OCSVMprofiling: Environmental profiling with One-Classification Support...

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

View source: R/OCSVMprofiling.R

Description

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

Usage

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

Arguments

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

Details

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.

Value

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

Author(s)

M. Iturbide

References

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.

See Also

svm, backgroundGrid

Examples

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## 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")

mopa documentation built on May 2, 2019, 6:47 a.m.