orange

Spherical Descriptors of Geographic Distributions

This package is a collation of tools and metrics to characterize distribution data on the surface of a sphere. The primary group of these metrics is those that describe the extent of a distribution, i.e. geographic ranges/range sizes (depending on who you talk to). The calculation of geographic ranges can be executed using point coordinate data, cells on a discretized sphere, vector polygons and rasters. Besides ensuring the use a geometrically correct implementations, the package offers the exploration of partial results for visual diagnostics and further post-processing.

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Dependencies

The functions of the package are dependent on geographic discretization structures. Due to its utility, the only hard dependency is icosa, which implements near equal area gridding of the sphere. Additional spatial structures include vector-spatial and raster objects implmented in the sf and terra packages, respectively.

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Example use

library(orange)

# background map
library(chronosphere)
ne <- fetch("NaturalEarth", verbose=FALSE)

# some example raw data (Pinna nobilis from OBIS)
data(pinna)
nobilis <- pinna[pinna$species=="Pinna nobilis", ]

# only coords
coords <- unique(nobilis[, c("decimalLongitude", "decimalLatitude")]) 
# rename to standard
colnames(coords) <- c("long", "lat") 

# omit issue localities
coords <- coords[-c(127,155), ]

# basic plot
plot(ne$geometry, reset=FALSE, xlim=c(-15, 40), ylim=c(30, 50),
    col="#ffe7ba", border=NA)
points(coords, pch=3, col="#5d7327", cex=2)

# Maximum great circle distance
mgcd <- mgcd(coords, plot=TRUE)

# Occupancy on a hexagonal grid
hex <- hexagrid(deg=2, sf=TRUE) # from package icosa
occ <- occupancy(coords, s=hex, plot=TRUE)

# Minimum spanning tree length
mst <- mstlength(coords, plot=TRUE, plot.args=list(lwd=3))


# centroid-circle hull
cc <- shull(coords, method="centroidcircle")
plot(cc, add=TRUE)

The Maximum great circle distance:

# Maximum great circle distance
mgcd

## [1] 3452.84

Count of occupied cells:

# Occupancy count 
occ

## [1] 25

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This is a pre-alpha version, and like R, comes with absolutely no warranty.