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Reduce viral load testing for PLHIV on ART #1520

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merged 17 commits into from
Dec 17, 2024
Merged

Reduce viral load testing for PLHIV on ART #1520

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691110d
add new parameter to scale-up VMMC from 2019 onwards to match reporte…
tdm32 Aug 20, 2024
b11db90
Merge branch 'master' into tara_scaleupVMMC_from2019
tbhallett Sep 4, 2024
4904d5d
reduce viral load testing to occur every 2 years
tdm32 Nov 19, 2024
73878c9
remove mihpsa sheet in ResourceFile_HIV.xlsx
tdm32 Nov 19, 2024
6cc6eb0
Merge remote-tracking branch 'refs/remotes/origin/tara_scaleupVMMC_fr…
tdm32 Nov 19, 2024
1730145
merge in PR 1456 - increase VMMC after 2019
tdm32 Nov 19, 2024
bd1d845
merge in PR 1456 - increase VMMC after 2019
tdm32 Nov 19, 2024
a56ebef
address comments in PR #1456
tdm32 Nov 19, 2024
442222f
Merge branch 'master' into tara_reduce_VL_testing
tdm32 Dec 10, 2024
9706e0a
revert analysis script
tdm32 Dec 10, 2024
2714dcd
Merge branch 'master' into tara_reduce_VL_testing
tdm32 Dec 11, 2024
33eb5cd
Merge branch 'master' into tara_reduce_VL_testing
tbhallett Dec 13, 2024
ee868f5
Merge branch 'master' into tara_reduce_VL_testing
tdm32 Dec 16, 2024
99d6ba5
Merge branch 'refs/heads/master' into tara_reduce_VL_testing
tdm32 Dec 17, 2024
1e165d9
remove ResourceFile_HIV.xlsx and add new parameter into csv file
tdm32 Dec 17, 2024
3a9988a
remove references to ResourceFile_HIV.xlsx
tdm32 Dec 17, 2024
5b44480
add parameter increase_in_prob_circ_2019 to parameters.csv
tdm32 Dec 17, 2024
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4 changes: 2 additions & 2 deletions resources/ResourceFile_HIV/parameters.csv
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2 changes: 1 addition & 1 deletion src/scripts/hiv/projections_jan2023/calibration_script.py
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Expand Up @@ -69,7 +69,7 @@ def __init__(self):
self.runs_per_draw = runs_per_draw

self.sampled_parameters = pd.read_excel(
os.path.join(self.resources, "../../../../resources/ResourceFile_HIV.xlsx"),
os.path.join(self.resources, "../../../../resources/ResourceFile_HIV/parameters.csv"),
sheet_name="LHC_samples",
)

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2 changes: 1 addition & 1 deletion src/scripts/hiv/projections_jan2023/output_plots.py
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Expand Up @@ -90,7 +90,7 @@ def make_plot(model=None, data_mid=None, data_low=None, data_high=None, title_st
data_tb_ntp = data_tb_ntp.drop(columns=["year"])

# HIV resourcefile
xls = pd.ExcelFile(resourcefilepath / "ResourceFile_HIV.xlsx")
xls = pd.ExcelFile(resourcefilepath / "ResourceFile_HIV/parameters.csv")

# HIV UNAIDS data
data_hiv_unaids = pd.read_excel(xls, sheet_name="unaids_infections_art2021")
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