simulates a CRNN ode model with extra work

This function calls a C function which solves an initial value problem, derived from a CRNN.

Usage

gsl_odeiv2_CRNN(
  name,
  experiments,
  l,
  nu,
  m,
  abs.tol = 1e-06,
  rel.tol = 1e-05,
  initial.step.size = 0.001,
  method = 0
)

Arguments

name

either the name of a file (shared library file) or the name of an ODE model to simulate (a shared library of the same name will be dynamically loaded and needs to be created first). If the name of the model is given, then the so file must have the same name in the current directory or a comment indicates its location.

experiments

a list of N simulation experiments (time, parameters, initial value, events).

l

a matrix of parameters with M columns, in log-space.

nu

a stoichiometry matrix (N×R) where N is the number of state variables and R the number of reactions, all reactions are assumed to be reversible.

m

modifiers -- similar to stoichiometry, but indicates whether the species takes part in the reaction without being consumed.

abs.tol

absolute tolerance, real scalar.

rel.tol

relative tolerance, real scalar.

initial.step.size

initial value for the step size; the step size will adapt to a value that observes the tolerances, real scalar.

Value

a list of the solution trajectories y(t;p) for all experiments (named like the experiments), as well as the output functions.

Examples

if (FALSE) {
  f <- uqsa_example("AKAR4")
  m <- model_from_tsv(f)
  ex <- experiments(m,as_ode(m,cla=FALSE))
  nu <- stoichiometric_matrix(m)
  l <- matrix(c(log(values(m$Parameter)),0),2,2,dimnames=list(rownames(m$Reaction),c("fwd","bwd")))
  C <- CRNN(NCOL(nu),initialValues=values(m$Compound),funcValues=formulae(m$Output))
  c.file <- tempfile("AKAR4_",fileext=".c")
  cat(C,file=c.file,sep='\n')
  so.file <- shlib(c.file,model.name="AKAR4")
  y <- gsl_odeiv2_CRNN(so.file,ex,l,nu,nu*0)
}