coldspots function

Computes biodiversity coldspots and hotspots

coldspots and hotspots map areas or grid cells with lowest or highest values, respectively, of a biodiversity metric e.g. species richness, species endemism or degree of threat.

coldspots(x, prob = 2.5, na.rm = TRUE, ...)

hotspots(x, prob = 2.5, na.rm = TRUE, ...)

Arguments

• x: a vector on which to compute coldspots
• prob: The threshold quantile for representing the lowest (coldspots) or highest (hotspots) proportion of biodiversity in an area. By default, the threshold is set to prob = 2.5 percent.
• na.rm: logical; if true, any NA and NaN's are removed from x before the quantiles are computed.
• ...: Further arguments passed to or from other methods.

Returns

A vector of integers of 1s and 0s with 1 corresponding to the coldspots or hotspots

Examples

library(terra)
data(africa)
p <- vect(system.file("ex/sa.json", package = "phyloregion"))

Endm <- weighted_endemism(africa$comm)
C <- coldspots(Endm) # coldspots
H <- hotspots(Endm) # hotspots

## Merge endemism values to shapefile of grid cells.
DF <- data.frame(grids=names(C), cold=C, hot=H)
m <- merge(p, DF, by = "grids", all = TRUE)

plot(p, border = "grey", col = "lightgrey",
     main = "Weighted Endemism Hotspots and Coldspots")
plot(m[(m$cold == 1), ], col = "blue", add = TRUE, border = NA)
plot(m[(m$hot == 1), ], col = "red", add = TRUE, border = NA)
legend("bottomleft", fill = c("blue", "red", "yellow", "green"),
       legend = c("coldspots", "hotspots"), bty = "n", inset = .092)

References

Myers, M., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B. & Kent, J. (2000) Biodiversity hotspots for conservation priorities. Nature 403 : 853–858.

Ceballos, G. & Ehrlich, P.R. (2006) Global mammal distributions, biodiversity hotspots, and conservation. Proceedings of the National Academy of Sciences USA 103 : 19374–19379.

Orme, C.D., Davies, R.G., Burgess, M., Eigenbrod, F., Pickup, N. et al. (2005) Global hotspots of species richness are not congruent with endemism or threat. Nature 436 : 1016–1019.

Daru, B.H., Van der Bank, M. & Davies, T.J. (2015) Spatial incongruence among hotspots and complementary areas of tree diversity in southern Africa. Diversity and Distributions 21 : 769-780.

Author(s)

Barnabas H. Daru darunabas@gmail.com