## Main functions

Essential functionality

mkinmod

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

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

## Show results

Functions working with mkinfit objects

plot.mkinfit

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

summary print

Summary method for class "mkinfit"

mkinresplot

Function to plot residuals stored in an mkin object

mkinparplot

Function to plot the confidence intervals obtained using mkinfit

endpoints

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

mkinerrmin

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

## Work with mmkin objects

Functions working with aggregated results

[.mmkin

Subsetting method for mmkin objects

plot

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

## Datasets and known results

FOCUS_2006_datasets

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)

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

test_data_from_UBA_2014

Three experimental datasets from two water sediment systems and one soil

mkinds

A dataset class for mkin

print

Print mkinds objects

## Helper functions

geometric_mean

Calculate the geometric mean

mkinsub

Function to set up a kinetic submodel for one state variable

max_twa_parent

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

mkinpredict

Produce predictions from a kinetic model using specific parameters

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

print

Print mkinmod objects

transform_odeparms backtransform_odeparms

Functions to transform and backtransform kinetic parameters for fitting

ilr invilr

Function to perform isometric log-ratio transformation

sigma_rl

Two component error model of Rocke and Lorenzato

## 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

## Generate synthetic datasets

add_err

mkinplot