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taxo_distance(), mrca(),
distance_matrix(), closest_relative(),
compare_lineages(), shared_clades(),
is_member(), filter_clade(),
lineage_depth(), check_coverage(),
clear_cache()taxo_cluster(): hierarchical clustering of taxa by
taxonomic distance.taxo_ordinate(): ordination (PCoA) of taxa in taxonomic
distance space.save_cache(): serialises the session lineage cache to
an .rds file.load_cache(): restores a previously saved cache,
avoiding redundant network requests.taxo_path(): returns the full node-by-node path between
two taxa as a tidy data frame, ascending from taxon A to their MRCA and
descending to taxon B.Statistical Applications of taxodist) demonstrating the
integration of taxodist with ape (tree
plotting) and vegan (taxonomic distinctness, Mantel tests,
and PERMANOVA).vegan to Suggests in
DESCRIPTION.distance_matrix()
output with vegan functions (taxondive(),
mantel(), adonis2()).taxo_cluster() results
into phylo objects using ape::as.phylo().[crown]) being matched across different lineages as if
they were the same ancestor.Cohort,
Subcohort, Magnorder, Grandorder,
Parvorder, Legion) that were being retained as
bare rank names instead of the actual clade names (e.g.,
Placentalia, Boreoeutheria,
Galloanserae).These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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