OCSVMprofiling: Environmental profiling with One-Classification Support...
In mopa: Species Distribution MOdeling with Pseudo-Absences

Description Usage Arguments Details Value Author(s) References See Also Examples

Presence-only modeling and classification of coordinates predicted as presence and absence

1	OCSVMprofiling(xy, varstack, background = NULL, nu = 0.5)

`xy`	Data frame or list of data frames with coordinates (each row is a point)
`varstack`	RasterStack of variables for modeling
`background`	Object derived from function `backgroundGrid`. If NULL (default), the background is extracted from varstack. Matrix or list of matrixes of the background xy coordinates in columns.
`nu`	Parameter needed for one-classification `svm`. Default is 0.5

This function constitutes the first step from a three-step proccess to generate pseudo-absences, and is aimed at excluding the suitable areas for the species (xy records) from the background from which pseudo-absences are sampled.

A list with two components:

`absence`	Matrix or list of matrixes with xy coordinates predicted as absence
`presence`	Matrix or list of matrixes with xy coordinates predicted as presence

M. Iturbide

Iturbide, M., Bedia, J., Herrera, S., del Hierro, O., Pinto, M., Gutierrez, J.M., 2015. A framework for species distribution modelling with improved pseudo-absence generation. Ecological Modelling. DOI:10.1016/j.ecolmodel.2015.05.018.

svm, backgroundGrid

## Load presence data
data(Oak_phylo2)

## Load climate data
destfile <- tempfile()
data.url <- "https://raw.githubusercontent.com/SantanderMetGroup/mopa/master/data/biostack.rda"
download.file(data.url, destfile)
load(destfile, verbose = TRUE)

## Spatial reference
projection(biostack$baseline) <- CRS("+proj=longlat +init=epsg:4326")
r <- biostack$baseline[[1]]
## Background of the whole study area
bg <- backgroundGrid(r)

## Environmental profiling
bg.profiled <- OCSVMprofiling(xy = Oak_phylo2, varstack = biostack$baseline, 
                              background = bg$xy)
## Plot
plot(bg.profiled$absence$H11, pch="*")
points(bg.profiled$presence$H11, pch="*", col= "pink")