addCovariates: Add Covariates to Mask or Traps

In secr: Spatially Explicit Capture-Recapture

Add Covariates to Mask or Traps

Description

Tools to construct spatial covariates for existing mask or traps objects from a spatial data source.

Usage

addCovariates(object, spatialdata, columns = NULL, strict = FALSE, replace = FALSE)

Arguments

object	mask, traps or popn object
spatialdata	spatial data source (see Details)
columns	character vector naming columns to include (all by default)
strict	logical; if TRUE a check is performed for points in object that lie outside spatialdata (mask data sources only)
replace	logical; if TRUE then covariates with duplicate names are replaced; otherwise a new column is added

Details

The goal is to obtain the value(s) of one or more spatial covariates for each point (i.e. row) in object. The procedure depends on the data source spatialdata, which may be either a spatial coverage (raster or polygon) or an object with covariate values at points (another mask or traps object). In the first case, an overlay operation is performed to find the pixel or polygon matching each point. In the second case, a search is conducted for the closest point in spatialdata.

If spatialdata is a character value then it is interpreted as the name of a polygon shape file (excluding ‘.shp’).

If spatialdata is a SpatialPolygonsDataFrame, SpatialGridDataFrame or 'sf' object from sf then it will be used in an overlay operation as described.

If package terra has been installed then spatialdata may also be a RasterLayer from package raster or SpatRaster from terra. If provided counts should be a single name that will be used for the values (otherwise 'raster' will be used).

If spatialdata is a mask or traps object then it is searched for the closest point to each point in object, and covariates are drawn from the corresponding rows in covariates(spatialdata). By default (strict = FALSE), values are returned even when the points lie outside any cell of the mask.

Value

An object of the same class as object with new or augmented covariates attribute. Column names and types are derived from the input.

Warning

Use of a SpatialGridDataFrame for spatialdata is untested.

See Also

make.mask, read.mask, read.traps

Examples

## In the Lake Station skink study (see ?skink), habitat covariates were
## measured only at trap sites. Here we extrapolate to a mask, taking
## values for each mask point from the nearest trap.

LSmask <- make.mask(LStraps, buffer = 30, type = "trapbuffer")
tempmask <- addCovariates(LSmask, LStraps)
## show first few lines
head(covariates(tempmask))

secr documentation built on Oct. 18, 2023, 1:07 a.m.