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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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Simple Implementations of Freyja and Alcov models with unit tests #25

Open danerkestey opened 4 months ago

danerkestey commented 4 months ago

Implemented simple versions of Freyja and Alcov models with respective unit tests using example data. Freyja uses lasso regression and Alcov is a simple linear regression -- both without intercepts.

danerkestey commented 4 months ago

Recreating with R instead of Python.

DBecker7 commented 4 months ago

Great work!

To make this more user friendly, it would be nice to have either of the following changes:

  1. Modify the functions to have the same inputs and outputs as provoc_optim(), then implement a method = "freyja" and method = "alcov" argument to the main provoc function. This would mean all of the same plotting, printing, etc. functions will work with this output.
  2. Make the output objects of class provoc, with all of the attributes. Again, this means we can use all the same methods, rather than re-implementing a plotting function.