malaria hiv interactions #1101
malaria hiv interactions #1101
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# Conflicts: # resources/ResourceFile_HIV.xlsx # resources/ResourceFile_TB.xlsx
make test for linear model harder - set whole population to be at risk of clinical/severe malaria and allow iptp to have protective effect
make test for linear model harder - set whole population to be at risk of clinical/severe malaria and allow iptp to have protective effect
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Tests are failing on this one. Investigating.... ..... One problem is that ... pushing a quick fix for that, to see if that solves everything magically! |
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Wow. It did! |
Ah great thanks Tim. |
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@tbhallett I'm just working on this - in another branch - where I'm decoupling malaria from HIV and TB. Any conditions which are reliant on properties set by module Hiv now have checks, so you can run malaria with or without Hiv Update: This is now committed to this branch. |
Allow malaria to run without HIV (which also requires TB)
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Thanks. So this is ready for review and merging? |
Yes please |
| @@ -2534,13 +2541,15 @@ def do_at_initiation(self, person_id): | |||
| df = self.sim.population.props | |||
| person = df.loc[person_id] | |||
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| # Check if drugs are available, and provide drugs: | |||
| # Check if drugs are available, and provide drugs | |||
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It would be safer for this to be dict or named tuple so that we don't have to remember the special ordering.
Ie for example return
{"art": True, "contrim": False}
src/tlo/methods/malaria.py
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| ) | ||
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| # prevalence of malaria in HIV population | ||
| prev_malaria_in_hiv_population = coinfection_num / hiv_infected |
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Careful about division of values than could be 0. Use safety around this: eg
X if y > 0 else 0
src/tlo/methods/malaria.py
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| df[df.is_alive & (df.ma_inf_type != 'none')] | ||
| ) | ||
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| prop_malaria_cases_with_hiv = coinfection_num / malaria_infected |
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Same as above and elsewhere
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changed here and wherever appropriate
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@tbhallett the suggested changes have been made and this is ready for final review. Thanks very much! |
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Thanks @tdm32 --- there's a conflict on this branch now. (ResourceFile_malaria.xlsx ... so it's hard for me to work out which version to choose). Please could you resolve through merging-in |
add missing parameter to Malaria module
Hi @tbhallett, I've merged in master this morning. The conflict arose I think because the file location moved. The correct version is in this branch. |
This branch incorporates interactions between malaria and HIV.
Specific changes are:
Plots below are small population (2000) and show some stochastic noise but are within reasonable tolerance of reported data.