R using LibBi

library(rbi)

sir.bi <- "
model sir {
  const N = 403
  const timestep = 0.1
  state S, I, R, Y
  param bet, gamm, iota
  noise infection, recovery
  sub parameter {
    bet <- 2.62110617498984
    gamm <- 0.5384615384615384
    iota <- 0.5
  }
  sub initial {
    S <- 60
    I <- 1
    R <- 342
    Y <- 0    
  }
  sub transition (delta=timestep) {
    inline lambd = bet*(I+iota)/N
    inline ifrac = 1.0-exp(-lambd*timestep)
    inline rfrac = 1.0-exp(-gamm*timestep)
    infection ~ binomial(S,ifrac)
    recovery ~ binomial(I,rfrac)
    S <- S - infection
    I <- I + infection - recovery
    R <- R + recovery
    Y <- Y + infection
  }
}
"

sir.bi.model <- bi_model(lines=sir.bi)
sir.bi.obj <- libbi(model=sir.bi.model)
sir.bi.sample <- sample(sir.bi.obj,
                        target="joint",
                        end_time=54.0,
                        nsamples=1000,
                        seed=1)
sir.bi.results <- bi_read(sir.bi.sample$output_file_name)

sir.bi.results