Main functionsEssential functionality 


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

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

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

Fit nonlinear mixedeffects models built from one or more kinetic degradation models and one or more error models 

GenericsGeneric functions introduced by the package 

Extract model parameters 

Method to get status information for fit array objects 


Method to get the names of illdefined parameters 
Function to calculate endpoints for further use from kinetic models fitted with mkinfit 

Calculate Akaike weights for model averaging 

Show resultsFunctions working with mkinfit objects 

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

Summary method for class "mkinfit" 

Confidence intervals for parameters of mkinfit objects 

Update an mkinfit model with different arguments 

Likelihood ratio test for mkinfit models 

Lackoffit test for models fitted to data with replicates 

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

Export a list of datasets format to a CAKE study file 

Work with mmkin objectsFunctions working with aggregated results 

Subsetting method for mmkin objects 

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

Calculate the AIC for a column of an mmkin object 

Summary method for class "mmkin" 

Mixed modelsCreate and work with nonlinear hierarchical models 

Read datasets and relevant meta information from a spreadsheet file 

Create an nlme model for an mmkin row object 


Fit nonlinear mixed models with SAEM 
Fit nonlinear mixedeffects models built from one or more kinetic degradation models and one or more error models 

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

Summary method for class "nlme.mmkin" 

Summary method for class "saem.mmkin" 

Anova method for saem.mmkin objects 

logLik method for saem.mmkin objects 

Helper functions to create nlme models from mmkin row objects 

Retrieve a degradation function from the mmkin namespace 

Create a mixed effects model from an mmkin row object 

Objects exported from other packages 

Confidence intervals for parameters in saem.mmkin objects 

Perform a hierarchical model fit with multiple starting values 

Plot the distribution of log likelihoods from multistart objects 

Plot parameter variability of multistart objects 

Datasets and known results 

Synthetic data for hierarchical kinetic degradation models 

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

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


Datasets A to F from the FOCUS Kinetics report from 2006 
Results of fitting the SFO model to Datasets A to F of FOCUS (2006) 

Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) 

Results of fitting the HS model to Datasets A to F of FOCUS (2006) 

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

Example datasets from the NAFTA SOP published 2015 

Example datasets from Attachment 1 to the NAFTA SOP published 2015 

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

Metabolism data set used for checking the software quality of KinGUI 

Synthetic datasets for one parent compound with two metabolites 

Experimental datasets used for development and testing of error models 

Three experimental datasets from two water sediment systems and one soil 

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

A dataset class for mkin 

A class for dataset groups for mkin 

NAFTA guidance 

Evaluate parent kinetics using the NAFTA guidance 

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

Utility functions 

Wrap the output of a summary function in tex listing environment 

Normalisation factors for aerobic soil degradation according to FOCUS guidance 

Set nondetects and unquantified values in residue series without replicates 


Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit 
Convert a dataframe with observations over time into long format 

Convert a dataframe from long to wide format 

Helper functions mainly used internally 

Produce predictions from a kinetic model using specific parameters 

Functions to transform and backtransform kinetic parameters for fitting 

Function to perform isometric logratio transformation 

Calculated the loglikelihood of a fitted mkinfit object 

Extract residuals from an mkinfit model 

Number of observations on which an mkinfit object was fitted 

Function to plot residuals stored in an mkin object 

Function to plot the confidence intervals obtained using mkinfit 

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

Calculate mean degradation parameters for an mmkin row object 

Create degradation functions for known analytical solutions 

Analytical solutionsParent only model solutions 

Single FirstOrder kinetics 

FirstOrder MultiCompartment kinetics 

Double FirstOrder in Parallel kinetics 

Single FirstOrder Reversible Binding kinetics 

HockeyStick kinetics 

Indeterminate order rate equation kinetics 

Logistic kinetics 

Generate synthetic datasets 

Add normally distributed errors to simulated kinetic degradation data 

Twocomponent error model 

Deprecated functionsFunctions that have been superseded 

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