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ropensci / taxa

taxonomic classes for R
https://docs.ropensci.org/taxa
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Add function to add placeholder taxa to force ranks to occur at a specific level/depth #169

Open zachary-foster opened 6 years ago

zachary-foster commented 6 years ago

This idea was in response to a comment made by @hollybik when reviewing the F1000 taxa paper:

How does "taxa" deal with (or allow manipulation / correction of) taxonomic hierarchies with non-homologous taxonomic levels. For example, a set of input hierarchies where level 4 represents "Order" level in Fungi but "Subclass" level in protists. This is a very common scenario for metabarcoding datasets - ideally you want to introduce gaps/placeholders for hierarchies that do not contain a certain level, so that users can automatically or manually standardize their taxonomic levels all rows in a dataset (e.g. making Level 7 correspond to "Family" level across all taxa).

It would also be useful as an intermediate step when converting the taxonomy information in a taxmap or taxonomy object into a table with ranks as columns.