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Create resistance mutations module#219

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pineapple-cat wants to merge 37 commits intodevelopmentUCL/hivpy:developmentfrom resistance-mutationsUCL/hivpy:resistance-mutationsCopy head branch name to clipboard

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Commits

Commits on Dec 6, 2024

• Started resistance mutations module and moved some variable inits from HIV status.

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• Updated viral load column to store past timestep and changed multi-timestep column naming to avoid issues with previous code.

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Commits on Dec 17, 2024

• Added new mutation probability multiplier matrix and some new revelant columns.

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• Merge branch 'development' into resistance-mutations

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• Style unification.

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• Fixing tests via further style update.

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Commits on Dec 20, 2024

• Added new mutation probability calculation.

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Commits on Jan 9, 2025

• Added CD4 delta multiplier matrix.

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• Updated new mutation matrix format to fit with CD4 delta matrix.

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• Added matrix value retrieval function.

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• Added more ART drug columns.

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• Added CD4 delta calculation.

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Commits on Jan 10, 2025

• Added base viral load matrix.

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• Updated matrix lookup.

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• Added viral load and viral load delta calculation.

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• Reorganising file.

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Commits on Jan 13, 2025

• Added more HIV columns for viral load and CD4 changes.

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• Added viral load update function.

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• Updated viral load range.

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• Added CD4 update function.

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• Restricted new mutation probability to not exceed 100%.

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Commits on Jan 16, 2025

• Added new mutation risk multiplier.

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• Simplified conditions in CD4 calculation for finding people on ARVs.

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• Removed unused viral load delta column.

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• Added column for continuous time on ARVs.

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Commits on Jan 17, 2025

• Updated viral load matrix values.

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• Added all antiretroviral drug columns.

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• Updated resistance mutation columns with more unified names.

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• Moved ART columns to one place and rehomed resistance mutation count.

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Commits on Jan 20, 2025

• Added resistance init to population and update to evolution.

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• Fixing variables with previous timestep columns.

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• Debugging fixes.

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• Added matrix retrieval test.

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• Added tests for viral load and new mutation probability calculations.

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• Added CD4 calculation test.

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• Style fixes.

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Commits on Jan 21, 2025

• Adjusted CD4 calculation ordering to make sense.

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