R: Taxonomic Distance and Phylogenetic Lineage Computation

# Taxonomic Distance and Phylogenetic Lineage Computation

## Documentation for package ‘taxodist’ version 0.5.0

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

## Help Pages

taxodist-package | taxodist: Taxonomic Distance and Phylogenetic Lineage Computation
cache_info | Inspect the current taxodist lineage cache
check_coverage | Check whether a taxon is covered by The Taxonomicon
clear_cache | Clear the taxodist lineage cache
closest_relative | Find the closest relative of a taxon among a set of candidates
compare_lineages | Compare lineages of two taxa side by side
distance_matrix | Compute pairwise taxonomic distances for a set of taxa
filter_clade | Filter a vector of taxa to those belonging to a given clade
focal_distances | Compute distances from a focal taxon to a community of taxa
get_lineage | Retrieve the full taxonomic lineage of a taxon by name
get_lineage_by_id | Retrieve the full taxonomic lineage of a taxon
get_taxonomicon_id | Find the Taxonomicon ID for a taxon name
is_member | Test whether one taxon is nested within another
lineage_depth | Get the lineage depth of a taxon
load_cache | Load a previously saved taxodist cache from disk
mrca | Compute the most recent common ancestor of two taxa
plot.taxodist_cluster | Plot method for taxodist_cluster objects
plot.taxodist_ord | Plot method for taxodist_ord objects
print.taxodist_focal | Print method for taxodist_focal objects
print.taxodist_path | Print method for taxodist_path objects
print.taxodist_result | Print method for taxodist distance results
save_cache | Save the taxodist lineage cache to disk
shared_clades | List all clades shared between two taxa
summary.taxodist_ord | Summary method for taxodist_ord objects
taxobase | Reference Taxonomic Dataset (taxobase)
taxodist | taxodist: Taxonomic Distance and Phylogenetic Lineage Computation
taxo_cluster | Cluster taxa by taxonomic distance
taxo_distance | Compute the phylogenetic distance between two taxa
taxo_heatmap | Plot a taxonomic heatmap
taxo_ordinate | Ordinate taxa in taxonomic distance space
taxo_path | Get the taxonomic path between two taxa
taxo_search | Search The Taxonomicon for a taxon name