Updates to HTM Swtiching Method to Fix Issue #1411 #1413
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…ty as small population size over 7 days will not schedule VMMC through HIV module. Remove HIV_Prevention_Circumcision in assert statement for HIV services delivered in one week
…x with updated NTP2019 TB data
# Conflicts: # resources/malaria/ResourceFile_malaria.xlsx # src/tlo/methods/hiv.py # src/tlo/methods/malaria.py
# Conflicts: # resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xlsx # resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES.xlsx # src/tlo/methods/malaria.py # tests/test_malaria.py
# Conflicts: # resources/ResourceFile_HIV.xlsx # src/tlo/methods/hiv.py
…rdioMetabolicDisorders
…or hiv infection and add comments
…nd_horizontal_progs
…(HIV, TB, MALARIA)
…onths, increase to 1
| @@ -660,7 +660,7 @@ def update_all_properties(self, df): | |||
| :param df: The population dataframe """ | |||
| # get months since last poll | |||
| now = self.module.sim.date | |||
| months_since_last_poll = round((now - self.date_last_run) / np.timedelta64(1, "M")) | |||
| months_since_last_poll = round((now - self.date_last_run) / np.timedelta64(1, "m")) | |||
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rolled back. Coding for month is "M", which is what we want and what was there originally. ("m" is the the code for minutes".
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I don't know why but this causes errors on my machine! It won't run with "M"... I'll check out why this is happening when I'm back.
src/tlo/methods/hiv.py
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| # viral suppression rates | ||
| # adults already at 95% by 2020 | ||
| # change all column values | ||
| p["prob_start_art_or_vs"]["virally_suppressed_on_art"] = scaled_params["virally_suppressed_on_art"] | ||
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| # update exising linear models to use new scaled-up paramters | ||
| self.pre_initialise_population() |
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good logic. I think I'll factor it out into self.build_lms() (that is called from self.pre_initialise_population in case there are other things that need to go into self.pre_initialise_population that we don't want run at this point.
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I've refactored this
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Results from running analysis script show much the same results as found previously (per #1411)
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@tdm32 -- I've made some cleaning-up changes on here, and I think is ready to go in following your review. |
…al_progs_fixes3Jul
This fixes a problem with the implementation of the scale-up of HIV, TB and Malaria programs whereby the LinearModels were not rebuilt following parameter updates during the simulation. Now we rebuild the models after updating the model parameters.
We hoped that would fix #1411 but it doesn't quite do that (see below).
But, we do want it merged in anyway, as these are important fixes.