Flags Spatial Errors in Biological Collection Data Using
Specialists' Information
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Documentation for package ‘RuHere’ version 1.0.1
Help Pages
| available_datasets | Check the available distribution datasets for a set of species |
| bien_here | Download species distribution information from BIEN |
| bind_here | Bind occurrences after standardizing columns |
| check_countries | Check if the records fall in the country assigned in the metadata |
| check_states | Check if the records fall in the state assigned in the metadata |
| country_dictionary | Country dictionary for standardizing country names and codes |
| country_from_coords | Extract country from coordinates |
| create_metadata | Create metadata template |
| cultivated | Dictionary of terms used to flag cultivated individuals |
| fake_data | Fake occurrence data for testing coordinate validation functions |
| faunabr_here | Download the latest version of the Fauna do Brazil (Taxonomic Catalog of the Brazilian Fauna) |
| fix_countries | Identify and correct coordinates based on country information |
| fix_states | Identify and correct coordinates based on state information |
| flag_bien | Identify records outside natural ranges according to BIEN |
| flag_colors | Color palette for flagged records |
| flag_consensus | Get consensus across multiple flags |
| flag_cultivated | Flag occurrence records of cultived individuals |
| flag_duplicates | Flag duplicated records |
| flag_env_moran | Select Environmentally Thinned Occurrences Using Moran's I Autocorrelation |
| flag_faunabr | Identify records outside natural ranges according to Fauna do Brasil |
| flag_florabr | Identify records outside natural ranges according to Flora e Funga do Brasil |
| flag_fossil | Flag fossil records |
| flag_geo_moran | Select Spatially Thinned Occurrences Using Moran's I Autocorrelation |
| flag_inaturalist | Flag occurrence records sourced from iNaturalist |
| flag_iucn | Identify records outside natural ranges according to the IUCN |
| flag_names | Flag name dictionary |
| flag_wcvp | Identify records outside natural ranges according to the World Checklist of Vascular Plants |
| flag_year | Flag records outside a year range |
| florabr_here | Download the latest version of Flora e Funga do Brasil database |
| format_columns | Format and standardize column names and data types of an occurrence dataset |
| get_bien | Download occurrence records from BIEN |
| get_env_bins | Identify Environmental Blocks and Group Nearby Records in Environmental Space |
| get_idigbio | get_idigbio |
| get_specieslink | Download occurrence records from SpeciesLink |
| ggmap_here | Static Visualization of Occurrence Flags with ggplot |
| ggrid_here | Static Visualization of Richness and Trait Maps |
| import_gbif | Import a download requested from GBIF |
| iucn_here | Download species distribution information from IUCN |
| map_here | Interactive Visualization of Occurrence Flags with mapview |
| moranfast | Fast Moran's I Autocorrelation Index |
| occurrences | Integrated occurrence dataset for three example species |
| occ_bien | Occurrence records of Yellow Trumpet Tree from BIEN |
| occ_flagged | Flagged occurrence records of _Araucaria angustifolia_ |
| occ_gbif | Occurrence records of _Araucaria angustifolia_ from GBIF |
| occ_idig | Occurrence records of azure jay from iDigBio |
| occ_splink | Occurrence records of azure jay from SpeciesLink |
| plot_env_bins | Plot Environmental Bins (2D Projection) |
| prepared_metadata | Metadata templates used internally by 'format_columns()' |
| prepare_gbif_download | Prepare data to request GBIF download |
| puma_atlanticr | Occurrence records of _Puma concolor_ from AtlanticR |
| relocate_after | Relocate a column in a data frame |
| relocate_before | Relocate a column in a data frame |
| remove_accent | Remove accents and special characters from strings |
| remove_flagged | Remove flagged records |
| remove_invalid_coordinates | Identify and remove invalid coordinates |
| request_gbif | Submit a request to download occurrence data from GBIF. |
| richness_here | Species Richness and Occurrence Summary Mapping |
| set_gbif_credentials | Store GBIF credentials |
| set_iucn_credentials | Store SpeciesLink credential |
| set_specieslink_credentials | Store SpeciesLink credential |
| spatialize | Spatialize occurrence records |
| spatial_kde | Kernel Density Estimation (Heatmap) for occurrence data |
| standardize_countries | Standardize country names |
| standardize_states | Standardize state names |
| states | Administrative Units (States, Provinces, and Regions) |
| states_dictionary | States dictionary for standardizing state and province names and codes |
| states_from_coords | Extract state from coordinates |
| summarize_flags | Summarize flags |
| thin_env | Flag records that are close to each other in the enviromnetal space |
| thin_geo | Flag records that are close to each other in the geographic space |
| wcvp_here | Download distribution data from the World Checklist of Vascular Plants (WCVP) |
| world | World Countries |
| worldclim | Bioclimatic Variables from WorldClim (bio_1, bio_7, bio_12) |