parus: Parus major population dynamics

In pomp: Statistical Inference for Partially Observed Markov Processes

Parus major population dynamics

Description

Size of a population of great tits (Parus major) from Wytham Wood, near Oxford.

Details

Provenance: Global Population Dynamics Database dataset #10163. (NERC Centre for Population Biology, Imperial College (2010) The Global Population Dynamics Database Version 2. https://www.imperial.ac.uk/cpb/gpdd2/). Original source: McCleer and Perrins (1991).

References

\McCleery

1991

See Also

More data sets provided with pomp: blowflies, bsflu, childhood_disease_data, dacca(), ebola

Examples

 # takes too long for R CMD check
  parus |>
    pfilter(Np=1000,times="year",t0=1960,
      params=c(K=190,r=2.7,sigma=0.2,theta=0.05,N.0=148),
      rprocess=discrete_time(
        function (r, K, sigma, N, ...) {
          e <- rnorm(n=1,mean=0,sd=sigma)
          c(N = exp(log(N)+r*(1-N/K)+e))
        },
        delta.t=1
      ),
      rmeasure=function (N, theta, ...) {
        c(pop=rnbinom(n=1,size=1/theta,mu=N+1e-10))
      },
      dmeasure=function (pop, N, theta, ..., log) {
        dnbinom(x=pop,mu=N+1e-10,size=1/theta,log=log)
      },
      partrans=parameter_trans(log=c("sigma","theta","N_0","r","K")),
      paramnames=c("sigma","theta","N_0","r","K")
    ) -> pf

  pf |> logLik()

  pf |> simulate() |> plot()

pomp documentation built on Sept. 13, 2024, 1:08 a.m.