R: Assign geographically-distinct k-folds to background/absence...

geoFoldContrast {enmSdmX}

R Documentation

Assign geographically-distinct k-folds to background/absence sites

Description

This function generates geographically-distinct cross-validation folds, or "geo-folds" of background or absence sites (i.e., "contrast" sites). Each contrast site is assigned to a fold based on the fold of the presence site that is closest. Typically, this function is run after geoFold is run to assign presences to folds.

Usage

geoFoldContrast(
  contrast,
  pres,
  presFolds,
  contrastLongLat = 1:2,
  presLongLat = 1:2,
  ...
)

Arguments

`contrast`	A "spatial points" object representing contrast sites: A `SpatVector` or `sf` vector with points A `data.frame` or `matrix`: Points will be assumed to have the WGS84 coordinate system (i.e., unprojected), and `contrastLongLat` should denote the columns with coordinates.
`pres`	A "spatial points" object representing presence sites: A `SpatVector` or `sf` vector with points A `data.frame` or `matrix`: Points will be assumed to have the WGS84 coordinate system (i.e., unprojected), and `presLongLat` should denote the columns with coordinates.
`presFolds`	Numeric vector: These provide the folds to which `pres` are assigned. There must be one value per point in `pres`.
`contrastLongLat`, `presLongLat`	Character or integer vector: A character or integer vector specifying the columns in `contrast` and `pres` corresponding to longitude and latitude (in that order). The default is to assume that the first two columns in `contrast` represent coordinates. These are ignored if `contrast` or `pres` are a `SpatVector` or an `sf` object.
`...`	Additional arguments (unused)

Value

A vector of integers the same length as the number of points in contrast. Each integer indicates which fold a point in contrast belongs to.

Examples

library(sf)
library(terra)

# lemur occurrence data
data(mad0)
data(lemurs)
crs <- getCRS('WGS84')
ll <- c('longitude', 'latitude')

# use occurrences of all species... easier to see on map
occs <- st_as_sf(lemurs, coords = ll, crs = getCRS('WGS84'))

# create 100 background points
mad0 <- vect(mad0)
bg <- spatSample(mad0, 100)

### assign 3 folds to occurrences and to background sites
k <- 3
minIn <- floor(nrow(occs) / k) # maximally spread between folds

presFolds <- geoFold(occs, k = k, minIn = minIn)
bgFolds <- geoFoldContrast(bg, pres = occs, presFolds = presFolds)

# number of sites per fold
table(presFolds)
table(bgFolds)

# map
plot(mad0, border = 'gray', main = paste(k, 'geo-folds'))
plot(bg, pch = 3, col = bgFolds + 1, add = TRUE)
plot(st_geometry(occs), pch = 20 + presFolds, bg = presFolds + 1, add = TRUE)

legend(
	'bottomright',
	legend = c(
		'presence fold 1',
		'presence fold 2',
		'presence fold 3',
		'background fold 1',
		'background fold 2',
		'background fold 3'
	),
	pch = c(21, 22, 23, 3, 3),
	col = c(rep('black', 3), 2, 3),
	pt.bg = c(2, 3, 4, NA, NA)
)