Description Usage Arguments Details Value Note References See Also Examples

The summed probability densities of both observed and unobserved individuals are computed for a fitted model and dataset.

1 |

`object` |
a fitted secr model |

`sessnum` |
session number if |

`mask` |
x- and y- coordinates of points at which density will be computed |

`ncores` |
integer number of cores to be used for parallel processing |

`...` |
other arguments passed to |

This function calls `fxi.secr`

for each detected animal and
overlays the results to obtain a summed probability density surface D.fx
for the locations of the home-range centres of detected individuals.

A separate calculation using `pdot`

provides the expected
spatial distribution of undetected animals, as another density
surface: crudely, D.nc(X) = D(X) * ( 1 – pdot(X)).

The pointwise sum of the two surfaces is sometimes used to represent the spatial distrbution of the population, but see Notes.

An object of class ‘Dsurface’ (a variety of mask) with a ‘covariates’ attribute that is a dataframe with columns –

`D.fx ` |
sum of |

`D.nc ` |
expected density of undetected (‘not caught’) individuals |

`D.sum ` |
sum of D.fx and D.nc |

All densities are in animals per hectare (the ‘scale’ argument of
`plot.Dsurface`

allows the units to be varied later).

The surface D.sum represents what is known from the data about a specific realisation of the spatial point process for home range centres: varying the intensity of sampling will change its shape. It is not an unbiased estimate of a biologically meaningful density surface. The surface will always tend to lack relief towards the edge of a habitat mask where the main or only contribution is from D.nc.

Borchers, D. L. and Efford, M. G. (2008) Spatially explicit maximum
likelihood methods for capture–recapture studies. *Biometrics*
**64**, 377–385.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
## Not run:
tmp <- fx.total(secrdemo.0)
## to plot we must name one of the covariates:
## the Dsurface default 'D.0' causes an error
plot(tmp, covariate = 'D.sum', col = terrain.colors(16),
plottype = 'shaded')
plot(tmp, covariate = 'D.sum', col = 'white', add = TRUE,
plottype = 'contour')
spotHeight(tmp, prefix = 'D.sum')
fxsurface <- fx.total(ovenbird.model.D, sessnum = 3)
plot(fxsurface, covariate = 'D.sum')
## End(Not run)
``` |

secr documentation built on March 18, 2018, 2:11 p.m.

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