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DASL-Lab / provoc

PROportions of Variants of Concern using counts, coverage, and a variant matrix.
https://dasl-lab.github.io/provoc/
MIT License
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Change astronomize to use built-in definitions. #3

Closed DBecker7 closed 8 months ago

DBecker7 commented 8 months ago

Currently, astronomimze() reads all of the data from the the constellations repo, allowing the user to keep the repo updated as they want (and, conversely, roll back to previous definitions that were relevant at the time of data collection).

However, this repo is no longer updated with the current omicron sub-lineages. Most of the definitions we're working with are unchanging. Built-in values are fine now, and this reduces the number of dependencies.

I believe the constellation_lists.rda file contains recent enough definitions. Change astronomize() to work with these by default, and a path to a clone of the constellations repo as an option.

Note that the function varmat_from_list() may be useful (it could also be programmed better).

DBecker7 commented 8 months ago

Fixed with commit 99d6d1b055edc858b4c692b67bdbb7cd36bdbdb7.