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scrnn returns a closure around gsl_odeiv2_CRNN()

scrnn.Rd

the returned value is a function of a variable p that encodes the CRNN in some way. Three user supplied functions are used to extract the three components of a CRNN:

Usage

scrnn(
  experiments,
  modelName,
  parMap = function(p) p$l,
  stoichiometry = function(p) p$nu,
  modifiers = function(p) p$m,
  method = 0
)

Arguments

experiments

list of experiments (inputs are ignored).

modelName

scalar string, can indicate a shared library with an attached comment attribute.

parMap

(function) extracts kinetic rate coefficients from its argument.

stoichiometry

(function) extracts the stoichiometry matrix from its argument.

modifiers

(function) extracts the modifier matrix from its argument.

method

(integer) integration method key (0:10) corresponds to these GSL methods: msbdf, msadams, bsimp, rk4imp, rk2imp, rk1imp, rk8pd, rkck, rkf45, rk4, rk2

Value

closure that maps one argument (p) to simulation results (y).

Details

  • kinetic rate coefficients (in log-space): l <- parMap(p)

  • stoichiometric matrix: nu <- stoichiometry(p)

  • modifier matrix: m <- modifiers(p)

these three components (one numeric vector, and two matrices) are passed to the simulation procedure. The vector l can be a matrix with M columns. In that case, one simulation per column is performed. The stoichiometry and modifiers remain unchanged throughout.

Examples

# \donttest{
  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_CRNN_",fileext=".c")
  cat(C,file=c.file,sep='\n')
  modelName <- "AKAR4"
  comment(modelName) <- shlib(c.file,model.name="AKAR4")
#> Error in shlib(c.file, model.name = "AKAR4"): unused argument (model.name = "AKAR4")
  s <- scrnn(ex, modelName)
  p <- list(l=l,nu=nu,m=nu*0)
  y <- s(p)
#> looking for ./AKAR4.so
#> Warning: [gsl_odeiv2_CRNN] for model name «AKAR4», file «./AKAR4.so» not found.
#> Error in gsl_odeiv2_CRNN(modelName, experiments, l, nu, m, method = 0): [dlopen] ./AKAR4.so: cannot open shared object file: No such file or directory.
# }