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

- - -

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).

Print mkinmod objects in a way that the user finds his way to get to its -components.

- -

mkinmod(
-  ...,
-  use_of_ff = "max",
-  name = NULL,
-  speclist = NULL,
-  quiet = FALSE,
-  verbose = FALSE,
-  dll_dir = NULL,
-  unload = FALSE,
-  overwrite = FALSE
-)
-
-# S3 method for mkinmod
-print(x, ...)
-
-mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)

- -

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" -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. -In print.mkinmod, this argument is currently not used.
use_of_ff: Specification of the use of formation fractions in the -model equations and, if applicable, the coefficient matrix. If "max", -formation fractions are always used (default). If "min", a minimum use of -formation fractions is made, i.e. each first-order pathway to a metabolite -has its own rate constant.
name: A name for the model. Should be a valid R object name.
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.
dll_dir: Directory where an DLL object, if generated internally by -inline::cfunction(), should be saved. The DLL will only be stored in a -permanent location for use in future sessions, if 'dll_dir' and 'name' -are specified. This is helpful if fit objects are cached e.g. by knitr, -as the cache remains functional across sessions if the DLL is stored in -a user defined location.
unload: If a DLL from the target location in 'dll_dir' is already -loaded, should that be unloaded first?
overwrite: If a file exists at the target DLL location in 'dll_dir', -should this be overwritten?
x: An mkinmod object.
submodel: Character vector of length one to specify the submodel type. -See mkinmod for the list of allowed submodel names.
to: Vector of the names of the state variable to which a -transformation shall be included in the model.
sink: Should a pathway to sink be included in the model in addition to -the pathways to other state variables?
full_name: An optional name to be used e.g. for plotting fits -performed with the model. You can use non-ASCII characters here, but then -your R code will not be portable, i.e. may produce unintended plot -results on other operating systems or system configurations.

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.

A list for use with mkinmod.

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"))
-#> Temporary DLL for differentials generated and loaded
-print(SFO_SFO)
-#> <mkinmod> model generated with
-#> Use of formation fractions $use_of_ff: max 
-#> Specification $spec:
-#> $parent
-#> $type: SFO; $to: m1; $sink: TRUE
-#> $m1
-#> $type: SFO; $sink: TRUE
-#> Coefficient matrix $coefmat available
-#> Compiled model $cf available
-#> Differential equations:
-#> d_parent/dt = - k_parent * parent
-#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
-
-# \dontrun{
- fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
-#> Warning: Observations with value of zero were removed from the data
-
- # Now supplying compound names used for plotting, and write to user defined location
- # We need to choose a path outside the session tempdir because this gets removed
- DLL_dir <- "~/.local/share/mkin"
- if (!dir.exists(DLL_dir)) dir.create(DLL_dir)
- SFO_SFO.2 <- mkinmod(
-   parent = mkinsub("SFO", "m1", full_name = "Test compound"),
-   m1 = mkinsub("SFO", full_name = "Metabolite M1"),
-   name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE)
-#> Temporary DLL for differentials generated and loaded
-#> Copied DLL from /tmp/RtmpiGRJ6t/file5c7f7365e02a0.so to /home/jranke/.local/share/mkin/SFO_SFO.so
-# Now we can save the model and restore it in a new session
-saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds")
-# Terminate the R session here if you would like to check, and then do
-library(mkin)
-SFO_SFO.3 <- readRDS("~/SFO_SFO.rds")
-fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
-#> Warning: Observations with value of zero were removed from the data
-
-# 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 diffs ( 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: }
-#> Temporary DLL for differentials generated and loaded
-
-# 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: 0x555558bd6708>
-
-# 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"),
- quiet = TRUE)
-
-fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
-  synthetic_data_for_UBA_2014[[12]]$data,
-  quiet = TRUE)
-# }
-
-

- -