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Updated schistosomiasis model #1587

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Updated schistosomiasis model #1587

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@tdm32 tdm32 commented Feb 12, 2025

This updated version of the schistosomiasis code has the following features:

  • all input data are updated (MDA coverage, infection burden)
  • many key parameters are updated
  • two diagnostic tests for different species, both have varying sensitivity and specificity based on individual worm burden
  • individuals now have a susceptibility property, which determines whether they are susceptible to schisto infection, this is calibrated to match infection prevalence
  • effects of WASH properties on schisto risk (proportion susceptible) now incorporated
  • updated logging includes person-years of infection by species and infection intensity (and district / age-group)
  • new test added
  • correct consumables dosage (by individual weight by age if treatment, by average weight of age-group if through MDA)
  • functionality to manipulate future MDA schedules as parameter inputs to module
  • background risk of infection dependent on deviation from baseline prevalence, when disease prevalence increases, background risk also increases reflecting higher likelihood of new infections (and reduces stochastic fadeout in small populations)
  • symptoms now linked with moderate/high worm burden and assigned probabilistically
  • links to bladder cancer and HIV included where relevant
  • can assign all individuals in simulation to one district through module keyword

tdm32 added 30 commits March 19, 2024 12:43
@tdm32
remove all scenario set-up code from tb.py
fb48774
@tdm32
remove all shorter tb regimens
fbbd113
@tdm32
test runs
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@tdm32
remove parameter rr_bcg_inf from tb.py
9901edd
@tdm32
test runs
7a7b2a9
@tdm32
move scenario update parameters to function within HIV module
e1fe062
@tdm32
test runs
30b127c
@tdm32
add in end-date for malaria logger for new cases to avoid counting th…
9297608 
…ose with scheduled symptoms in the future
@tdm32
update definition of ma_is_infected
fe5b7dc
@tdm32
update selection criteria for new asym infections to avoid over-writi…
34a0e23 
…ng scheduled clinical/severe infections
@tdm32
test runs
f6e06d0
@tdm32
clear malaria treatment once cured
e67ef03 
make sure treatment only has effect on current infection (date_treated after date_infection)
@tdm32
test runs
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@tdm32
test runs
3eb5b2a
@tdm32
test runs
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@tdm32
Merge branch 'master' into tara_feb2024_updates_clean
62e5c04 
# Conflicts:
#	src/tlo/methods/tb.py
@tdm32
edit comment in initialise_simulation
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@tdm32
test runs
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@tdm32
Merge branch 'tara_hiv_ncd_feb2024' into tara_feb2024_updates_clean
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# Conflicts:
#	resources/ResourceFile_HIV.xlsx
#	resources/ResourceFile_TB.xlsx
#	src/tlo/methods/hiv.py
#	src/tlo/methods/tb.py
@tdm32
fix parameter name error
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@tdm32
update parameters
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@tdm32
test runs
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@tdm32
test runs
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@tdm32
if scenario 2|5 modify tb function calculate_untreated_proportion to …
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…return 1. So TB treatment will have no effect on incidence
@tdm32
test runs
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@tdm32
set up full runs
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@tdm32
set up full runs
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@tdm32
edit and fix flake8 errors
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@tdm32
fix failing test
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@tdm32
update ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xlsx
8bba11c
@tdm32 tdm32 requested a review from tbhallett March 6, 2025 12:34
@tdm32 tdm32 assigned tamuri and unassigned tamuri Mar 6, 2025
@tdm32 tdm32 requested a review from tamuri March 6, 2025 12:35
@tdm32 tdm32 marked this pull request as ready for review March 6, 2025 12:35
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tdm32 commented Mar 6, 2025

@tbhallett @tamuri this is the revised schisto module. I'd appreciate a review of both the modelling, but also whether there are any efficiency gains to be had given this update frequently crashes during full model runs. I have tried to avoid making copies of the dataframe and switching individual level events to population events to reduce memory usage. Please do let me know if you have other ideas though. Thanks so much.

@tbhallett tbhallett added the epi label Apr 2, 2025
tdm32 and others added 2 commits May 29, 2025 10:04
@tdm32
Update schisto.py
92b79a7 
delay juvenile worms maturing for 2 months
update WASH effects on susceptibility 
update ordering of events
@tdm32
updates from working branch
0f5894f
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tdm32 commented May 29, 2025

@tbhallett @tamuri this is the revised schisto module. I'd appreciate a review of both the modelling, but also whether there are any efficiency gains to be had given this update frequently crashes during full model runs. I have tried to avoid making copies of the dataframe and switching individual level events to population events to reduce memory usage. Please do let me know if you have other ideas though. Thanks so much.

Just addressing this point- memory problems are no longer an issue following updates to methods here and to master.

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@tbhallett tbhallett Awaiting requested review from tbhallett

@tamuri tamuri Awaiting requested review from tamuri

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@tdm32 @tamuri @tbhallett