aoh: aoh: mapping the AOH of species

In thaisdoria/habitaR: Tools for mapping the species’ area of habitat (AOH) from geospatial data

Description

Provide the area of habitat (AOH) of a given species through refinement of its known geographic distribution

Usage

aoh(eooSp = NULL, lc = NULL, alt = NULL, altPref = NULL,
habPref = NULL, climSuit = NULL, threshold = 0.5, resolution = NULL,
continuous = FALSE, shpOut = FALSE, extentOut = NULL,
progress = FALSE)

Arguments

eooSp	SpatialPolygons of the spatial distribution of the species or path for a folder with spatial distribution shapefiles (ESRI shapefile format). The name of the species must be on the second column of the attribute table of the shapefile.
lc	'RasterLayer', 'RasterBrick' or 'RasterStack' object of the land use map reclassified for the categories of habitat.
alt	'RasterLayer' object of the elevation map. Optional.
altPref	Data.frame with altitudinal range of species. First column must be the species name, second column the minimum value of altitude and the third column the maximum value of altitude
habPref	Data.frame 0/1 of habitat preference of the species. First column must be the species name. The posterior columns must be named after the categories of habitat as following the lc classification. prefHab can help obtain this data.
climSuit	List containing RasterLayers objects of the climatic suitability of the species. The itens of the list must be named after their corresponding species. Optional.
threshold	Numeric value indicating the threshold of the cell coverage by the species to the species be considered present (values between 0 and 1). Only used if continuous = FALSE and a coarser resolution is provided or the resolution of lc and alt are different or shpOut is TRUE.
resolution	Numeric value indicating the preferred resolution for the rasters. Resolution must coarser than the resolution of lc and alt.
continuous	(logical) Whether the output should be continuous instead binary for the rasters. Only used if resolution provided or when the resolution of lc and alt are different.
shpOut	(logical) Whether the output should be a shapefile as opposed to a raster.
extentOut	Extent object or a vector of four numbers indicating the preferred output for the rasters. Optional.
progress	(logical) A bar showing the progress of the function.

Details

The function map the 'area of habitat' (AOH) within the polygon of geographical distribution (SpatialPolygon) representing the 'extent of occurrence' (EOO). This mapping is made considering the specific preference for habitats of a given species.

Value

By default, aoh returns 'aoh' object corresponding to a list with two elements:

• A data.frame detailing if the function was able (1) or not (0) to refinate the species distribution.

• A list of 'RasterLayer' or 'SpatialPolygons' object representing the refined distribution of the species. For the 'RasterLayer' the value of 0 indicates the cells where the species were considered as present before the refinement. Values higher than 0 indicates the coverage of cell by the spatial distribution after the species habitat's mapping.

Author(s)

Daniel Gonçalves-Souza & Thaís Dória

References

1. Rondinini C., Di Marco M., Chiozza F., Santulli G., Baisero D., Visconti P., and Boitani L. (2011). Global habitat suitability models of terrestrial mammals. Philosophical Transactions of the Royal Society B, 366:2633–2641.

2. Ficetola G.F., Rondinini C., Bonardi A., Baisero D., and Padoa-Schippa E. (2015). Habitat availability for amphibians and extinction threat: a global analysis. Diversity and Distributions, 21(3):302–311.

3. Brooks T.M., Pimm S.L., Akçakaya H.R., Buchanan G.M., Butchart S.H.M, Foden W., Hilton-Taylor C., Hoffmann M., Jenkins C.N., Joppa L., Li B.V., Menon V., Ocampo-Peñuela N., and Rondinini C. (2019). Measuring Terrestrial Area of Habitat (AOH) and Its Utility for the IUCN Red List. Trends in Ecology & Evolution, 34(11):977–986.

Examples

### Raster Output ###

aoh_ras <- aoh(eooSp = eoo_birdShp, lc = lc_map, alt = alt_map,
altPref = alpref_bird, habPref = habpref_bird, climSuit = climSuit_bird,
continuous = TRUE, shpOut = FALSE, progress = FALSE)

### Shapefile Output ###

aoh_shp <- aoh(eooSp = eoo_birdShp, lc = lc_map, alt = alt_map,
altPref = alpref_bird,habPref = habpref_bird, climSuit = climSuit_bird,
resolution = 0.05, shpOut = TRUE, progress = FALSE)

thaisdoria/habitaR documentation built on Dec. 18, 2020, 8:09 p.m.