funC: Generate C code for a function and compile it

In dlill/cOde2ndsens: Automated C Code Generation for Use with the 'deSolve' and 'bvpSolve' Packages

Description

Generate C code for a function and compile it

Usage

funC(f, forcings = NULL, outputs = NULL, jacobian = c("none", "full",
  "inz.lsodes", "jacvec.lsodes"), rootfunc = NULL, boundary = NULL,
  compile = TRUE, fcontrol = c("nospline", "einspline"),
  nGridpoints = 500, precision = 1e-05, modelname = NULL,
  verbose = FALSE)

Arguments

f	Named character vector containing the right-hand sides of the ODE. You may use the key word time in your equations for non-autonomous ODEs.
forcings	Character vector with the names of the forcings
outputs	Named character vector for additional output variables, see arguments nout and outnames of lsode
jacobian	Character, either "none" (no jacobian is computed), "full" (full jacobian is computed and written as a function into the C file) or "inz.lsodes" (only the non-zero elements of the jacobian are determined, see lsodes)
rootfunc	Named character vector. The root function (see lsoda). Besides the variable names (names(f)) also other symbols are allowed that are treated like new parameters.
boundary	data.frame with columns name, yini, yend specifying the boundary condition set-up. NULL if not a boundary value problem
compile	Logical. If FALSE, only the C file is written
fcontrol	Character, either "nospline" (default, forcings are handled by deSolve) or "einspline" (forcings are handled as splines within the C code based on the einspline library).
nGridpoints	Integer, defining the number of grid points between tmin and tmax where the ODE is computed in any case. Indicates also the number of spline nodes if fcontrol = "einspline".
precision	Numeric. Only used when fcontrol = "einspline".
modelname	Character. The C file is generated in the working directory and is named <modelname>.c. If NULL, a random name starting with ".f" is chosen, i.e. the file is hidden on a UNIX system.
verbose	Print compiler output to R command line.

Details

The function replaces variables by arrays y[i], etc. and replaces "^" by pow() in order to have the correct C syntax. The file name of the C-File is derived from f. I.e. funC(abc, ... will generate a file abc.c in the current directory. Currently, only explicit ODE specification is supported, i.e. you need to have the right-hand sides of the ODE.

Value

the name of the generated shared object file together with a number of attributes

Examples

## Not run: 
# Exponential decay plus constant supply
f <- c(x = "-k*x + supply")
func <- funC(f, forcings = "supply")

# Example 2: root function
f <- c(A = "-k1*A + k2*B", B = "k1*A - k2*B")
rootfunc <- c(steadyState = "-k1*A + k2*B - tol")

func <- funC(f, rootfunc = rootfunc, modelname = "test")

yini <- c(A = 1, B = 2)
parms <- c(k1 = 1, k2 = 5, tol = 0.1)
times <- seq(0, 10, len = 100)

odeC(yini, times, func, parms)

## End(Not run)

dlill/cOde2ndsens documentation built on May 30, 2019, 1:37 p.m.