Description Usage Arguments Value References Examples
Calls the summaryHTML rmd file information and displays the quantitative and spatial results content.
1 2 3 4 5 6 7 8 9 10 | SummaryHTML(
Species_list,
Occurrence_data,
Raster_list,
Buffer_distance = 50000,
Ecoregions_shp = NULL,
Pro_areas = NULL,
Output_Folder,
writeRasters
)
|
Species_list |
A species list to calculate 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 representing the species distribution models for the species list provided loaded in raster format. This list must match the same order as the species list. |
Buffer_distance |
Geographical distance used to create circular buffers around germplasm. Default: 50000 that is 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() |
Pro_areas |
A raster file representing protected areas information. If Pro_areas=NULL the funtion will use a protected area raster file provided for your use after run GetDatasets() |
Output_Folder |
A path to save the HTML file resulting of this function |
writeRasters |
Boolean field (default=FALSE) to indicate if raster files should be saved |
This function returns a data frame file saved at a specified folder
Khoury et al. (2019) Diversity and Distributions 26(2):209-225. doi: 10.1111/DDI.13008
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ##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 protected areas raster
data(ProtectedAreas)
##Obtaining ecoregions shapefile
data(ecoregions)
##Get datasets
GetDatasets()
##Running SummaryHTML function
summaryHTML_file <- SummaryHTML(Species_list=Cucurbita_splist,
Occurrence_data = CucurbitaData,
Raster_list=CucurbitaRasters,
Pro_areas=ProtectedAreas,
Buffer_distance=50000,
Ecoregions_shp=ecoregions,
Output_Folder=tempdir(),
writeRasters=FALSE)
|
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