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Create resistance mutations module #219

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Create resistance mutations module #219

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pineapple-cat
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Addresses #211.

@pineapple-cat pineapple-cat linked an issue Dec 17, 2024 that may be closed by this pull request
Implement HIV progression on ART #211
Open
@pineapple-cat
Fixing tests via further style update.
36eb9d4
@pineapple-cat
Added new mutation probability calculation.
c695e3d
@pineapple-cat
Added CD4 delta multiplier matrix.
fbfb2da
@pineapple-cat
Updated new mutation matrix format to fit with CD4 delta matrix.
d4afed0
@pineapple-cat
Added matrix value retrieval function.
b45b3f4
@pineapple-cat
Added more ART drug columns.
53a56a9
@pineapple-cat
Added CD4 delta calculation.
b4ac9b8
@pineapple-cat
Added base viral load matrix.
be0ce52
@pineapple-cat
Updated matrix lookup.
b1d8d0c
@pineapple-cat
Added viral load and viral load delta calculation.
3cdb220
@pineapple-cat
Reorganising file.
a29ff28
@pineapple-cat
Added more HIV columns for viral load and CD4 changes.
3791957
@pineapple-cat
Added viral load update function.
6259831
@pineapple-cat
Updated viral load range.
833643e
@pineapple-cat
Added CD4 update function.
698a565
@pineapple-cat
Restricted new mutation probability to not exceed 100%.
78c40b2
@pineapple-cat
Added new mutation risk multiplier.
099939d
@pineapple-cat
Simplified conditions in CD4 calculation for finding people on ARVs.
385ea36
@pineapple-cat
Removed unused viral load delta column.
ca78dd6
@pineapple-cat
Added column for continuous time on ARVs.
ddc29ff
@pineapple-cat
Updated viral load matrix values.
7fd1393
@pineapple-cat
Added all antiretroviral drug columns.
46e6ee5
@pineapple-cat
Updated resistance mutation columns with more unified names.
37fce51
@pineapple-cat
Moved ART columns to one place and rehomed resistance mutation count.
bf3f5fe
@pineapple-cat pineapple-cat marked this pull request as ready for review January 20, 2025 18:41
pineapple-cat
pineapple-cat commented Jan 24, 2025
View reviewed changes
src/hivpy/resistance_mutations.py

def get_viral_load_matrix(self, max_viral_load):
# viral_load_matrix[active_drugs][cont_on_art][adherence]
# FIXME: is there a better way to do this?
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This is ridiculously inefficient for population sizes of 100k+, but even switching to a static matrix containing a, b, and c values for a a * max_viral_load + b + c * min_vl_on_art calculation isn't much better because the main problem appears to be that a separate calculation is happening for every person in the population.

I think it looks like the vl calculation will have to be separated into more transform_group-able chunks to improve performance.

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@mmcleod89 mmcleod89 Awaiting requested review from mmcleod89

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Implement HIV progression on ART
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@pineapple-cat