GapAnalysis (version 1.0.2)

ERSex: Ecological representativeness score ex situ

Description

The ERSex process provides an ecological measurement of the proportion of a species range that can be considered to be conserved in ex situ repositories. The ERSex calculates the proportion of terrestrial ecoregions (The Nature Conservancy Geospatial Conservation Atlas 2019) represented within the G buffered areas out of the total number of ecoregions occupied by the distribution model.

Usage

ERSex(
  Species_list,
  Occurrence_data,
  Raster_list,
  Buffer_distance = 50000,
  Ecoregions_shp = NULL,
  Gap_Map = FALSE
)

Arguments

Species_list

A vector of characters with the species names to calculate the GRSex metrics.

Occurrence_data

A data frame object with the species name, geographical coordinates, and type of records (G or H) for a given species

Raster_list

A list of rasters representing the species distribution models for the species list provided in Species_list. The order of rasters in this list must match the same order as Species_list.

Buffer_distance

Geographical distance used to create circular buffers around germplasm. Default: 50000 (50 km) around germplasm accessions (CA50)

Ecoregions_shp

A shapefile representing Ecoregions information with a field ECO_ID_U representing Ecoregions Ids. If Ecoregions=NULL the function will use a shapefile provided for use after running GetDatasets()

Gap_Map

logical, if TRUE the function will calculate gap maps for each species analyzed and will return a list with with two slots ERSex and gap_maps, or three slots ERSex, buffer_list, and gap_maps

Value

This function returns a dataframe as main result with two columns:

species	Species name	ERSex
ERSex value calculated	species	Species name

References

Castaneda-Alvarez et al. (2016) Nature Plants 2(4):16022. doi: 10.1038/nplants.2016.22 Khoury et al. (2019) Ecological Indicators 98:420-429. doi: 10.1016/j.ecolind.2018.11.016 The Nature Conservancy Geospatial Conservation Atlas. 2019. Terrestrial Ecoregions

Examples

# NOT RUN {
##Obtaining occurrences from example
data(CucurbitaData)
Cucurbita_splist <- unique(CucurbitaData$species)
## Obtaining rasterList object. ##
data(CucurbitaRasters)
CucurbitaRasters <- raster::unstack(CucurbitaRasters)
##Obtaining ecoregions shapefile
data(ecoregions)
#Running ERSex
ERSex_df <- ERSex(Species_list = Cucurbita_splist,
                    Occurrence_data = CucurbitaData,
                    Raster_list = CucurbitaRasters,
                    Buffer_distance = 50000,
                    Ecoregions_shp=ecoregions,
                    Gap_Map=FALSE)

# }