Write C code

This function expects a list of character vectors, as returned by as_ode(). This list describes an ODE model (initial values, default parameters, transformation events, output functions). This function uses this information, calculates Jacobians via Ryacas and returns a character vector with C source code for the solvers in the GNU Scientific Library (GSL).

Usage

generateCode(odeModel)

Arguments

odeModel

a list that represents an ODE

Value

a character vector with the generated code, one vector-element is one line of code.

Details

The value can be written to a file: cat(generateCode(odeModel),sep="\n",file=...). This file can be compiled into a shared library.

Examples

f <- uqsa_example("AKAR4")
m <- model_from_tsv(f)
C <- generateCode(as_ode(m))
#> Warning: This function will start a background yacas process via Ryacas.
#> There is currently no working way to reset/restart that process.
#>  It is therefore not advisable to generate the code for two different models in the same R session.
#> The definitions for the two models will be mixed up. 
cat(head(C,12),sep='\n')
#> #include <stdlib.h>
#> #include <math.h>
#> #include <string.h>
#> #include <gsl/gsl_errno.h>
#> #include <gsl/gsl_odeiv2.h>
#> #include <gsl/gsl_math.h>
#> 
#> /* Enums will be used for indexing purposes.   */
#> enum stateVariable { _AKAR4p, _C, numStateVar };
#> enum param { _kf_C_AKAR4, _kb_C_AKAR4, _kcat_AKARp, _AKAR4_C_ConservedConst, _AKAR4_ConservedConst, numParam };
#> enum func { _AKAR4pOUT, numFunc };
#>