pomp (version 3.2)

parus: 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

R. McCleery and C. Perrins. Effects of predation on the numbers of Great Tits, Parus major. In: C.M. Perrins, J.-D. Lebreton, and G.J.M. Hirons (eds.), Bird Population Studies, pp. 129--147, Oxford. Univ. Press, 1991.

See Also

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

More examples provided with pomp: blowflies, bsflu, dacca(), ebola, gompertz(), measles, ou2(), pomp_examples, ricker(), rw2(), sir_models, verhulst()

Examples

# NOT RUN {
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()

# }