`mkinmod.Rd`

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.

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

... | For each observed variable, a list has to be specified as an
argument, containing at least a component |
---|---|

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 |

A list of class `mkinmod`

for use with `mkinfit`

,
containing, among others,

A vector of string representations of differential equations, one for each modelling variable.

A list containing named character vectors for each observed variable, specifying the modelling variables by which it is represented.

The content of `use_of_ff`

is passed on in this list component.

The coefficient matrix, if the system of differential equations can be represented by one.

The likelihood function, taking the parameter vector as the first argument.

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

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

.

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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

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

# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...) SFO <- mkinmod(parent = list(type = "SFO")) # One parent compound, one metabolite, both single first order SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))#># \dontrun{ # 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)#> Compilation argument: #> /usr/lib/R/bin/R CMD SHLIB file12cd48616f1.c 2> file12cd48616f1.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: #> 3: #> 4: static double parms [3]; #> 5: #define k_parent_sink parms[0] #> 6: #define k_parent_m1 parms[1] #> 7: #define k_m1_sink parms[2] #> 8: #> 9: void initpar(void (* odeparms)(int *, double *)) { #> 10: int N = 3; #> 11: odeparms(&N, parms); #> 12: } #> 13: #> 14: #> 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { #> 16: #> 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0]; #> 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1]; #> 19: }#># 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) # }