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Port PMD error model from BEAST1 #22

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kche309 opened this issue Mar 1, 2022 · 3 comments
Open

Port PMD error model from BEAST1 #22

kche309 opened this issue Mar 1, 2022 · 3 comments
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enhancement New feature or request

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@kche309
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kche309 commented Mar 1, 2022 •
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Port DNA damage model from BEAST1

See related Git Issue from the Beast2 repo
CompEvol/beast2#173

Preliminary version to be implemented in April.
@kche309 kche309 added the enhancement New feature or request label Mar 1, 2022
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kche309 commented Jul 14, 2022 •
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Work in progress on branch https://github.com/bioDS/beast-phylonco/tree/PMDErrorModel

TODOs:

  • refactor ErrorModel superclass to take branching time t
  • In Likelihood class, pass branch time into error models methods
  • Unit testing
  • Example XML template for PMD error model

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kche309 commented Jul 16, 2022

Refactored error model class to take in branch time t 9c058c4
Added a taxa exclusion list, which means the excluded taxa are assumed to be error-free 9c058c4

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kche309 commented Jul 16, 2022

Unit testing is underway

@ddkapan ddkapan mentioned this issue Oct 26, 2022
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