Description Usage Arguments Value References Examples
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
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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 |
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 |
Khoury et al. (2019) Ecological Indicators 98:420-429. doi: 10.1016/j.ecolind.2018.11.016
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ##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)
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