simCJS {AHMbook} R Documentation

## Simulate individual capture-histories under a Cormack-Jolly-Seber (CJS) survival model

### Description

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.

### Usage

```simCJS(n.occ = 6, n.marked = 20, phi = 0.7, p = 0.4, show.plot = TRUE)
```

### Arguments

 `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.

### Value

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.

### Author(s)

Marc Kéry & Andy Royle, based on code written by Michael Schaub for Chapter 7 of Kéry & Schaub (2012).

### References

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.

### Examples

```# Run with the default arguments and look at the structure of the output:
set.seed(123)
tmp <- simCJS()
str(tmp)
colSums(tmp\$ch)
```

[Package AHMbook version 0.2.3 Index]