simSpatialDSte {AHMbook} | R Documentation |

## Simulate data for replicate line transect surveys with temporary emigration

### Description

This simulates line transect distance sampling data with a spatial distribution of objects in a heterogeneous landscape where the parameter beta controls the effect of habitat. Multiple sample occasions are simulated and temporary emigration is allowed (parameter phi). Habitat is simulated according to a Gaussian random field model defined within the function. Uses a half normal detection model (if perp = TRUE) or a Gaussian hazard model (perp = FALSE).

To recreate the data sets used in the book with R 3.6.0 or later, include `sample.kind="Rounding"`

in the call to `set.seed`

. This should only be used for reproduction of old results.

### Usage

```
simSpatialDSte(nsites=28, dim=10, beta=1, lam0=2.5, nsurveys=4, sigma=3,
phi=0.6, theta=2, show.plots=3)
```

### Arguments

`nsites` |
number of sites |

`dim` |
number of pixels along each side of the square site |

`beta` |
the effect of habitat on the number of individuals in a pixel. |

`lam0` |
expected population size at each site |

`nsurveys` |
the number of replicate surveys |

`sigma` |
scale of half-normal detection function |

`phi` |
probability an individual is available for detection, ie, not temporarily emigrated. |

`theta` |
exponential correlation in the spatial covariate. |

`show.plots` |
the number of sites for which plots should be displayed; set to 0 to suppress plotting. |

### Value

A list with the values of the input arguments and the following additional elements:

`npixels` |
the number of pixels in each site (= dim^2) |

`B` |
distance from line to edge of square (= dim/2) |

`M` |
true number of individuals at each site |

`d` |
perpendicular distance of each pixel from the line |

`Habitat` |
pixels x sites matrix, value of habitat covariate for each pixel |

`y` |
sites x pixels x surveys array, number of animals detected |

`Counts` |
sites x surveys matrix, number of animals detected (summed over pixels) |

### Author(s)

Mizel et al (2018) Appendix S1, based in turn on Kéry & Royle (2016).

### References

Kéry, M. & Royle, J.A. (2016) *Applied Hierarchical Modeling in Ecology*.

Mizel, J.D., Schmidt, J.H., & Lindberg, M.S. (2018) Accommodating temporary emigration in spatial distance sampling models. *Journal of Applied Ecology*, 55, 1456-1464.

Kéry, M. & Royle, J.A. (2021) *Applied Hierarchical Modeling in Ecology* AHM2 - 11.

### Examples

```
# Run the function with default values and look at the output
str(tmp <- simSpatialDSte())
```

*AHMbook*version 0.2.9 Index]