Taxonomic Distance and Phylogenetic Lineage Computation

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Documentation for package ‘taxodist’ version 0.2.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

taxodist-package	taxodist: Taxonomic Distance and Phylogenetic Lineage Computation
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
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_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
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