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)
```

*AHMbook*version 0.2.9 Index]