synthpops.pop module¶
This module provides the layer for communicating with the agent-based model Covasim.
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class
synthpops.pop.
Pop
(n=None, max_contacts=None, ltcf_pars=None, school_pars=None, with_industry_code=False, with_facilities=False, use_default=False, use_two_group_reduction=True, average_LTCF_degree=20, ltcf_staff_age_min=20, ltcf_staff_age_max=60, with_school_types=False, school_mixing_type='random', average_class_size=20, inter_grade_mixing=0.1, average_student_teacher_ratio=20, average_teacher_teacher_degree=3, teacher_age_min=25, teacher_age_max=75, with_non_teaching_staff=False, average_student_all_staff_ratio=15, average_additional_staff_degree=20, staff_age_min=20, staff_age_max=75, rand_seed=None, country_location=None, state_location=None, location=None, sheet_name=None, household_method='infer_ages', smooth_ages=False, window_length=7, do_make=True)¶ Bases:
sciris.sc_utils.prettyobj
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generate
(verbose=False)¶ Actually generate the network.
- Parameters
verbose (bool) – If True, print statements about the population and networks as they’re being generated.
- Returns
A dictionary of the full population with ages, connections, and other attributes.
- Return type
network (dict)
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to_dict
()¶ Export to a dictionary – official way to get the popdict.
Example:
popdict = pop.to_dict()
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to_json
(filename, indent=2, **kwargs)¶ Export to a JSON file.
Example:
pop.to_json('my-pop.json')
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save
(filename, **kwargs)¶ Save population to an binary, gzipped object file.
Example:
pop.save('my-pop.pop')
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static
load
(filename, *args, **kwargs)¶ Load from disk from a gzipped pickle.
- Parameters
filename (str) – the name or path of the file to load from
kwargs – passed to sc.loadobj()
Example:
pop = sp.Pop.load('my-pop.pop')
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count_pop_ages
()¶ Create an age count of the generated population.
- Returns
Dictionary of the age count of the generated population.
- Return type
dict
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get_enrollment_by_school_type
(*args, **kwargs)¶ Get enrollment sizes by school types in popdict.
- Returns
List of generated enrollment sizes by school type.
- Return type
list
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plot_people
(*args, **kwargs)¶ Placeholder example of plotting the people in a population.
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plot_contacts
(*args, **kwargs)¶ Plot matrices of the contacts for a given layer or layers.
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plot_ages
(*args, **kwargs)¶ Plot a comparison of the expected and generated age distribution.
Example:
pars = {'n': 10e3, location='seattle_metro', state_location='Washington', country_location='usa'} pop = sp.Pop(**pars) fig, ax = pop.plot_ages()
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plot_enrollment_rates_by_age_comparison
(*args, **kwargs)¶ Plot a comparison of the expected and generated enrollment rates by age.
Example:
pars = {'n': 10e3, location='seattle_metro', state_location='Washington', country_location='usa'} pop = sp.Pop(**pars) fig, ax = pop.plot_age_distribution_comparison()
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plot_school_sizes
(*args, **kwargs)¶ Plot a comparison of the expected and generated school size distributions by school type.
Example:
pars = {'n': 10e3, location='seattle_metro', state_location='Washington', country_location='usa'} pop = sp.Pop(**pars) fig, ax = pop.plot_school_sizes()
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synthpops.pop.
make_population
(*args, **kwargs)¶ Interface to sp.Pop().to_dict(). Included for backwards compatibility.
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synthpops.pop.
generate_synthetic_population
(*args, **kwargs)¶ For backwards compatibility only.