Internal {secr}

R Documentation

Internal Functions

Description

Various functions called internally by secr and not exported.

Usage

boundarytoSF (poly)

esaPlotsecr (object, max.buffer = NULL, max.mask = NULL,
    thin = 0.1, poly = NULL, poly.habitat = TRUE, session = 1, plt = TRUE, 
    type = "density", add = FALSE, overlay = TRUE, conditional = FALSE, ...)

Arguments

poly	data to define one or more polygons
object	secr object output from secr.fit
max.buffer	maximum width of buffer in metres
max.mask	mask object
thin	proportion of mask points to retain in plot and output
poly.habitat	logical as in make.mask
session	vector of session indices (used if object spans multiple sessions)
plt	logical to plot results
type	character; see esaPlot
add	logical to add line to an existing plot
overlay	logical; if TRUE then automatically add = TRUE for plots after the first
conditional	logical; see esaPlot
...	other arguments not used (boumndarytoSF, Dfn2) or graphical arguments passed to plot() and lines() (esaPlotsecr)

Details

The function boundarytoSF converts various possible polygon input formats to a standard form (sfc).

Possible inputs are:

Input	From	Note
2-column matrix or dataframe	base R
SpatialPolygons	sp
SpatialPolygonsDataFrame	sp
SpatVector	terra
sf	sf	geometry type POLYGON or MULTIPOLYGON
sfc	sf	geometry type POLYGON or MULTIPOLYGON

Matrix input defines a single polygon.

esaPlotsecr provides a wrapper for esaPlot that is called internally from esaPlot when it is presented with an secr object. Arguments of esaPlot such as detectfn are inferred from the fitted model.

The optional ‘poly’ argument of esaPlotsecr is a matrix of two columns interpreted as the x and y coordinates of a bounding polygon.

If max.mask is not specified then a maximal mask of type ‘trapbuffer’ is constructed using max.buffer and the spacing of the mask in object. In this case, if max.buffer is not specified then it is set either to the width of the existing plot (add = TRUE) or to 10 x sigma-hat from the fitted model in object (add = FALSE).

Value

boundarytoSF – Spatial object of sf class sfc, containing a geometry set of type POLYGON or MULTIPOLYGON. NULL input results in NULL output.

esaPlotsecr – see esaPlot

References

Hijmans, R. J. (2022) terra: Spatial Data Analysis. R package version 1.5-14. https://rspatial.org/terra/

Pebesma, E. (2018) Simple features for R: standardized support for spatial vector data. The R Journal 10(1), 439–446. https://doi.org/10.32614/RJ-2018-009

Pebesma, E.J. and Bivand, R. S. (2005) Classes and methods for spatial data in R. R News 5(2), 9–13. https://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdf.

See Also

pointsInPolygon, secr-spatialdata.pdf,

Examples

## Not run: 

poly <- cbind(x = c(0,6,6,0,0), y = c(0,0,6,6,0))  
secr:::boundarytoSF(poly)


## End(Not run)

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