simDM {AHMbook} | R Documentation |

Simulation for multiple-visit data (from `pcountOpen`

help file in package unmarked). `simDM0`

has no covariates while `simDM`

allows for covariates. Both functions assume constant time intervals between primary periods.

simDM0(nsites = 50, nsurveys = 3, nyears = 5, lambda = 4, gamma = 1.5, phi = 0.8, p = 0.7, show.plots=TRUE) simDM(nsites = 50, nsurveys = 3, nyears = 5, mean.lambda = 4, mean.gamma.rel = 0.5, mean.phi = 0.8, mean.p = 0.7, beta.lam = 1, beta.gamma = 1, beta.phi = -1, beta.p = -1, show.plots=TRUE)

`nsites` |
number of sites. |

`nsurveys` |
number of replicate (secondary) samples within period of closure. |

`nyears` |
number of primary samples: years, seasons etc. |

`lambda` |
Initial expected abundance. |

`gamma` |
recruitment rate. |

`phi` |
apparent survival rate. |

`p` |
detection probability. |

`mean.lambda` |
Initial expected abundance at cov.lam = 0. |

`mean.gamma.rel` |
recruitment rate at cov.gamma = 0. |

`mean.phi` |
apparent survival rate at cov.phi = 0. |

`mean.p` |
detection probability at cov.p = 0. |

`beta.lam` |
the slope of parameter lambda (link transformed) on the cov.lam covariate |

`beta.gamma` |
the slope of parameter gamma (link transformed) on the cov.gamma covariate |

`beta.phi` |
the slope of parameter phi (link transformed) on the cov.phi covariate |

`beta.p` |
the slope of parameter p (link transformed) on the cov.p covariate |

`show.plots` |
if TRUE, plots are produced. Set this to FALSE when running simulations. |

For `simDM0`

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

`N ` |
true number of individuals, nsites x nyears |

`S ` |
number of survivors, nsites x (nyears-1) |

`R ` |
number of recruits, nsites x (nyears-1) |

`y ` |
number detected, nsites x nyears x nsurveys |

`yy ` |
number detected as a matrix, nsites x (nyears*nsurveys) |

`simDM`

has the following additional elements:

`cov.lam ` |
covariate for lambda generated from Uniform(-1, 1), nsites vector |

`cov.gamma ` |
covariate for gamma generated from Uniform(-1, 1), nsites vector |

`cov.phi ` |
covariate for phi generated from Uniform(-1, 1), nsites vector |

`cov.p ` |
covariate for p generated from Uniform(-1, 1), nsites x nyears x nsurveys |

`ccov.p ` |
cov.p formatted as a matrix, nsites x (nyears*nsurveys) |

Marc Kéry & Andy Royle, based in part on code written by Richard Chandler.

Dail, D. & Madsen, L. (2011) Models for estimating abundance from repeated counts of an open metapopulation. *Biometrics*, 67, 577-587.

Kéry, M. & Royle, J.A. (2021) *Applied Hierarchical Modeling in Ecology* AHM2 - 2.5.

# Simulate a data set with the default arguments and look at the structure of the output: tmp0 <- simDM0() str(tmp0) tmp <- simDM() str(tmp)

[Package *AHMbook* version 0.2.3 Index]