fx.total | R Documentation |

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

```
fx.total(object, sessnum = 1, mask = NULL, ncores = NULL, ...)
```

`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 threads 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.

Setting `ncores = NULL`

uses the existing value from the environment variable
RCPP_PARALLEL_NUM_THREADS (see `setNumThreads`

).

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.

`fxi.secr`

, `fxi.contour`

, `pdot`

```
## 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')
if (interactive()) {
spotHeight(tmp, prefix = 'D.sum')
}
fxsurface <- fx.total(ovenbird.model.D, sessnum = 3)
plot(fxsurface, covariate = 'D.sum')
## End(Not run)
```

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