In ropenscilabs/taxa: Classes for Storing and Manipulating Taxonomic Data

Talk outline

Introduction (0.5 min)

Taxonomic information in the wild (1 min)

• sequence databases
• BLAST results
• Sepcies occurance databases
• museum records

The purpose of the taxa package (0.5 min)

The classes (3 min total)

The basic classes (1 min)

Taxonomy and Taxmap (2 min)

Taxon attributes (4.5 min total)

Ranks, names, and IDs (0.5 min)

• taxon_names, taxon_ranks, taxon_ids

Parts of the tree (3 min)

• branches, internodes, leaves, roots, stems, supertaxa, subtaxa

Numbers of supertaxa/subtaxa/data (1 min)

• n_supertaxa, n_subtaxa, n_obs, n_supertaxa_1, n_subtaxa_1, n_obs_1

Parsing (5 min total)

Vectors (1 min)

Tables (2 min)

Complex strings (2 min)

Manipulation (4 min total)

Subsetting the taxonomy (2 min)

Subsetting user data (1.5 min)

Adding user data (0.5 min)

Compatibility with other packages (3 min total)

Metacoder (2.5 min)

Taxize (0.5 min)

Conclusion

ropenscilabs/taxa documentation built on Feb. 23, 2024, 6:31 p.m.