simOpenSCR: Simulate data from an open population SCR study with fixed or...
In benaug/OpenPopSCR: Open Population Spatial Capture-recapture MCMC algorithms

Description Usage Arguments Value Author(s)

View source: R/simOpenSCR.R

This function simulates data from an open population SCR model.

simOpenSCR(N = c(40, 60, 80), gamma = NULL, phi = rep(0.8, 2),
  lam0 = rep(0.2, 3), sigma = rep(0.5, 3), K = rep(10, 3), X = X,
  t = 3, M = M, sigma_t = NULL, buff = 3, obstype = "bernoulli",
  ACtype = "fixed", vertices = NA, maxprop = 10000, dSS = NA,
  primary = NA)

`N`	a vector indicating the number of individuals to simulate. If size 1, provide one or multiple gammas (see gamma below) to determine N in subsequent primary periods. Otherwise, size is t, the number of primary periods.
`gamma`	a vector containing the per capita recruitment rates between primary periods. If size 1, gamma is fixed across primary periods. Otherwise, size is t-1. Do not enter a gamma if N for all primary periods specified.
`phi`	a vector containing the survival rates between primary periods. If size 1, phi is fixed across primary periods. Otherwise, size is t-1.
`lam0`	a vector containing the detection function expected number of captures at distance 0. If size 1, a constant rate across primary periods is assumed. Otherwise, size is t, the number of primary periods.
`sigma`	a vector containing the detection function spatial scale parameter. If size 1, sigma is fixed across primary periods. #' Otherwise, size is t, the number of primary periods.
`K`	a vector containing the number of capture occasions in each of the t primary periods
`X`	a list of trap locations in each primary period. Each list element is a J[l] x 2 matrix of trap locations, with J[l] being the number of traps in primary period l.
`M`	an integer indicating the level of data augmentation to use during simulation. This should be larger than the total number of individuals ever alive.
`sigma_t`	a numeric indicating the between primary period spatial scale parameter for ACtypes "metamu" "metamu2", "markov" and "markov2" This is the only parameter that is not primary period-specific. Very rich data sets would be required to estimate a year-specific sigma_t.
`buff`	the distance to buffer the trapping array in the X and Y dimensions to produce the state space in which the population lives
`obstype`	observation type, either "bernoulli" or "poisson"
`ACtype`	A character indicating the type of activity centers. "fixed" activity centers do not move between primary periods, "metamu" assumes there is a meta activity center around which the primary period activity centers distributed following a bivariate normal distribution with spatial scale parameter sigma_t. Primary period activity centers are required to stay inside the state space. "metamu2" is identical to "metamu" except primary period activity centers are allowed to leave the state space. markov" assumes activity centers in primary period 1 are distributed uniformly across the state space and the activy centers in primary period l+1 are a bivariate normal draw centered around the activity center in primary period l (but must stay within the state space). "markov2" is the same as "markov" except each dispersal considers the available distances to disperse to in a use vs. availability framework. Discrete state space is required. Finally, "independent" assumes animals randomly mix between primary periods. (spatial uniformity in all primary periods with independence between primary periods).
`vertices`	an optional list of polygon vertices to use for the state space. Each list element should be a matrix with 2 columns, corresponding to the X and Y coordinates of polygon vertices. The vertices must close the polygon (e.g. the first and last vertices should be the same). Cannot enter both vertices and dSS.
`dSS`	an optional (N_SS x 2) matrix of discrete state space locations. The matrix should have 2 columns corresponding to the X and Y coordinates of each state space element. Cannot enter both vertices and dSS.
`primary`	a vector of length T with entries 1 if the population is to be observed in primary period l and 0 otherwise.