Function reference
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mkinmod()
print(<mkinmod>)
mkinsub()
- Function to set up a kinetic model with one or more state variables
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mkinfit()
- Fit a kinetic model to data with one or more state variables
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mmkin()
print(<mmkin>)
- Fit one or more kinetic models with one or more state variables to one or more datasets
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mhmkin()
`[`(<mhmkin>)
print(<mhmkin>)
- Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
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parms()
- Extract model parameters
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status()
print(<status.mmkin>)
print(<status.mhmkin>)
- Method to get status information for fit array objects
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illparms()
print(<illparms.mkinfit>)
print(<illparms.mmkin>)
print(<illparms.saem.mmkin>)
print(<illparms.mhmkin>)
- Method to get the names of ill-defined parameters
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endpoints()
- Function to calculate endpoints for further use from kinetic models fitted with mkinfit
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aw()
- Calculate Akaike weights for model averaging
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plot(<mkinfit>)
plot_sep()
plot_res()
plot_err()
- Plot the observed data and the fitted model of an mkinfit object
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summary(<mkinfit>)
print(<summary.mkinfit>)
- Summary method for class "mkinfit"
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confint(<mkinfit>)
- Confidence intervals for parameters of mkinfit objects
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update(<mkinfit>)
- Update an mkinfit model with different arguments
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lrtest(<mkinfit>)
lrtest(<mmkin>)
- Likelihood ratio test for mkinfit models
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loftest()
- Lack-of-fit test for models fitted to data with replicates
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mkinerrmin()
- Calculate the minimum error to assume in order to pass the variance test
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CAKE_export()
- Export a list of datasets format to a CAKE study file
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`[`(<mmkin>)
- Subsetting method for mmkin objects
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plot(<mmkin>)
- Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
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AIC(<mmkin>)
BIC(<mmkin>)
- Calculate the AIC for a column of an mmkin object
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summary(<mmkin>)
print(<summary.mmkin>)
- Summary method for class "mmkin"
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hierarchical_kinetics()
- Hierarchical kinetics template
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read_spreadsheet()
- Read datasets and relevant meta information from a spreadsheet file
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nlme(<mmkin>)
print(<nlme.mmkin>)
update(<nlme.mmkin>)
- Create an nlme model for an mmkin row object
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saem()
print(<saem.mmkin>)
saemix_model()
saemix_data()
- Fit nonlinear mixed models with SAEM
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mhmkin()
`[`(<mhmkin>)
print(<mhmkin>)
- Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models
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plot(<mixed.mmkin>)
- Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
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summary(<nlme.mmkin>)
print(<summary.nlme.mmkin>)
- Summary method for class "nlme.mmkin"
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summary(<saem.mmkin>)
print(<summary.saem.mmkin>)
- Summary method for class "saem.mmkin"
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anova(<saem.mmkin>)
- Anova method for saem.mmkin objects
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logLik(<saem.mmkin>)
- logLik method for saem.mmkin objects
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nlme_function()
nlme_data()
- Helper functions to create nlme models from mmkin row objects
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get_deg_func()
- Retrieve a degradation function from the mmkin namespace
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mixed()
print(<mixed.mmkin>)
- Create a mixed effects model from an mmkin row object
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intervals(<saem.mmkin>)
- Confidence intervals for parameters in saem.mmkin objects
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multistart()
print(<multistart>)
best()
which.best()
- Perform a hierarchical model fit with multiple starting values
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llhist()
- Plot the distribution of log likelihoods from multistart objects
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parplot()
- Plot parameter variability of multistart objects
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ds_mixed
ds_sfo
ds_fomc
ds_dfop
ds_hs
ds_dfop_sfo
- Synthetic data for hierarchical kinetic degradation models
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D24_2014
- Aerobic soil degradation data on 2,4-D from the EU assessment in 2014
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dimethenamid_2018
- Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018
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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
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FOCUS_2006_SFO_ref_A_to_F
- Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
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FOCUS_2006_FOMC_ref_A_to_F
- Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
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FOCUS_2006_HS_ref_A_to_F
- Results of fitting the HS model to Datasets A to F of FOCUS (2006)
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FOCUS_2006_DFOP_ref_A_to_B
- Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
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NAFTA_SOP_Appendix_B
NAFTA_SOP_Appendix_D
- Example datasets from the NAFTA SOP published 2015
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NAFTA_SOP_Attachment
- Example datasets from Attachment 1 to the NAFTA SOP published 2015
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mccall81_245T
- Datasets on aerobic soil metabolism of 2,4,5-T in six soils
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schaefer07_complex_case
- Metabolism data set used for checking the software quality of KinGUI
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synthetic_data_for_UBA_2014
- Synthetic datasets for one parent compound with two metabolites
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experimental_data_for_UBA_2019
- Experimental datasets used for development and testing of error models
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test_data_from_UBA_2014
- Three experimental datasets from two water sediment systems and one soil
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focus_soil_moisture
- FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
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print(<mkinds>)
- A dataset class for mkin
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print(<mkindsg>)
- A class for dataset groups for mkin
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nafta()
print(<nafta>)
- Evaluate parent kinetics using the NAFTA guidance
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plot(<nafta>)
- Plot the results of the three models used in the NAFTA scheme.
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summary_listing()
tex_listing()
html_listing()
- Display the output of a summary function according to the output format
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f_time_norm_focus()
- Normalisation factors for aerobic soil degradation according to FOCUS guidance
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set_nd_nq()
set_nd_nq_focus()
- Set non-detects and unquantified values in residue series without replicates
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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
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mkin_wide_to_long()
- Convert a dataframe with observations over time into long format
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mkin_long_to_wide()
- Convert a dataframe from long to wide format
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mkinpredict()
- Produce predictions from a kinetic model using specific parameters
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transform_odeparms()
backtransform_odeparms()
- Functions to transform and backtransform kinetic parameters for fitting
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logLik(<mkinfit>)
- Calculated the log-likelihood of a fitted mkinfit object
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residuals(<mkinfit>)
- Extract residuals from an mkinfit model
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nobs(<mkinfit>)
- Number of observations on which an mkinfit object was fitted
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mkinresplot()
- Function to plot residuals stored in an mkin object
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mkinparplot()
- Function to plot the confidence intervals obtained using mkinfit
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mkinerrplot()
- Function to plot squared residuals and the error model for an mkin object
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mean_degparms()
- Calculate mean degradation parameters for an mmkin row object
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create_deg_func()
- Create degradation functions for known analytical solutions
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SFO.solution()
- Single First-Order kinetics
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FOMC.solution()
- First-Order Multi-Compartment kinetics
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DFOP.solution()
- Double First-Order in Parallel kinetics
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SFORB.solution()
- Single First-Order Reversible Binding kinetics
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HS.solution()
- Hockey-Stick kinetics
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IORE.solution()
- Indeterminate order rate equation kinetics
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logistic.solution()
- Logistic kinetics
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add_err()
- Add normally distributed errors to simulated kinetic degradation data
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sigma_twocomp()
- Two-component error model
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mkinplot()
- Plot the observed data and the fitted model of an mkinfit object