GapAnalysis (version 1.0.2)

SummaryHTML: Creating a summary HTML document for each taxon

Description

Calls the summaryHTML rmd file information and displays the quantitative and spatial results content.

Usage

SummaryHTML(
  Species_list,
  Occurrence_data,
  Raster_list,
  Buffer_distance = 50000,
  Ecoregions_shp = NULL,
  Pro_areas = NULL,
  Output_Folder,
  writeRasters
)

Arguments

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

Value

This function returns a data frame file saved at a specified folder

References

Khoury et al. (2019) Diversity and Distributions 26(2):209-225. doi: 10.1111/DDI.13008

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 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)
# }
# NOT RUN {
# }