mkinmod. mkin 0.9.44.9000

Usage

mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)

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Arguments

...: - For each observed variable, a list has to be specified as an argument, containing - at least a component type, specifying the type of kinetics to use - for the variable. Currently, single first order kinetics "SFO", - indeterminate order rate equation kinetics "IORE", or - single first order with reversible binding "SFORB" are implemented for all - variables, while - "FOMC", "DFOP" and "HS" can additionally be chosen for the first - variable which is assumed to be the source compartment. - Additionally, each component of the list can include a character vector to, - specifying names of variables to which a transfer is to be assumed in the - model. - If the argument use_of_ff is set to "min" (default) and the model for - the compartment is "SFO" or "SFORB", an additional component of the list - can be "sink=FALSE" effectively fixing the flux to sink to zero. -
use_of_ff: - Specification of the use of formation fractions in the model equations and, if - applicable, the coefficient matrix. If "min", a minimum use of formation - fractions is made in order to avoid fitting the product of formation fractions - and rate constants. If "max", formation fractions are always used. -
speclist: - The specification of the observed variables and their submodel types and - pathways can be given as a single list using this argument. Default is NULL. -
quiet: - Should messages be suppressed? -
verbose: - If TRUE, passed to cfunction if applicable to give - detailed information about the C function being built. -

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Description

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The function usually takes several expressions, each assigning a compound name to - a list, specifying the kinetic model type and reaction or transfer to other - observed compartments. Instead of specifying several expressions, a list - of lists can be given in the speclist argument.

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For the definition of model types and their parameters, the equations given - in the FOCUS and NAFTA guidance documents are used.

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Value

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diffs: A vector of string representations of differential equations, - one for each modelling variable.
parms: A vector of parameter names occurring in the differential equations.
map: A list containing named character vectors for each observed variable, specifying - the modelling variables by which it is represented.
use_of_ff: The content of use_of_ff is passed on in this list component.
coefmat: The coefficient matrix, if the system of differential equations can be - represented by one.

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Note

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The IORE submodel is not well tested (yet). When using this model for metabolites, - you may want to read the second note in the help page to - mkinfit.

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References

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FOCUS (2006) “Guidance Document on Estimating Persistence and - Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://focus.jrc.ec.europa.eu/dk

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NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental - Media

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Examples

# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
-SFO <- mkinmod(parent = list(type = "SFO"))
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-# One parent compound, one metabolite, both single first order
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
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-Successfully compiled differential equation model from auto-generated C code.
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-## Not run: 
-# # The above model used to be specified like this, before the advent of mkinsub()
-# SFO_SFO <- mkinmod(
-#   parent = list(type = "SFO", to = "m1"),
-#   m1 = list(type = "SFO"))
-# 
-# # Show details of creating the C function
-# SFO_SFO <- mkinmod(
-#   parent = mkinsub("SFO", "m1"),
-#   m1 = mkinsub("SFO"), verbose = TRUE)
-# 
-# # If we have several parallel metabolites 
-# # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
-# m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-#                            M1 = mkinsub("SFO"),
-#                            M2 = mkinsub("SFO"),
-#                            use_of_ff = "max", quiet = TRUE)
-# 
-# fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 
-#                           synthetic_data_for_UBA_2014[[12]]$data,
-#                           quiet = TRUE)
-# ## End(Not run)
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Author

- - Johannes Ranke - - -

- Function to set up a kinetic model with one or more state variables -