pred extract for extraction of environmnetal data

pred_extract. For extraction of environmental data used for species distribution modeling.

pan-european use case AquaINFRA R

Inputs
Id Title Data Type Description
input_data Occurrence data string URL to a table containing the occurrences from any source. This can be the outcome of the check-names process.
input_raster_url_or_name Input raster string URL of a cloud-optimized raster to be used (will not be downloaded but accessed remotely), or the name of one of the static rasters on the server. Currently only worldclim is available, for testing purposes.
study_area_extent Area of Interest as a Shapefile string URL to the input shapefile containing the study areas inside which you would like to delineate the bounding box or extent for study area.
study_area_geojson_url Area of Interest as a GeoJSON string URL to the input GeoJSON file containing the study areas inside which you would like to delineate the bounding box or extent for study area.
study_area_geojson Area of Interest as GeoJSON object object Directly post the GeoJSON containing the study areas inside which you would like to delineate the bounding box or extent for study area.
colname_lat Column name including Latitude string Column name lat. Example: "decimalLatitude"
colname_lon Column name including Longitude string Column name lon. Example: "decimalLongitude"
colname_species Column name including Species string Column name species. Example: "speciescheck"
mininmum_sprecords Minimum points to consider from the species dataset integer The minimum number of points in a dataset to allow species retained in the dataset. Example: 10, is species dataset is less than 10 records will be ignored.
bool_merge Merge extracted data boolean This allows to return the full dataset with merged with extracted data
bool_list Return a list of dataframe for species if they are more than 1 boolean For multiple species, if set to TRUE, then a list of species dataframes are returned. If false, then a dataframe is returned.
bool_coords Attach the original coordinates boolean If YES, the original records used for data extraction will be attached on the dataset. Easy to tract the slight changes in coordinates during data extraction.
bool_remove_nas Remove NAs after data extraction boolean If YES, the NAs created when the coordinates did not retrun records and left in the dataset.
bool_remove_duplicates Remove duplicates boolean If YES, duplicates records will be removed.
minimum_sprecordsallow Minimum species records to consider before using data in species distribution modeling boolean In species distribution models, species with fewer records needs to be removed but normal data extraction this parameter should be set to FALSE to retain all species.
Outputs
Id Title Description
multiprecleaned Records extracted from raster files. The environmental variables extracted from raster files such as WORLDCLIM, CHELSA, and Copernicus data.

Educational resources and documentation

Jobs

Browse jobs

Links

Execution modes

  • Synchronous
  • Asynchronous