aohVal: aohVal: evaluate the AOH mapping

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

Description

Provide the summary of validation results based on comparison between an independent occurrence records of species and the extent of occurrence (EOO) and area of habitat (AOH) following Rondinini et al. (2011)

Usage

# method for signature 'SpatialPolygonsDataFrame', 'RasterLayer',
'RasterStack', a 'list' of 'RasterLayer' or 'aoh' object (see
 aoh to generate the latter object)

aohVal(eooSp, aohSp, plot=TRUE, progress=FALSE)

Arguments

eooSp	Spatial distribution data of the species representing the original (i.e. not refined) extent of occurrence (EOO). It might correspond to 'SpatialPolygonsDataFrame' (see readShp to obtain such class of object), a 'RasterLayer', a 'RasterStack', or a 'list' with 'RasterLayer' class of features (see readRas to obtain such object).
aohSp	Spatial distribution data of the species representing the area of habitat (AOH). It might correspond to 'SpatialPolygonsDataFrame' (see readShp to obtain such class of object), a 'RasterLayer', a 'RasterStack', a 'list' with 'RasterLayer' class of features (see readRas to obtain such object), or a 'aoh' (see aoh to obtain such class of object).
plot	(logical) Whether the output should also return a plot representing the graphical result of validation (see Rondinini et al. 2011). Default is TRUE.
progress	(logical) A bar showing the progress of the function. Default is FALSE.

Details

The function gives the summary of validation steps followed to evaluate the quality of models as described and performed by Rondidini et al. (2011) and Ficetola et al. (2015).

Value

By default, aohVal returns a data.frame with a summary of results for each species which aoh was evaluated. It gives the number of records matching with the EOO ("MATCH.EOO) and with the AOH ("MATCH.AOH) and the values of prevalence of points ("PP", Rondinini et al. 2011) through the proportion of occurrences spatially congruent with suitable cells, and of model prevalence ("MP", Rondinini et al. 2011), which represents EOOs proportion assigned as suitable). AOH predict species occurrences correctly when all available records match with its suitable cells (PP = 1). The evaluation of AOHs performance is based on difference between PP and MP. If PP > MP, AOH performs better than EOO in predict presences (Ficetola et al. 2015).

If plot is TRUE, the function return also a plot with a graphical representation of validation results (see Rondinini et al. 2011). If plot FALSE, the function return a data.frame

Author(s)

Thaís Dória & Daniel Gonçalves-Souza

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

### Fictitious birds data

# Example for signature 'SpatialPolygonsDataFrame' (eoo) and 'aoh' (aoh) with
a 'RasterLayer' class of features.

birdVal1<-aohVal(eoo = eoo_birdShp, aoh = aoh_birdRas, plot = TRUE, progress = TRUE)
# Example for signature 'RasterLayer' or 'RasterStack' (eoo) and 'aoh' (aoh) with
a 'RasterLayer' class of features.

birdVal2<-aohVal(eoo = eoo_birdRas, aoh = aoh_birdRas, plot = TRUE, progress = TRUE)

# Example for signature 'SpatialPolygonsDataFrame' (eoo) and 'aoh' (aoh) with
a 'SpatialPolygonsDataFrame' class of features.

birdVal3<-aohVal(eoo = eoo_birdShp, aoh = aoh_birdShp, plot = TRUE, progress = TRUE)

# Example for signature 'RasterLayer' or 'RasterStack' (eoo) and 'aoh' (aoh) with
a 'SpatialPolygonsDataFrame' class of features.

birdVal4<-aohVal(eoo = eoo_birdRas, aoh = aoh_birdShp, plot = TRUE, progress = TRUE)

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