Reference

Indexing and download functions The safedata package maintains a local index of the datasets available in the SAFE dataset repository, used to check the availability of datasets and to download and verify dataset files. These commands are used to generate the local index, validate record ids against the index and to download data.
safedata	Finding and using data from the SAFE Project.
set_safe_dir()	Set the local SAFE data directory
validate_record_ids() print(<safe_record_set>) `&`(<safe_record_set>) `|`(<safe_record_set>)	Validates dataset record ids from user input
download_safe_files()	Download SAFE dataset files
set_example_safe_dir() unset_example_safe_dir()	Functions to use an example data directory for package examples
Data discovery These functions provide an interface to the dataset metadata search API provided by the SAFE Project website
search_dates() search_fields() search_authors() search_taxa() search_text() search_spatial()	SAFE dataset search functions.
Metadata display SAFE datasets contain a considerable amount of metadata about at the dataset, data worksheet and field level. These functions display the metadata available at each of these levels.
show_concepts() show_record() show_worksheet()	Show SAFE dataset metadata
Loading data These functions load data from a SAFE dataset and allow users to explore the taxa and locations associated with a dataset and to match taxa and locations into a loaded data worksheet.
load_safe_data() str(<safedata>) print(<safedata>)	Loads data from a SAFE dataset.
insert_dataset()	Inserts local copies of files from a dataset into a SAFE data directory
get_taxa()	Obtaining taxonomy for a SAFE dataset.
get_taxon_coverage()	Retrieve the current taxon index
igraph_to_phylo() get_phylogeny()	Getting a phylogeny for a dataset
get_taxon_graph()	Get a graph of the taxa in a dataset
add_taxa()	Add a taxonomic hierarchy to a SAFE data worksheet.
get_locations()	Obtaining locations for a SAFE dataset.
add_locations()	Adds location data to a SAFE data worksheet.
Accessing files These functions help users get access to the files stored in a safedata directory.
get_file_details()	Get file details for a record
Internal functions The following internal functions are not included in the package namespace but are documented here briefly.
safedata_env	Index file memory cache
get_data_dir()	Checks the data directory is set and returns it
verbose_message()	Message function that can be globally muted
download_index()	Downloads the current dataset index
download_gazetteer()	Downloads the current SAFE gazetteer
download_location_aliases()	Downloads the current SAFE location aliases
load_index()	Load and cache the dataset index
load_gazetteer()	Load and cache the SAFE gazetteer
load_location_aliases()	Load and cache the SAFE location aliases
fetch_record_metadata() load_record_metadata()	Get and load SAFE dataset metadata
safe_api_search() validate_query_param()	Internal SAFE dataset API search functions
taxon_index_to_taxon_table()	Add taxon hierarchy to taxon metadata
try_to_download()	Attempt to download a URL resource, failing gracefully.
safedata_network	Network resources and the safedata package.