Function reference

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 on mkinfit objects

• plot.mkinfit(plot_sep)
  Plot the observed data and the fitted model of an mkinfit object
• summary.mkinfit(print.summary.mkinfit)
  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.mmkin
  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(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)
• mccall81_245T
  Datasets on aerobic soil metabolism of 2,4,5-T in six soils
• schaefer07_complex_case(schaefer07_complex_results)
  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

Helper functions

• 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
• mkinsub
  Function to set up a kinetic submodel for one state variable
• mkinds
  A dataset class for mkin
• print.mkinds
  Print mkinds objects
• print.mkinmod
  Print mkinmod objects
• 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
• geometric_mean
  Calculate the geometric mean

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

Deprecated functions

Functions that have been superseeded

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

Other

• add_err
  Add normally distributed errors to simulated kinetic degradation data