R/parus.R

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

##' Parus major population dynamics
##'
##' Size of a population of great tits (\emph{Parus major}) from Wytham Wood, near Oxford.
##'
##' Provenance: Global Population Dynamics Database dataset #10163.
##' (NERC Centre for Population Biology, Imperial College (2010)
##' The Global Population Dynamics Database Version 2.
##' \url{http://www.sw.ic.ac.uk/cpb/cpb/gpdd.html}).
##'
##' Original source: McCleer and Perrins (1991).
##'
##' @name parus
##' @rdname parus
##' @docType data
##' @family datasets
##'
##' @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.
##'
##' @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()
##'
NULL