Package index • RuHere

All functions

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
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
occurrences: Integrated occurrence dataset for three example species
plot_env_bins(): Plot Environmental Bins (2D Projection)
prepare_gbif_download(): Prepare data to request GBIF download
prepared_metadata: Metadata templates used internally by format_columns()
puma_atlanticr: Occurrence records of Puma concolor from AtlanticR
relocate_after() 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
spatial_kde(): Kernel Density Estimation (Heatmap) for occurrence data
spatialize(): Spatialize occurrence records
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)