ensemble.spatialThin: Thinning of presence point coordinates in geographical or...

In BiodiversityR: Package for Community Ecology and Suitability Analysis

Thinning of presence point coordinates in geographical or environmental space

Description

Function ensemble.spatialThin creates a randomly selected subset of point coordinates where the shortest distance (geodesic) is above a predefined minimum. The geodesic is calculated more accurately (via distGeo) than in the spThin or red packages.

Usage

ensemble.spatialThin(x, thin.km = 0.1, 
    runs = 100, silent = FALSE, verbose = FALSE, 
    return.notRetained = FALSE)

ensemble.spatialThin.quant(x, thin.km = 0.1, 
    runs = 100, silent = FALSE, verbose = FALSE, 
    LON.length = 21, LAT.length = 21)

ensemble.environmentalThin(x, predictors.stack = NULL, 
    extracted.data=NULL, thin.n = 50,
    runs = 100, pca.var = 0.95, silent = FALSE, verbose = FALSE,
    return.notRetained = FALSE)

ensemble.environmentalThin.clara(x, predictors.stack = NULL, thin.n = 20,
    runs = 100, pca.var = 0.95, silent = FALSE, verbose = FALSE,
    clara.k = 100)

ensemble.outlierThin(x, predictors.stack = NULL, k = 10,
    quant = 0.95, pca.var = 0.95, 
    return.outliers = FALSE)

Arguments

x	Point locations provided in 2-column (lon, lat) format.
thin.km	Threshold for minimum distance (km) in final point location data set.
runs	Number of runs to maximize the retained number of point coordinates.
silent	Do not provide any details on the process.
verbose	Provide some details on each run.
return.notRetained	Return in an additional data set the point coordinates that were thinned out.
LON.length	Number of quantile limits to be calculated from longitudes; see also quantile
LAT.length	Number of quantile limits to be calculated from latitudes; see also quantile
predictors.stack	RasterStack object (stack) containing environmental layers that define the environmental space of point observations.
extracted.data	Data set with the environmental data at the point locations. If this data is provided, then this data will be used in the analysis and data will not be extracted from the predictors.stack.
thin.n	Target number of environmentally thinned points.
pca.var	Minimum number of axes based on the fraction of variance explained (default value of 0.95 indicates that at least 95 percent of variance will be explained on the selected number of axes). Axes and coordinates are obtained from Principal Components Analysis (scores).
clara.k	The number of clusters in which the point coordinates will be divided by clara. Clustering is done in environmental space with point coordinates determined from Principal Components Analysis.
k	The number of neighbours for the Local Outlier Factor analysis; see lof
quant	The quantile probability above with local outlier factors are classified as outliers; see also quantile
return.outliers	Return in an additional data set the point coordinates that were flagged as outliers.

Details

Locations with distances smaller than the threshold distance are randomly removed from the data set until no distance is smaller than the threshold. The function uses a similar algorithm as functions in the spThin or red packages, but the geodesic is more accurately calculated via distGeo.

With several runs (default of 100 as in the red package or some spThin examples), the (first) data set with the maximum number of records is retained.

Function ensemble.spatialThin.quant was designed to be used with large data sets where the size of the object with pairwise geographical distances could create memory problems. With this function, spatial thinning is only done within geographical areas defined by quantile limits of geographical coordinates.

Function ensemble.environmentalThin performs an analysis in environmental space similar to the analysis in geographical space by ensemble.spatialThin. However, the target number of retained point coordinates needs to be defined by the user. Coordinates are obtained in environmental space by a principal components analysis (function rda). Internally, first points are randomly selected from the pair with the smallest environmental distance until the selected target number of retained point coordinates is reached. From the retained point coordinates, the minimum environmental distance is determined. In a second step (more similar to spatial thinning), locations are randomly removed from all pairs that have a distance larger than the minimum distance calculated in step 1.

Function ensemble.environmentalThin.clara was designed to be used with large data sets where the size of the object with pairwise environmental distances could create memory problems. With this function, environmental thinning is done sequentially for each of the clusters defined by clara. Environmental space is obtained by by a principal components analysis (function rda). Environmental distances are calculated as the pairwise Euclidean distances between the point locations in the environmental space.

Function ensemble.outlierThin selects point coordinates that are less likely to be local outliers based on a Local Outlier Factor analysis (lof). Since LOF does not result in strict classification of outliers, a user-defined quantile probability is used to identify outliers.

Value

The function returns a spatially or environmentally thinned point location data set.

