examples/userdata.R

In kidusasfaw/pomp: Statistical Inference for Partially Observed Markov Processes

## The familiar Ricker example
## For some bizarre reason, we wish to pass 'phi' via the userdata facility.

## C snippet approach:

simulate(times=1:100,t0=0,
  phi=as.double(100),
  params=c(r=3.8,sigma=0.3,N.0=7),
  rprocess=discrete_time(
    step.fun=Csnippet("
      double e = (sigma > 0.0) ? rnorm(0,sigma) : 0.0;
      N = r*N*exp(-N+e);"
    ),
    delta.t=1
  ),
  rmeasure=Csnippet("
       double phi = *(get_userdata_double(\"phi\"));
       y = rpois(phi*N);"
  ),
  paramnames=c("r","sigma"),
  statenames="N",
  obsnames="y"
) -> rick1

## The same problem solved using 'globals':
simulate(times=1:100,t0=0,
  globals=Csnippet("static double phi = 100;"),
  params=c(r=3.8,sigma=0.3,N.0=7),
  rprocess=discrete_time(
    step.fun=Csnippet("
      double e = (sigma > 0.0) ? rnorm(0,sigma) : 0.0;
      N = r*N*exp(-N+e);"
    ),
    delta.t=1
  ),
  rmeasure=Csnippet("
       y = rpois(phi*N);"
  ),
  paramnames=c("r","sigma"),
  statenames="N",
  obsnames="y"
) -> rick2

## Finally, the R function approach:

simulate(times=1:100,t0=0,
  phi=100,
  params=c(r=3.8,sigma=0.3,N_0=7),
  rprocess=discrete_time(
    step.fun=function (r, N, sigma, ...) {
      e <- rnorm(n=1,mean=0,sd=sigma)
       c(N=r*N*exp(-N+e))
    },
    delta.t=1
  ),
  rmeasure=function(phi, N, ...) {
      c(y=rpois(n=1,lambda=phi*N))
  }
) -> rick3