parus {pomp} | R Documentation |
Size of a population of great tits (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. https://www.imperial.ac.uk/cpb/gpdd2/). Original source: McCleer and Perrins (1991).
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.
Other datasets: blowflies
,
bsflu
, dacca
,
ebola
, measles
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()