hiv

Defines classes and methods for HIV natural history

Classes

Name	Description
HIVsim	A class based around performing operations on a self.pars dict.

hiv.HIVsim(sim, art_datafile, hiv_datafile, hiv_pars)

A class based around performing operations on a self.pars dict.

Name	Description
check_hiv_death	Check for new deaths from HIV
finalize	Compute prevalence, incidence.
get_hiv_data	Load HIV incidence and art coverage data, if provided
init_states	Add HIV-related states to the people states
load_data	Load any data files that are used to create additional parameters, if provided
new_hiv_infections	Apply HIV infection rates to population
set_hiv_prognoses	Set HIV outcomes
step	Wrapper method that checks for new HIV infections, updates prognoses, etc.
update_cd4	Update CD4 counts
update_hiv_results	Update the HIV results
update_hpv_progs	Update people’s relative susceptibility, severity, and immunity

hiv.HIVsim.check_hiv_death(people)

Check for new deaths from HIV

hiv.HIVsim.finalize(sim)

Compute prevalence, incidence.

hiv.HIVsim.get_hiv_data(hiv_datafile=None, art_datafile=None, add_lower=False)

Load HIV incidence and art coverage data, if provided

Name	Type	Description	Default
location	str	must be provided if you want to run with HIV dynamics	required
hiv_datafile	str	must be provided if you want to run with HIV dynamics	`None`
art_datafile	str	must be provided if you want to run with HIV dynamics	`None`
verbose	bool	whether to print progress	required

Name	Type	Description
hiv_inc	dict	dictionary keyed by sex, storing arrays of HIV incidence over time by age
art_cov	dict	dictionary keyed by sex, storing arrays of ART coverage over time by age

hiv.HIVsim.init_states(people)

Add HIV-related states to the people states

hiv.HIVsim.load_data(hiv_datafile=None, art_datafile=None)

Load any data files that are used to create additional parameters, if provided

hiv.HIVsim.new_hiv_infections(people, year=None)

Apply HIV infection rates to population

hiv.HIVsim.set_hiv_prognoses(people, inds)

Set HIV outcomes

hiv.HIVsim.step(people=None, year=None)

Wrapper method that checks for new HIV infections, updates prognoses, etc.

hiv.HIVsim.update_cd4(people)

Update CD4 counts

hiv.HIVsim.update_hiv_results(people, hiv_inds)

Update the HIV results

hiv.HIVsim.update_hpv_progs(people)

Update people’s relative susceptibility, severity, and immunity