Access Tree of Life Data Releases

Documentation for package ‘rtreeoflife’ version 0.1.0

Help Pages

tol_attach_fasta	Attach parsed FASTA data to a download plan
tol_base_url	Kew Tree of Life base URL
tol_build_gene_tree	Build an illustrative tree from one shared gene
tol_common_genes	Choose a gene shared by multiple downloaded FASTA files
tol_data_dir	Local data directory for downloaded files
tol_download	Download files from a Kew Tree of Life release
tol_download_bundle	Download a predefined Kew Tree of Life bundle
tol_download_directory	Download and validate one directory from a Kew Tree of Life release
tol_download_fasta	Download FASTA files for selected species records
tol_download_release	Download and validate a complete Kew Tree of Life release
tol_export_fasta	Export downloaded FASTA files and a manifest
tol_fasta_long	Convert attached FASTA data to a tidy long table
tol_fasta_summary	Summarise FASTA content by species record
tol_index	List files and directories in a Kew Tree of Life remote index
tol_known_bundle	Known download bundles
tol_known_bundles	Known download bundles
tol_manifest	Read a downloaded Kew Tree of Life manifest
tol_match_species	Match requested species names against the Kew Tree of Life index
tol_plot_fasta_summary	Plot FASTA summary with ggplot2
tol_plot_gene_recovery	Plot recovered gene counts with ggplot2
tol_plot_tree	Plot an hclust tree with ggplot2
tol_read_fasta	Read a FASTA file
tol_release_url	Build a URL for a Kew Tree of Life release
tol_resolve_fasta	Resolve FASTA download targets for selected species records
tol_save_fasta	Save downloaded FASTA files to a permanent directory
tol_search_species	Search Kew Tree of Life species records
tol_set_base_url	Set the Kew Tree of Life base URL for the current R session
tol_species	Kew Tree of Life species index
tol_species_index	Read the Kew Tree of Life species index