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

Source: R/mkinmod.R

This function is usually called using a call to mkinsub() for each observed variable, specifying the corresponding submodel as well as outgoing pathways (see examples).

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

Arguments

...

For each observed variable, a list as obtained by mkinsub() has to be specified as an argument (see examples). 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", "HS" and "logistic" can additionally be chosen for the first variable which is assumed to be the source compartment. Additionally, mkinsub() has an argument 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 mkinsub() argument 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 inline::cfunction() if applicable to give detailed information about the C function being built.

Value

A list of class mkinmod for use with mkinfit(), containing, among others,

diffs

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

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.

deg_func

If generated, a function containing the solution of the degradation model.

coefmat

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

cf

If generated, a compiled function calculating the derivatives as returned by cfunction.

Details

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

For kinetic models with more than one observed variable, a symbolic solution of the system of differential equations is included in the resulting mkinmod object in some cases, speeding up the solution.

If a C compiler is found by pkgbuild::has_compiler() and there is more than one observed variable in the specification, C code is generated for evaluating the differential equations, compiled using inline::cfunction() and added to the resulting mkinmod object.

Note

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

References

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

Author

Johannes Ranke

Examples


# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
SFO <- mkinmod(parent = mkinsub("SFO"))

# One parent compound, one metabolite, both single first order
SFO_SFO <- mkinmod(
  parent = mkinsub("SFO", "m1"),
  m1 = mkinsub("SFO"))

#> Successfully compiled differential equation model from auto-generated C code.

# \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"))

#> Successfully compiled differential equation model from auto-generated C code.

# Show details of creating the C function
SFO_SFO <- mkinmod(
  parent = mkinsub("SFO", "m1"),
  m1 = mkinsub("SFO"), verbose = TRUE)

#> Program source:
#>   1: #include <R.h>
#>   2: 
#>   3: 
#>   4: static double parms [3];
#>   5: #define k_parent parms[0]
#>   6: #define f_parent_to_m1 parms[1]
#>   7: #define k_m1 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 * y[0];
#>  18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];
#>  19: }
#> Successfully compiled differential equation model from auto-generated C code.

# The symbolic solution which is available in this case is not
# made for human reading but for speed of computation
SFO_SFO$deg_func

#> function (observed, odeini, odeparms) 
#> {
#>     predicted <- numeric(0)
#>     with(as.list(odeparms), {
#>         t <- observed[observed$name == "parent", "time"]
#>         predicted <<- c(predicted, SFO.solution(t, odeini["parent"], 
#>             k_parent))
#>         t <- observed[observed$name == "m1", "time"]
#>         predicted <<- c(predicted, (((k_m1 - k_parent) * odeini["m1"] - 
#>             f_parent_to_m1 * k_parent * odeini["parent"]) * exp(-k_m1 * 
#>             t) + f_parent_to_m1 * k_parent * odeini["parent"] * 
#>             exp(-k_parent * t))/(k_m1 - k_parent))
#>     })
#>     return(predicted)
#> }
#> <environment: 0x55555b726d88>

# 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)

#> Warning: Shapiro-Wilk test for standardized residuals: p =  0.000174
# }