getEnvVar: Extract environmental data to presence locations

In ppmlasso: Point Process Models with LASSO-Type Penalties

Extract environmental data to presence locations

Description

Given a matrix of quadrature points and a list of species presences, this function extracts environmental data to presence locations using bilinear interpolation.

Usage

getEnvVar(sp.xy, env.grid, env.scale, coord = c("X", "Y"), envfilename = "SpEnvData", 
tol = 0.01, writefile = TRUE)

Arguments

sp.xy	A matrix of species locations containing at least one column representing longitude and one column representing latitude.
env.grid	The geo-referenced matrix of environmental grids.
env.scale	The spatial resolution of the quadrature scheme from which the environmental data is extracted.
coord	A vector containing the names of the longitude and latitude coordinates, as in sampleQuad.
envfilename	An optional argument containing the name of the saved file. Setting envfilename = "SpEnvData" will save a matrix sp.dat containing the species presence locations and the interpolated environmental data to the file "SpEnvData.RData".
tol	An optional argument to specify the tolerance level of coordinate error passed to an internal call to the griddify function, set to 0.01 by default.
writefile	A logical argument to determine whether the output should be written to a file or not. If TRUE (the default), the output will be saved with the file name as described in the envfilename argument.

Details

At a given species location with coordinates (x, y), the interpolated value of the environmental variable z is calculated as a weighted average of z at four reference quadrature points (x^{(1)}, y^{(1)}), (x^{(1)}, y^{(2)}), (x^{(2)}, y^{(1)}) and (x^{(2)}, y^{(2)}) that form a square of nominated side length env.scale surrounding (x, y).

Value

A matrix containing locations of species presences in the first two columns and the interpolated environmental data in the remaining columns.

Author(s)

Ian W. Renner

Examples

data(BlueMountains)
species.env = getEnvVar(BlueMountains$eucalypt, env.grid = BlueMountains$env, env.scale = 0.5,
envfilename = NA, writefile = FALSE)

ppmlasso documentation built on Dec. 1, 2022, 5:09 p.m.