From 91a5834dd701211f929fd25419dc34561ce3b4e7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Feb 2025 09:15:20 +0100 Subject: Initialize dev docs --- docs/dev/reference/index.html | 735 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 735 insertions(+) create mode 100644 docs/dev/reference/index.html (limited to 'docs/dev/reference/index.html') diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html new file mode 100644 index 00000000..476b8804 --- /dev/null +++ b/docs/dev/reference/index.html @@ -0,0 +1,735 @@ + +Package index • mkin + Skip to contents + + +
+
+
+ +

Package index

+
+ +
+

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
+
+
+ + +
+ + + + + + + -- cgit v1.2.1