Updated schistosomiasis model #1587

tdm32 · 2025-02-12T12:57:39Z

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

…effects only

extract deaths per py

# Conflicts: # resources/ResourceFile_HIV.xlsx # resources/ResourceFile_TB.xlsx # src/tlo/methods/malaria.py # src/tlo/methods/tb.py

set up test runs

# Conflicts: # resources/ResourceFile_HIV.xlsx # src/tlo/methods/enhanced_lifestyle.py # src/tlo/methods/hiv.py

add new property susceptibility add susceptibility when initialising population

…or future MDA programs

…care seeking as no longer used

tdm32 · 2025-07-07T07:49:36Z

@tbhallett This is now ready for review again. Symptoms have been simplified, ReallySimplifiedBirths has been removed and some duplicative code has been restructured.

src/tlo/methods/demography.py

…s (so that log file always look the same)

tamuri

Some changes needed for idiomatic pandas.

src/tlo/methods/enhanced_lifestyle.py

src/tlo/methods/schisto.py

add in update_infection_symtpoms for initial population

Co-authored-by: Asif Tamuri <tamuri@gmail.com>

…chisto_for_PR

…toms

src/tlo/methods/demography.py

All resolved

tdm32 · 2025-07-09T15:36:57Z

@tamuri this is ready to go now I think

tamuri · 2025-07-11T08:27:56Z

src/tlo/methods/schisto.py

+        self.sim.modules['SymptomManager'].register_symptom(
+            Symptom(name='ss_sm_moderate'))
+
+        self.sim.modules['SymptomManager'].register_symptom(
+            Symptom(name='ss_sm_heavy'))
+
+        self.sim.modules['SymptomManager'].register_symptom(
+            Symptom(name='ss_sh_moderate'))
+
+        self.sim.modules['SymptomManager'].register_symptom(
+            Symptom(name='ss_sh_heavy'))


Is it right that these are symptoms - wouldn't the symptom be "itchiness" or something like that, and these be a property of the individual? (Not suggesting we change this at this stage)

We did have that originally, but each set of symptoms was linked with one schisto species and an intensity level, so it was cleaner to just assign a generic "symptom" corresponding to each set. Each symptom has a fixed probability of healthcare seeking, diagnosis and the same treatment and treatment success rates so there was no benefit really to having all the separate symptoms (bladder pathology, dysuria, ascites... etc).

tdm32 and others added 30 commits April 15, 2024 17:46

add dalys per person-years with plot

9c3a3d9

add dalys per person-years with plot

41c15c0

additional calculations of life expectancy and differences in deaths

c10163b

Merge branch 'master' into tara_feb2024_updates_clean

a1f0da9

add adjusted mortality rates for life expectancy modified for direct …

98e806c

…effects only

edit figures

50f0715

extract deaths per py

population pyramid

7117c6e

set up HS outputs

cb6a12a

Merge branch 'tara_feb2024_updates_clean' into tara_htm_impact_mar2024

ccb706c

# Conflicts: # resources/ResourceFile_HIV.xlsx # resources/ResourceFile_TB.xlsx # src/tlo/methods/malaria.py # src/tlo/methods/tb.py

merge in latest version with HTM updates

24aa740

set up test runs

test runs

c28879a

Merge branch 'master' into tara_htm_impact_mar2024

5821816

update resourcefiles

d85dad9

update script for full runs

786333c

json file for runs

442d0e6

add logging for WASH properties

435af82

Merge branch 'tara_htm_impact_mar2024' into tara_schisto_glide

6f053a0

# Conflicts: # resources/ResourceFile_HIV.xlsx # src/tlo/methods/enhanced_lifestyle.py # src/tlo/methods/hiv.py

merge in branch tara_htm_impact_mar2024 and resolve conflicts

cfb27e8

add logger for WASH

6ec1f59

add new parameters for revised schisto model

8476171

edit new parameters in resourcefile and schisto

e8b58ba

add new property susceptibility add susceptibility when initialising population

test runs, add proportion susceptible

b52ddae

add updated reservoir of infection for initial population

1ac282a

long runs to check endemic equilibium

c171305

save outputs

3d778c8

add equal_allocation_by_district

7cbd233

edit groupby argument

2262b23

test runs

184d067

switch off MDA and run

a194a8f

set up long runs for calibration

5cd1bff

tdm32 and others added 5 commits July 6, 2025 11:01

update improved_healthsystem_and_care_seeking to include parameters f…

008d586

…or future MDA programs

remove prob_lab_sent_to_test_children and adults from improved health…

bedecc0

…care seeking as no longer used

check param type=float in improved healthcare seeking sheet

d5718e0

Update schisto.py

80c1c67

Update schisto.py

b40aa8f

loc to is_alive

5d22ae4

tbhallett reviewed Jul 7, 2025

View reviewed changes

src/tlo/methods/demography.py Outdated Show resolved Hide resolved

tbhallett added 2 commits July 7, 2025 12:51

removing 'if' clauses for logging of district specific scaling factor…

3f3d15f

…s (so that log file always look the same)

roll back incidental changes

e09036a

tbhallett approved these changes Jul 7, 2025

View reviewed changes

tamuri previously requested changes Jul 7, 2025

View reviewed changes

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src/tlo/methods/schisto.py Outdated Show resolved Hide resolved

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tdm32 and others added 8 commits July 8, 2025 16:15

remove contact_rates series with value 1 for all entries

0d5ca94

add in update_infection_symtpoms for initial population

Update src/tlo/methods/enhanced_lifestyle.py

c26d713

Co-authored-by: Asif Tamuri <tamuri@gmail.com>

Merge remote-tracking branch 'origin/tara_schisto_for_PR' into tara_s…

0f03746

…chisto_for_PR

update the WASH logger in enhanced_lifestyle.py

a449f23

update update_infection_symptoms to clear only specified schisto symp…

d59b8c4

…toms

avoid division by 0 in logger

b2963bf

fix failing test

6e57e62

Merge branch 'master' into tara_schisto_for_PR

abcc191

tamuri reviewed Jul 9, 2025

View reviewed changes

src/tlo/methods/demography.py Outdated Show resolved Hide resolved

Update demography.py

f4e5445

tamuri self-requested a review July 9, 2025 13:29

tamuri added 2 commits July 11, 2025 09:20

Simplify

f1fcaf6

Slice index rather than dataframe

472b926

tamuri reviewed Jul 11, 2025

View reviewed changes

tamuri merged commit 9b8112d into master Jul 11, 2025
62 checks passed

tamuri deleted the tara_schisto_for_PR branch July 11, 2025 14:05

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Updated schistosomiasis model #1587

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tdm32 commented Feb 12, 2025

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Updated schistosomiasis model #1587

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