Using the Open Tree of Life for your Research -- with R!: Glossary

Key Points

Package version	Package version is key for science reproducibility, and you can document it using the function packageVersion().
Finding your taxa in the Open Tree of Life Taxonomy	Open Tree of Life Taxonomy ids, or OTT ids are unique numeric identifiers for individual taxa that the Open Tree of Life project uses to handle taxonomy. You can go from a scientific name to an OTT id using TNRS matching. You can not go from a common name to OTT id using the Open Tree of Life tools.
Getting a piece of the Synthetic Open Tree of Life	OTT ids and node ids allow us to interact with the synthetic OpenTree. Portions of the synthetic OpenTree can be extracted from a single OTT id or from a bunch of OTT ids It is not possible to get a subtree from an OTT id that is not in the synthetic tree.
Dealing with "broken" and "invalid" taxa	It is not possible to get a subtre from an OTT id that is not in the synthetic tree. OTT ids and node ids allow us to interact with the synthetic OpenTree.
Getting an induced subtree of all taxa within a taxonomic rank	It is possible to get all types of subsets from the synthetic tree, as long as you can get the OTT ids!
Getting studies and trees supporting relationships in a synthetic subtree	Supporting trees usually contain more taxa than the ones we are interested in.
Getting branch length information (proportional to time) for you taxa	datelife stores all chronograms from the Open Tree of Life phylesystem. chronograms are stored in the `opentree_chronograms` object. source chronograms are retrieved at the species level only (for now).
Summarizing branch length information	Source chronograms have a wide range of variation in age estimates.

Glossary

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