R: Flags Spatial Errors in Biological Collection Data Using Specialists' Information

# Flags Spatial Errors in Biological Collection Data Using Specialists' Information

## Documentation for package ‘RuHere’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

atlantic_amphibians | Amphibian communities from the Atlantic Forest
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
cite_datapaper | Cite data papers retrieved from get_datapaper
country_dictionary | Country dictionary for standardizing country names and codes
country_from_coords | Extract country from coordinates
count_flags | Count the number of flags for each record
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_datapaper | Download and merge biodiversity data papers
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
inventory_completeness | Estimation of inventory completeness and coverage deficit
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.
request_gbif_specieslist | Download a list of species recorded inside a spatial polygon 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)