

lrtest(<mkinfit>) lrtest(<mmkin>)

Likelihood ratio test for mkinfit models

loftest()

Lack-of-fit test for models fitted to data with replicates

mkinerrmin()

Calculate the minimum error to assume in order to pass the variance test

CAKE_export()

Export a list of datasets format to a CAKE study file

Work with mmkin objects

Functions working with aggregated results

`[`(<mmkin>)

Subsetting method for mmkin objects

plot(<mmkin>)

Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object

AIC(<mmkin>) BIC(<mmkin>)

Calculate the AIC for a column of an mmkin object

summary(<mmkin>) print(<summary.mmkin>)

Summary method for class "mmkin"

Mixed models

Create and work with nonlinear hierarchical models

read_spreadsheet()

Read datasets and relevant meta information from a spreadsheet file

nlme(<mmkin>) print(<nlme.mmkin>) update(<nlme.mmkin>)

Create an nlme model for an mmkin row object

saem() print(<saem.mmkin>) saemix_model() saemix_data() parms(<saem.mmkin>)

Fit nonlinear mixed models with SAEM

mhmkin() `[`(<mhmkin>) print(<mhmkin>)

Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models

plot(<mixed.mmkin>)

Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object

summary(<nlme.mmkin>) print(<summary.nlme.mmkin>)

Summary method for class "nlme.mmkin"

summary(<saem.mmkin>) print(<summary.saem.mmkin>)

Summary method for class "saem.mmkin"

anova(<saem.mmkin>)

Anova method for saem.mmkin objects

logLik(<saem.mmkin>)

logLik method for saem.mmkin objects

nlme_function() nlme_data()

Helper functions to create nlme models from mmkin row objects

get_deg_func()

Retrieve a degradation function from the mmkin namespace

mixed() print(<mixed.mmkin>)

Create a mixed effects model from an mmkin row object

reexports intervals lrtest nlme

Objects exported from other packages

intervals(<saem.mmkin>)

Confidence intervals for parameters in saem.mmkin objects

multistart() print(<multistart>) best() which.best()

Perform a hierarchical model fit with multiple starting values

llhist()

Plot the distribution of log likelihoods from multistart objects

parplot()

Plot parameter variability of multistart objects

Datasets and known results

ds_mixed ds_sfo ds_fomc ds_dfop ds_hs ds_dfop_sfo

Synthetic data for hierarchical kinetic degradation models

D24_2014

Aerobic soil degradation data on 2,4-D from the EU assessment in 2014

dimethenamid_2018

Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018

FOCUS_2006_A FOCUS_2006_B FOCUS_2006_C FOCUS_2006_D FOCUS_2006_E FOCUS_2006_F

Datasets A to F from the FOCUS Kinetics report from 2006

FOCUS_2006_SFO_ref_A_to_F

Results of fitting the SFO model to Datasets A to F of FOCUS (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_DFOP_ref_A_to_B

Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

NAFTA_SOP_Appendix_B 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

mccall81_245T

Datasets on aerobic soil metabolism of 2,4,5-T in six soils

schaefer07_complex_case

Metabolism data set used for checking the software quality of KinGUI

synthetic_data_for_UBA_2014

Synthetic datasets for one parent compound with two metabolites

experimental_data_for_UBA_2019

Experimental datasets used for development and testing of error models

test_data_from_UBA_2014

Three experimental datasets from two water sediment systems and one soil

focus_soil_moisture

FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar

print(<mkinds>)

A dataset class for mkin

print(<mkindsg>)

A class for dataset groups for mkin

NAFTA guidance

nafta() print(<nafta>)

Evaluate parent kinetics using the NAFTA guidance

plot(<nafta>)

Plot the results of the three models used in the NAFTA scheme.

Utility functions

tex_listing()

Wrap the output of a summary function in tex listing environment

f_time_norm_focus()

Normalisation factors for aerobic soil degradation according to FOCUS guidance

set_nd_nq() set_nd_nq_focus()

Set non-detects and unquantified values in residue series without replicates

max_twa_parent() max_twa_sfo() max_twa_fomc() max_twa_dfop() max_twa_hs()

Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit

mkin_wide_to_long()

Convert a dataframe with observations over time into long format

mkin_long_to_wide()

Convert a dataframe from long to wide format

Helper functions mainly used internally

mkinpredict()

Produce predictions from a kinetic model using specific parameters

transform_odeparms() backtransform_odeparms()

Functions to transform and backtransform kinetic parameters for fitting

ilr() invilr()

Function to perform isometric log-ratio transformation

logLik(<mkinfit>)

Calculated the log-likelihood of a fitted mkinfit object

residuals(<mkinfit>)

Extract residuals from an mkinfit model

nobs(<mkinfit>)

Number of observations on which an mkinfit object was fitted

mkinresplot()

Function to plot residuals stored in an mkin object

mkinparplot()

Function to plot the confidence intervals obtained using mkinfit

mkinerrplot()

Function to plot squared residuals and the error model for an mkin object

mean_degparms()

Calculate mean degradation parameters for an mmkin row object

create_deg_func()

Create degradation functions for known analytical solutions

Analytical solutions

Parent only model solutions

SFO.solution()

Single First-Order kinetics

FOMC.solution()

First-Order Multi-Compartment kinetics

DFOP.solution()

Double First-Order in Parallel kinetics

SFORB.solution()

Single First-Order Reversible Binding kinetics

HS.solution()

Hockey-Stick kinetics

IORE.solution()

Indeterminate order rate equation kinetics

logistic.solution()

Logistic kinetics

Generate synthetic datasets

add_err()

Add normally distributed errors to simulated kinetic degradation data

sigma_twocomp()

Two-component error model

Deprecated functions

Functions that have been superseded

mkinplot()

Plot the observed data and the fitted model of an mkinfit object