Main functions

Essential functionality

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

• mkinmod

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

• mkinfit

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

• mmkin

Show results

Functions working with mkinfit objects

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

• plot.mkinfit
• plot_sep

Summary method for class "mkinfit"

• summary.mkinfit
• print.summary.mkinfit

Function to plot residuals stored in an mkin object

• mkinresplot

Function to plot the confidence intervals obtained using mkinfit

• mkinparplot

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

• endpoints

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

• mkinerrmin

Work with mmkin objects

Functions working with aggregated results

Subsetting method for mmkin objects

• [.mmkin

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

• plot.mmkin

Datasets and known results

Datasets A to F from the FOCUS Kinetics report from 2006

• FOCUS_2006_A
• FOCUS_2006_B
• FOCUS_2006_C
• FOCUS_2006_D
• FOCUS_2006_E
• FOCUS_2006_F

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

• FOCUS_2006_SFO_ref_A_to_F

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

• FOCUS_2006_FOMC_ref_A_to_F

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

• FOCUS_2006_HS_ref_A_to_F

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

• FOCUS_2006_DFOP_ref_A_to_B

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

• mccall81_245T

Metabolism data set used for checking the software quality of KinGUI

• schaefer07_complex_case
• schaefer07_complex_results

Synthetic datasets for one parent compound with two metabolites

• synthetic_data_for_UBA_2014

A dataset class for mkin

• mkinds

Print mkinds objects

• print.mkinds

Helper functions

Convert a dataframe with observations over time into long format

• mkin_wide_to_long

Convert a dataframe from long to wide format

• mkin_long_to_wide

Function to set up a kinetic submodel for one state variable

• mkinsub

Print mkinmod objects

• print.mkinmod

Produce predictions from a kinetic model using specific parameters

• mkinpredict

Functions to transform and backtransform kinetic parameters for fitting

• transform_odeparms
• backtransform_odeparms

Function to perform isometric log-ratio transformation

• ilr
• invilr

Calculate the geometric mean

• geometric_mean

Analytical solutions

Parent only model solutions

Single First-Order kinetics

• SFO.solution

First-Order Multi-Compartment kinetics

• FOMC.solution

Double First-Order in Parallel kinetics

• DFOP.solution

Single First-Order Reversible Binding kinetics

• SFORB.solution

Hockey-Stick kinetics

• HS.solution

Indeterminate order rate equation kinetics

• IORE.solution

Generate synthetic datasets

Add normally distributed errors to simulated kinetic degradation data

• add_err

Deprecated functions

Functions that have been superseeded

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

• mkinplot