emodpy_hiv.demographics.HIVDemographics module

This module contains the classes and functions for creating demographics files for HIV simulations. For more information on EMOD demographics files, see Demographics file.

class emodpy_hiv.demographics.HIVDemographics.HIVDemographics(nodes, idref='Gridded world grump2.5arcmin', base_file=None)

Bases: emod_api.demographics.Demographics.Demographics

This class is derived from emod_api.demographics.Demographics.Demographics and sets certain defaults for HIV in construction.

Parameters

  • nodes – The number of nodes to create.

  • idref – Method describing how the latitude and longitude values are created for each of the nodes in a simulation. “Gridded world” values use a grid overlaid across the globe at some arcsec resolution. You may also generate the grid using another tool or coordinate system. For more information, see Metadata.

  • base_file – A basic demographics file used as a starting point for creating more complicated demographics files. For example, using a single node file to create a multi-node file for spatial simulations.

  • init_prev – The initial HIV prevalence of the population.

Returns

None

fertility(path_to_csv)

Set fertility based on data. Simulation shall concist of individual pregnancies with rates by woman’s age and year-of-simulation using data from provided csv.

mortality(file_male, file_female, interval_fit=[1970, 1980], which_point='mid', predict_horizon=2050, csv_out=False, n=0, results_scale_factor=0.0027397260273972603)

Calculate and set the expected natural mortality by age, sex, and year from data, predicting what it would have been without HIV.

apply_assortivity(category, rowmale_colfemale_matrix)

Add an assortivity matrix to Pair-Forming Algo. Right now only applies to RISK IP.

Parameters

  • category – “COMMERCIAL”, “INFORMAL”, “MARITAL”, or “TRANSITORY”

  • rowmale_colfemale_matrix – 3x3 matrix of assortivity values, row represents male, column represents female.

Returns

N/A.

emodpy_hiv.demographics.HIVDemographics.from_template_node(lat=0, lon=0, pop=1000000.0, name=1, forced_id=1)

Create a single-node HIVDemographics instance from the parameters you supply.

Parameters

  • lat – Latitude of the centroid of the node to create.

  • lon – Longitude of the centroid of the node to create.

  • pop – Human population of the node.

  • name – The name of the node. This may be a characteristic of the node, such as “rural” or “urban”, or an identifying integer.

  • forced_id – The node ID for the single node.

Returns

A HIVDemographics instance.

emodpy_hiv.demographics.HIVDemographics.from_pop_csv(pop_filename_in, pop_filename_out='spatial_gridded_pop_dir', site='No_Site')

Create a multi-node HIVDemographics instance from a CSV file describing a population.

Parameters

  • pop_filename_in – The path to the demographics file to ingest.

  • pop_filename_out – The path to the file to output.

  • site – A string to identify the country, village, or trial site.

Returns

A HIVDemographics instance.

emodpy_hiv.demographics.HIVDemographics.from_params(tot_pop=1000000.0, num_nodes=100, frac_rural=0.3, id_ref='from_params')

Create a multi-node HIVDemographics instance as a synthetic population based on a few parameters.

Parameters

  • tot_pop – The total human population in the node.

  • num_nodes – The number of nodes to create.

  • frac_rural – The fraction of the population that is rural.

  • id_ref – Method describing how the latitude and longitude values are created for each of the nodes in a simulation. “Gridded world” values use a grid overlaid across the globe at some arcsec resolution. You may also generate the grid using another tool or coordinate system. For more information, see Metadata.

Returns

A HIVDemographics instance.