gen_Nmix_open: gen_Nmix_open
In mrparker909/redNMix: An R package for N-mixtures models.

Description Usage Arguments Value Examples

Generate a population/observation pair with the structure of an open N-mixture model. Use cbind_pop() and rbind_pop() functions to combine sub-pops to easily add covariate structures.

1 2	gen_Nmix_open(num_sites, num_times, lambda, pdet, omega, gamma, starts = NULL)

`num_sites`	The number of observation sites.
`num_times`	The number of sampling occasions.
`lambda`	The population rate parameter (N_i \sim Poisson(λ)).
`pdet`	The probability of detection p (n_{it} \sim Binomial(N_i,p)).
`omega`	The probability of survival (S_{it} \sim Binomial(N_{it}, ω)). Either a single number, or a vector of length t-1 (omega for each sampling occassion after the first).
`gamma`	The recruitment rate parameter (G_{it} \sim Poisson(γ)). Either a single number, or a vector of length t-1 (gamma for each sampling occassion after the first).
`starts`	If not NULL, a vector of starting population values (used instead of lambda).

A list object with two named matrices. Nit contains the total population per site (each row represents a site, each column a sampling occasion). nit contains the observed counts (rows=sites, columns=sampling occasions).

pop <- gen_Nmix_open(num_sites = 5,
                     num_times = 10,
                     lambda = 50,
                     pdet = 0.4,
                     omega = 0.8,
                     gamma = 4)
pop

# example with time covariate for omega:
pop_a <- gen_Nmix_open(2,4,50,0.75,0.9,1) # survival=90%
pop_b <- gen_Nmix_open(2,4,50,0.75,0.1,1, starts=pop_a$Ni[,4]) # survival=10%, use last time observation from pop_a to start pop_b, then drop first time observation from pop_b (this makes a seamless transition between pop_a and pop_b)
pop_b <- list(Ni=pop_b$Ni[,-1], nit=pop_b$nit[,-1])
pop   <- cbind_pops(pop_a,pop_b) # combine to produce one population list
pop