GapAnalysis (version 1.0.2)

FCSex: Final conservation score ex situ

Description

This function calculates the average of the three ex situ conservation metrics returning a final conservation score summary table. It also assigns conservation priority categories

Usage

FCSex(
  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 three slots: FCSex, GRSex_maps,and ERSex_maps

Value

This function returns a data frame summarizing the ex-situ gap analysis scores:

species	Species name	SRSex
Sampling representativeness score ex situ	GRSex	Geographical representativeness score ex situ
ERSex	Ecological representativeness score ex situ	FCSex
Final conservation score ex situ	species	Species name

References

Khoury et al. (2019) Ecological Indicators 98:420-429. doi: 10.1016/j.ecolind.2018.11.016

Examples

# NOT RUN {
##Obtaining occurrences from example
data(CucurbitaData)
##Obtaining species names from the data
Cucurbita_splist <- unique(CucurbitaData$species)
##Obtaining raster_list
data(CucurbitaRasters)
CucurbitaRasters <- raster::unstack(CucurbitaRasters)
##Obtaining ecoregions shapefile
data(ecoregions)
#Running all three Ex-situ gap analysis steps using a unique function
FCSex_df <- FCSex(Species_list=Cucurbita_splist,
                                      Occurrence_data=CucurbitaData,
                                      Raster_list=CucurbitaRasters,
                                      Buffer_distance=50000,
                                      Ecoregions_shp=ecoregions,
                                      Gap_Map=TRUE)

# }