emodpy_malaria.demographics.MalariaDemographics module

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

class emodpy_malaria.demographics.MalariaDemographics.MalariaDemographics(nodes, idref='Gridded world grump2.5arcmin', base_file=None, init_prev=0.2, include_biting_heterogeneity=True)

Bases: emod_api.demographics.Demographics.Demographics

This class is derived from emod_api.demographics.Demographics.Demographics and sets certain defaults for malaria 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 malaria prevalence of the population.

Returns

None

set_risk_lowmedium()

Set initial risk for low-medium transmission settings per: https://wiki.idmod.org/display/MAL/Heterogeneous+biting+risk+in+simulations+vs+data.

set_risk_high()

Set initial risk for high transmission settings per: https://wiki.idmod.org/display/MAL/Heterogeneous+biting+risk+in+simulations+vs+data.

add_larval_habitat_multiplier(schema, hab_type, multiplier, species='ALL_SPECIES', node_id=0)

Add LarvalHabitatMultiplier to node(s).

Parameters

  • schema – Path to schema.json.

  • hab_type – Habitat type.

  • multiplier – Multiplier or Factor.

  • specices – Specific species (defaults to ALL).

  • node_id – Nodes for this LHM. Defaults to all.

Returns

Nothing.

emodpy_malaria.demographics.MalariaDemographics.from_template_node(lat=0, lon=0, pop=1000000.0, name=1, forced_id=1, init_prev=0.2, include_biting_heterogeneity=True)

Create a single-node MalariaDemographics 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.

  • init_prev – The initial malaria prevalence of the node.

Returns

A MalariaDemographics instance.

emodpy_malaria.demographics.MalariaDemographics.from_pop_csv(pop_filename_in, pop_filename_out='spatial_gridded_pop_dir', site='No_Site')

Create a multi-node MalariaDemographics 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 MalariaDemographics instance

emodpy_malaria.demographics.MalariaDemographics.from_csv(input_file, res=0.008333333333333333, id_ref='from_csv')

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

Parameters

  • input_file – The path to the csv file to ingest.

  • res – Resolution.

  • id_ref – A string to identify the file, needs to match other input files.

Returns

A MalariaDemographics instance

emodpy_malaria.demographics.MalariaDemographics.from_params(tot_pop=1000000.0, num_nodes=100, frac_rural=0.3, id_ref='from_params')

Create a multi-node MalariaDemographics 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 MalariaDemographics instance.