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The safedata package

This is an R package for discovering and using datasets produced by scientific research at the SAFE Project. See the following links:

Using safedata

The homepage for the package is at:

https://imperialcollegelondon.github.io/safedata/.

In particular, the following links provide:

Building safedata

The package repository structure and build processes are described here

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Version

Install

install.packages('safedata')

Monthly Downloads

96

Version

1.1.3

License

GPL-3

Maintainer

David Orme

Last Published

May 5th, 2023

Functions in safedata (1.1.3)

get_taxon_coverage

Retrieve the current taxon index
get_taxa

Obtaining taxonomy for a SAFE dataset.
get_index

Get the cached dataset index
get_locations

Obtaining locations for a SAFE dataset.
igraph_to_phylo

Getting a phylogeny for a dataset
load_location_aliases

Load and cache the SAFE location aliases
load_gazetteer

Load and cache the SAFE gazetteer
safedata

Finding and using data from the SAFE Project.
safedata_network

Network resources and the safedata package.
search_safe

SAFE dataset search functions.
show_concepts

Show SAFE dataset metadata
taxon_index_to_taxon_table

Add taxon hierarchy to taxon metadata
verbose_message

Message function that can be globally muted
validate_record_ids

Validates dataset record ids from user input
load_safe_data

Loads data from a SAFE dataset.
try_to_download

Attempt to download a URL resource, failing gracefully.
safe_api_search

Internal SAFE dataset API search functions
set_safe_dir

Set the local SAFE data directory
safedata_env

Index file memory cache
set_example_safe_dir

Functions to use an example data directory for package examples
download_index

Downloads the current dataset index
add_locations

Adds location data to a SAFE data worksheet.
download_safe_files

Download SAFE dataset files
get_file_details

Get file details for a record
add_taxa

Add a taxonomic hierarchy to a SAFE data worksheet.
get_taxon_graph

Get a graph of the taxa in a dataset
insert_dataset

Inserts local copies of files from a dataset into a SAFE data directory
download_gazetteer

Downloads the current SAFE gazetteer
download_location_aliases

Downloads the current SAFE location aliases
load_index

Load and cache the dataset index
get_data_dir

Checks the data directory is set and returns it
fetch_record_metadata

Get and load SAFE dataset metadata
file_status

Get file status for a dataset