`panel4pt2.fn` <- function(y,J=11,Nmax=100){ # This is the R construction of the likelihood for the two-state occupancy # model using a construction that is consistent with the Royle-Nichols model # (Panel 4.2) # lik<-function(parms){ p<-expit(parms[1]) lambda<-exp(parms[2]) pvec<-1-(1-p)^(0:1) pvec<-c(pvec[1],rep(pvec[2],Nmax)) gN<-dpois(0:Nmax,lambda) gN<-gN/sum(gN) lik<-rep(NA,nsites) for(i in 1:nsites){ lik[i]<-sum(dbinom(y[i],J,pvec)*gN) } -1*sum(log(lik)) } nsites<-length(y) nlm(lik,c(0,0),hessian=TRUE) }