hpvsim.hiv module

Defines classes and methods for HIV natural history

class HIVsim(sim, art_datafile, hiv_datafile, hiv_pars)

Bases: ParsObj

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

Initialization

update_pars(old_pars=None, new_pars=None, create=True)

static init_states(people)

Add HIV-related states to the people states

init_results(sim)

set_hiv_prognoses(people, inds, year=None, incident=True)

Set HIV outcomes

check_hiv_death(people)

Check for new deaths from HIV

update_cd4(people)

Update CD4 counts

step(people=None, year=None)

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

new_hiv_infections(people, year=None)

Apply HIV infection rates to population

update_hpv_progs(people)

Update people’s relative susceptibility, severity, and immunity

update_hiv_results(people, hiv_inds)

Update the HIV results

get_hiv_data(hiv_datafile=None, art_datafile=None)

Load HIV incidence and art coverage data, if provided

Parameters:

• location (str) – must be provided if you want to run with HIV dynamics

• hiv_datafile (str) – must be provided if you want to run with HIV dynamics

• art_datafile (str) – must be provided if you want to run with HIV dynamics

• verbose (bool) – whether to print progress

Returns:

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

Return type:

hiv_inc (dict)

load_data(hiv_datafile=None, art_datafile=None)

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

finalize(sim)

Compute prevalence, incidence.