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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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Remove "JAGS" models #1

Closed DBecker7 closed 7 months ago

DBecker7 commented 8 months ago

Ensure that nothing in provoc_jags is useful elsewhere, then delete.

There's no longer a need for the method = "jags" option in this package. The main provoc function can be purely the "optim" option.

JeremyFaria commented 8 months ago

Firstly, I will make a new branch for this issue. In that branch I will first ensure that none of the functions in provoc_jags are referenced anywhere else in the project. If a function is referenced I will take the appropiate measure in removing it, while maintaining that the function i'm removing it from still has the same functionality. I will commit every change I make to ensure I am making atomic commits. Once I ensured that nothin in provoc_jags is useful anywhere else I will delete the file.

Secondly I will check the files to change any functions with a method = jags option, by taking appropiate measures in removing that option for functions without changing the functionality of the function. This would include removing paths where JAGS and runjags are required.

Once all changes are committed I will merge the branch back to the main branch