simCJS {AHMbook} | R Documentation |
Function generates individual capture-histories under a CJS model with possibly time-dependent parameters. The number of values for interval-specific survival (phi) and time-specific detection (p) must be ensured to be equal to the number of occasions (n.occ) minus 1.
simCJS(n.occ = 6, n.marked = 20, phi = 0.7, p = 0.4, show.plot = TRUE)
n.occ |
The number of occasions (eg, years). |
n.marked |
The number of individuals marked per year except for the last year; scalar, or a vector of length (n.occ-1). |
phi |
The apparent survival probability between years; scalar, or a vector of length (n.occ-1). |
p |
The recapture probability for all except the first year; scalar, or a vector of length (n.occ-1). |
show.plot |
Choose whether to show plots or not. Set to FALSE when using function in simulations. |
A list with the values of the arguments entered and the following additional elements:
z |
n.ind x n.occ matrix, 1 if the individual is alive and in the study area, 0 otherwise. |
ch |
n.ind x n.occ matrix, 1 if the individual is captured, 0 otherwise. |
f |
n.ind vector, occasion the individual was first captured, and marked. |
n.ind |
scalar, total number of individuals marked. |
n.alive |
n.occ vector, number of animals alive and in the study area each year. |
Marc Kéry & Andy Royle, based on code written by Michael Schaub for Chapter 7 of Kéry & Schaub (2012).
Kéry, M. & Schaub, M. (2012) Bayesian population analysis using WinBUGS - a hierarchical perspective, Academic Press.
Kéry, M. & Royle, J.A. (2021) Applied Hierarchical Modeling in Ecology AHM2 - 3.2.2.
# Run with the default arguments and look at the structure of the output: set.seed(123) tmp <- simCJS() str(tmp) colSums(tmp$ch)