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Continuous PrEP usage #208

Merged
merged 23 commits into from
Nov 18, 2024
Merged

Continuous PrEP usage #208

merged 23 commits into from
Nov 18, 2024

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pineapple-cat
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@pineapple-cat pineapple-cat commented Nov 1, 2024 •
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Addresses #206.

@pineapple-cat pineapple-cat linked an issue Nov 1, 2024 that may be closed by this pull request
Re-starting, continuing, and switching PrEP #206
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pineapple-cat
pineapple-cat commented Nov 4, 2024
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src/hivpy/prep.py Outdated Show resolved Hide resolved
src/hivpy/prep.py Outdated Show resolved Hide resolved
@pineapple-cat
Minor fixes and updates, including new apply function for population …
0fbf6f5 
…dataframe.
@pineapple-cat
Undummied PrEP just started flags.
0d70a2a
@pineapple-cat
Added PrEP stop probabilities.
e10cd75
@pineapple-cat
Added PrEP continuation columns.
edb7c57
@pineapple-cat
Updated base PrEP start probability distribution to match SAS core.
596d3d6
@pineapple-cat
Removed some redundant sub-pop filtering for starting PrEP - HIV stat…
007190e 
…us is irrelevant as long as individuals are undiagnosed.
@pineapple-cat
Added continuing and switching PrEP.
b83fec5
@pineapple-cat
Fixed failing simulation tests.
5de9875
@pineapple-cat
Added PrEP stop date and updated starting and continuing PrEP date ou…
06999d4 
…tcomes.
@pineapple-cat
Updated starting PrEP test to check continuous and cumulative usage.
d0451a3
@pineapple-cat
Added continuous and cumulative use to starting PrEP after testing.
a92c098
@pineapple-cat
Added basic continuing PrEP unit test.
d894d3e
@pineapple-cat pineapple-cat marked this pull request as ready for review November 11, 2024 10:52
mmcleod89
mmcleod89 approved these changes Nov 18, 2024
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Looks good to me for now; we will need to update though to have the prep code not necessarily run for everyone every time step as previously discussed

@mmcleod89 mmcleod89 merged commit 2cda7ea into development Nov 18, 2024
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@pineapple-cat pineapple-cat deleted the prep-usage branch November 19, 2024 18:36
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@mmcleod89 mmcleod89 mmcleod89 approved these changes

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Re-starting, continuing, and switching PrEP
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@pineapple-cat @mmcleod89