Kinetic Evaluation of Chemical Degradation Data

add_err | Add normally distributed errors to simulated kinetic... |

AIC.mmkin | Calculate the AIC for a column of an mmkin object |

anova.saem.mmkin | Anova method for saem.mmkin objects |

aw | Calculate Akaike weights for model averaging |

CAKE_export | Export a list of datasets format to a CAKE study file |

confint.mkinfit | Confidence intervals for parameters of mkinfit objects |

create_deg_func | Create degradation functions for known analytical solutions |

D24_2014 | Aerobic soil degradation data on 2,4-D from the EU assessment... |

DFOP.solution | Double First-Order in Parallel kinetics |

dimethenamid_2018 | Aerobic soil degradation data on dimethenamid and... |

ds_mixed | Synthetic data for hierarchical kinetic degradation models |

endpoints | Function to calculate endpoints for further use from kinetic... |

experimental_data_for_UBA | Experimental datasets used for development and testing of... |

Extract.mmkin | Subsetting method for mmkin objects |

FOCUS_2006_datasets | Datasets A to F from the FOCUS Kinetics report from 2006 |

FOCUS_2006_DFOP_ref_A_to_B | Results of fitting the DFOP model to Datasets A to B of FOCUS... |

FOCUS_2006_FOMC_ref_A_to_F | Results of fitting the FOMC model to Datasets A to F of FOCUS... |

FOCUS_2006_HS_ref_A_to_F | Results of fitting the HS model to Datasets A to F of FOCUS... |

FOCUS_2006_SFO_ref_A_to_F | Results of fitting the SFO model to Datasets A to F of FOCUS... |

focus_soil_moisture | FOCUS default values for soil moisture contents at field... |

FOMC.solution | First-Order Multi-Compartment kinetics |

f_time_norm_focus | Normalisation factors for aerobic soil degradation according... |

get_deg_func | Retrieve a degradation function from the mmkin namespace |

hierarchical_kinetics | Hierarchical kinetics template |

HS.solution | Hockey-Stick kinetics |

illparms | Method to get the names of ill-defined parameters |

ilr | Function to perform isometric log-ratio transformation |

intervals.saem.mmkin | Confidence intervals for parameters in saem.mmkin objects |

IORE.solution | Indeterminate order rate equation kinetics |

llhist | Plot the distribution of log likelihoods from multistart... |

loftest | Lack-of-fit test for models fitted to data with replicates |

logistic.solution | Logistic kinetics |

logLik.mkinfit | Calculated the log-likelihood of a fitted mkinfit object |

logLik.saem.mmkin | logLik method for saem.mmkin objects |

lrtest.mkinfit | Likelihood ratio test for mkinfit models |

max_twa_parent | Function to calculate maximum time weighted average... |

mccall81_245T | Datasets on aerobic soil metabolism of 2,4,5-T in six soils |

mean_degparms | Calculate mean degradation parameters for an mmkin row object |

mhmkin | Fit nonlinear mixed-effects models built from one or more... |

mixed | Create a mixed effects model from an mmkin row object |

mkinds | A dataset class for mkin |

mkindsg | A class for dataset groups for mkin |

mkinerrmin | Calculate the minimum error to assume in order to pass the... |

mkinerrplot | Function to plot squared residuals and the error model for an... |

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

mkin_long_to_wide | Convert a dataframe from long to wide format |

mkinmod | Function to set up a kinetic model with one or more state... |

mkinparplot | Function to plot the confidence intervals obtained using... |

mkinplot | Plot the observed data and the fitted model of an mkinfit... |

mkinpredict | Produce predictions from a kinetic model using specific... |

mkinresplot | Function to plot residuals stored in an mkin object |

mkin_wide_to_long | Convert a dataframe with observations over time into long... |

mmkin | Fit one or more kinetic models with one or more state... |

multistart | Perform a hierarchical model fit with multiple starting... |

nafta | Evaluate parent kinetics using the NAFTA guidance |

NAFTA_SOP_2015 | Example datasets from the NAFTA SOP published 2015 |

NAFTA_SOP_Attachment | Example datasets from Attachment 1 to the NAFTA SOP published... |

nlme | Helper functions to create nlme models from mmkin row objects |

nlme.mmkin | Create an nlme model for an mmkin row object |

nobs.mkinfit | Number of observations on which an mkinfit object was fitted |

parms | Extract model parameters |

parplot | Plot parameter variability of multistart objects |

plot.mixed.mmkin | Plot predictions from a fitted nonlinear mixed model obtained... |

plot.mkinfit | Plot the observed data and the fitted model of an mkinfit... |

plot.mmkin | Plot model fits (observed and fitted) and the residuals for a... |

plot.nafta | Plot the results of the three models used in the NAFTA... |

read_spreadsheet | Read datasets and relevant meta information from a... |

reexports | Objects exported from other packages |

residuals.mkinfit | Extract residuals from an mkinfit model |

saem | Fit nonlinear mixed models with SAEM |

schaefer07_complex_case | Metabolism data set used for checking the software quality of... |

set_nd_nq | Set non-detects and unquantified values in residue series... |

SFORB.solution | Single First-Order Reversible Binding kinetics |

SFO.solution | Single First-Order kinetics |

sigma_twocomp | Two-component error model |

status | Method to get status information for fit array objects |

summary_listing | Display the output of a summary function according to the... |

summary.mkinfit | Summary method for class "mkinfit" |

summary.mmkin | Summary method for class "mmkin" |

summary.nlme.mmkin | Summary method for class "nlme.mmkin" |

summary.saem.mmkin | Summary method for class "saem.mmkin" |

synthetic_data_for_UBA_2014 | Synthetic datasets for one parent compound with two... |

test_data_from_UBA_2014 | Three experimental datasets from two water sediment systems... |

transform_odeparms | Functions to transform and backtransform kinetic parameters... |

update.mkinfit | Update an mkinfit model with different arguments |

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