R: Access Tree of Life Data Releases

# Access Tree of Life Data Releases

## Documentation for package ‘rtreeoflife’ version 0.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## 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