Author(s)

Roeland Kindt (World Agroforestry Centre)

References

Aiello-Lammens ME, Boria RA, Radosavljevic A, Vilela B and Anderson RP. 2015. spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography 38: 541-545

See Also

ensemble.batch

Examples

## Not run: 
# get predictor variables, only needed for plotting
library(dismo)
predictor.files <- list.files(path=paste(system.file(package="dismo"), '/ex', sep=''),
    pattern='grd', full.names=TRUE)
predictors <- stack(predictor.files)
# subset based on Variance Inflation Factors
predictors <- subset(predictors, subset=c("bio5", "bio6", 
    "bio16", "bio17", "biome"))
predictors
predictors@title <- "base"

# presence points
presence_file <- paste(system.file(package="dismo"), '/ex/bradypus.csv', sep='')
pres <- read.table(presence_file, header=TRUE, sep=',')[, -1]

# number of locations
nrow(pres)

par.old <- graphics::par(no.readonly=T)
par(mfrow=c(2,2))

pres.thin1 <- ensemble.spatialThin(pres, thin.km=100, runs=10, verbose=T)
plot(predictors[[1]], main="5 runs", ext=extent(SpatialPoints(pres.thin1)))
points(pres, pch=20, col="black")
points(pres.thin1, pch=20, col="red")

pres.thin2 <- ensemble.spatialThin(pres, thin.km=100, runs=10, verbose=T)
plot(predictors[[1]], main="5 runs (after fresh start)", ext=extent(SpatialPoints(pres.thin2)))
points(pres, pch=20, col="black")
points(pres.thin2, pch=20, col="red")

pres.thin3 <- ensemble.spatialThin(pres, thin.km=100, runs=100, verbose=T)
plot(predictors[[1]], main="100 runs", ext=extent(SpatialPoints(pres.thin3)))
points(pres, pch=20, col="black")
points(pres.thin3, pch=20, col="red")

pres.thin4 <- ensemble.spatialThin(pres, thin.km=100, runs=100, verbose=T)
plot(predictors[[1]], main="100 runs (after fresh start)", ext=extent(SpatialPoints(pres.thin4)))
points(pres, pch=20, col="black")
points(pres.thin4, pch=20, col="red")

graphics::par(par.old)

## thinning in environmental space

env.thin <- ensemble.environmentalThin(pres, predictors.stack=predictors, thin.n=60,
    return.notRetained=T)
pres.env1 <- env.thin$retained
pres.env2 <- env.thin$not.retained

# plot in geographical space
par.old <- graphics::par(no.readonly=T)
par(mfrow=c(1, 2))

plot(predictors[[1]], main="black = not retained", ext=extent(SpatialPoints(pres.thin3)))
points(pres.env2, pch=20, col="black")
points(pres.env1, pch=20, col="red")

# plot in environmental space
background.data <- data.frame(raster::extract(predictors, pres))
rda.result <- vegan::rda(X=background.data, scale=T)
# select number of axes
ax <- 2
while ( (sum(vegan::eigenvals(rda.result)[c(1:ax)])/
    sum(vegan::eigenvals(rda.result))) < 0.95 ) {ax <- ax+1}
rda.scores <- data.frame(vegan::scores(rda.result, display="sites", scaling=1, choices=c(1:ax)))
rownames(rda.scores) <- rownames(pres)
points.in <- rda.scores[which(rownames(rda.scores) %in% rownames(pres.env1)), c(1:2)]
points.out <- rda.scores[which(rownames(rda.scores) %in% rownames(pres.env2)), c(1:2)]
plot(points.out, main="black = not retained", pch=20, col="black", 
    xlim=range(rda.scores[, 1]), ylim=range(rda.scores[, 2]))
points(points.in, pch=20, col="red")

graphics::par(par.old)

## removing outliers
out.thin <- ensemble.outlierThin(pres, predictors.stack=predictors, k=10,
    return.outliers=T)
pres.out1 <- out.thin$inliers
pres.out2 <- out.thin$outliers

# plot in geographical space
par.old <- graphics::par(no.readonly=T)
par(mfrow=c(1, 2))

plot(predictors[[1]], main="black = outliers", ext=extent(SpatialPoints(pres.thin3)))
points(pres.out2, pch=20, col="black")
points(pres.out1, pch=20, col="red")

# plot in environmental space
background.data <- data.frame(raster::extract(predictors, pres))
rda.result <- vegan::rda(X=background.data, scale=T)
# select number of axes
ax <- 2
while ( (sum(vegan::eigenvals(rda.result)[c(1:ax)])/
    sum(vegan::eigenvals(rda.result))) < 0.95 ) {ax <- ax+1}
rda.scores <- data.frame(vegan::scores(rda.result, display="sites", scaling=1, choices=c(1:ax)))
rownames(rda.scores) <- rownames(pres)
points.in <- rda.scores[which(rownames(rda.scores) %in% rownames(pres.out1)), c(1:2)]
points.out <- rda.scores[which(rownames(rda.scores) %in% rownames(pres.out2)), c(1:2)]
plot(points.out, main="black = outliers", pch=20, col="black", 
    xlim=range(rda.scores[, 1]), ylim=range(rda.scores[, 2]))
points(points.in, pch=20, col="red")

graphics::par(par.old)


## End(Not run)

BiodiversityR documentation built on June 22, 2024, 11:57 a.m.