mkinmod. mkin 0.9-41

Usage

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

+ +

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. +

+ +

Description

+ +

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.

+ +

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

+ +

Value

+ +

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.

+ +

Note

+ +

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.

+ +

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://focus.jrc.ec.europa.eu/dk

+ +

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

+ +

Examples

# 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"))
+
+Successfully compiled differential equation model from auto-generated C code.
+
+# 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)
+
+Compilation argument:
+ /usr/lib/R/bin/R CMD SHLIB file5a355b71ca9.c 2> file5a355b71ca9.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: }
+
+Successfully compiled differential equation model from auto-generated C code.
+
+# 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)
+
+## Not run: 
+# fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 
+#                           synthetic_data_for_UBA_2014[[12]]$data,
+#                           quiet = TRUE)
+# ## End(Not run)
+

+ + + +

Author

+ + Johannes Ranke + + +

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