Package index • mkin

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

hierarchical_kinetics(): Hierarchical kinetics template

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(): 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

check_failed(): Check if fit within an mhmkin object failed

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

summary_listing() tex_listing() html_listing(): Display the output of a summary function according to the output format

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