parus {pomp} | R Documentation

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

### See Also

Other datasets: `blowflies`, `bsflu`, `dacca`, `ebola`, `measles`

### Examples

    library(magrittr)

    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()

[Package pomp version 2.3 Index]