people
Defines the People class and functions associated with making people and handling the transitions between states (e.g., from susceptible to infected).
Classes
| Name | Description |
|---|---|
| People | A class to perform all the operations on the people – usually not invoked directly. |
People
people.People(pars, strict=True, pop_trend=None, pop_age_trend=None, **kwargs)A class to perform all the operations on the people – usually not invoked directly.
This class is usually created automatically by the sim. The only required input argument is the population size, but typically the full parameters dictionary will get passed instead since it will be needed before the People object is initialized. However, ages, contacts, etc. will need to be created separately – see hpv.make_people() instead.
Note that this class handles the mechanics of updating the actual people, while hpv.BasePeople takes care of housekeeping (saving, loading, exporting, etc.). Please see the BasePeople class for additional methods.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| pars | dict | the sim parameters, e.g. sim.pars – alternatively, if a number, interpreted as n_agents | required |
| strict | bool | whether or not to only create keys that are already in self.meta.person; otherwise, let any key be set | True |
| pop_trend | dataframe |
a dataframe of years and population sizes, if available | None |
| kwargs | dict | the actual data, e.g. from a popdict, being specified | {} |
Examples::
ppl1 = hpv.People(2000)
sim = hpv.Sim()
ppl2 = hpv.People(sim.pars)Methods
| Name | Description |
|---|---|
| add_births | Add more people to the population |
| apply_death_rates | Apply death rates to remove people from the population |
| check_cancer | Check for new progressions to cancer |
| check_cancer_deaths | Check for new deaths from cancer |
| check_cin | Check for new progressions to CIN |
| check_clearance | Check for HPV clearance. |
| check_inds | Return indices for which the current state is false and which meet the date criterion |
| check_inds_true | Return indices for which the current state is true and which meet the date criterion |
| check_migration | Check if people need to immigrate/emigrate in order to make the population |
| check_progress | Wrapper function for all the new progression checks |
| create_partnerships | Create partnerships. All the hard work of creating the contacts is done by hppop.make_contacts, |
| dissolve_partnerships | Dissolve partnerships |
| increment_age | Let people age by one timestep |
| infect | Infect people and determine their eventual outcomes. |
| init_flows | Initialize flows to be zero |
| initialize | Perform initializations |
| make_naive | Make a set of people naive. This is used during dynamic resampling. |
| plot | Plot statistics of the population – age distribution, numbers of contacts, |
| remove_people | Remove people - used for death and migration |
| scale_flows | Return the scaled versions of the flows – replacement for len(inds) |
| set_prognoses | Assigns prognoses for all infected women on day of infection. |
| set_severity | Set severity levels for individual women |
| story | Print out a short history of events in the life of the specified individual. |
| update_states_post | State updates at the end of the current timestep |
| update_states_pre | Perform all state updates at the current timestep |
add_births
people.People.add_births(
year=None,
new_births=None,
ages=0,
immunity=None,
sex_ratio=0.5,
hiv_prevalence=None,
)Add more people to the population
Specify either the year from which to retrieve the birth rate, or the absolute number of new people to add. Must specify one or the other. People are added in-place to the current People instance.
apply_death_rates
people.People.apply_death_rates(year=None)Apply death rates to remove people from the population NB people are not actually removed to avoid issues with indices
check_cancer
people.People.check_cancer(genotype)Check for new progressions to cancer
check_cancer_deaths
people.People.check_cancer_deaths()Check for new deaths from cancer
check_cin
people.People.check_cin(genotype)Check for new progressions to CIN
check_clearance
people.People.check_clearance(genotype)Check for HPV clearance.
check_inds
people.People.check_inds(current, date, filter_inds=None)Return indices for which the current state is false and which meet the date criterion
check_inds_true
people.People.check_inds_true(current, date, filter_inds=None)Return indices for which the current state is true and which meet the date criterion
check_migration
people.People.check_migration(year=None)Check if people need to immigrate/emigrate in order to make the population size correct.
check_progress
people.People.check_progress(what, genotype)Wrapper function for all the new progression checks
create_partnerships
people.People.create_partnerships(
tind,
mixing,
layer_probs,
f_cross_layer,
m_cross_layer,
dur_pship,
acts,
age_act_pars,
)Create partnerships. All the hard work of creating the contacts is done by hppop.make_contacts, which in turn relies on hpu.create_edgelist for creating the edgelist. This method is just a light wrapper that passes in the arguments in the right format and the updates relationship info stored in the People class.
dissolve_partnerships
people.People.dissolve_partnerships(t=None)Dissolve partnerships
increment_age
people.People.increment_age()Let people age by one timestep
infect
people.People.infect(inds, g=None, layer=None)Infect people and determine their eventual outcomes. Method also deduplicates input arrays in case one agent is infected many times and stores who infected whom in infection_log list.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| inds | array | array of people to infect | required |
| g | int | int of genotype to infect people with | None |
| layer | str | contact layer this infection was transmitted on | None |
Returns
| Name | Type | Description |
|---|---|---|
| count | int | number of people infected |
init_flows
people.People.init_flows()Initialize flows to be zero
initialize
people.People.initialize(sim_pars=None)Perform initializations
make_naive
people.People.make_naive(inds)Make a set of people naive. This is used during dynamic resampling.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| inds | array | list of people to make naive | required |
plot
people.People.plot(*args, **kwargs)Plot statistics of the population – age distribution, numbers of contacts, and overall weight of contacts (number of contacts multiplied by beta per layer).
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| bins (arr) | age bins to use (default, 0-100 in one-year bins) | required | |
| width (float) | bar width | required | |
| font_size (float) | size of font | required | |
| alpha (float) | transparency of the plots | required | |
| fig_args (dict) | passed to pl.figure() | required | |
| axis_args (dict) | passed to pl.subplots_adjust() | required | |
| plot_args (dict) | passed to pl.plot() | required | |
| do_show (bool) | whether to show the plot | required | |
| fig (fig) | handle of existing figure to plot into | required |
remove_people
people.People.remove_people(inds, cause=None)Remove people - used for death and migration
scale_flows
people.People.scale_flows(inds)Return the scaled versions of the flows – replacement for len(inds) followed by scale factor multiplication
set_prognoses
people.People.set_prognoses(inds, g, gpars, dt)Assigns prognoses for all infected women on day of infection.
set_severity
people.People.set_severity(inds, g, gpars, dt, set_sev=True)Set severity levels for individual women Args: inds: indices of women to set severity for g: genotype index dt: timestep set_sev: whether or not to set initial severity
story
people.People.story(uid, *args)Print out a short history of events in the life of the specified individual.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| uid | int / list | the person or people whose story is being regaled | required |
| args | list | these people will tell their stories too | () |
Example::
sim = hpv.Sim(pop_type='hybrid', verbose=0)
sim.run()
sim.people.story(12)
sim.people.story(795)update_states_post
people.People.update_states_post(t, year=None)State updates at the end of the current timestep
update_states_pre
people.People.update_states_pre(t, year=None)Perform all state updates at the current timestep