health_data.py

The health_data object stores and manipulates built-in health data (population and incidence rates) from BenMAP. It inputs a dictionary of filepaths and two Boolean run options (verbose and race_stratified) to return dataframes of population, incidence, and combined population-incidence information (pop_inc).

Inputs

• pop_alloc: a geodataframe of population allocated to the ISRM grid geometry
• incidence_fp: a string containing the file path to the background incidence dataset
• verbose: a Boolean indicating whether or not detailed logging statements should be printed
• race_stratified: a Boolean indicating whether race-stratified incidence rates should be used
• debug_mode: a Boolean indicating whether or not to output debug statements

Calculated Attributes

• population: a geodataframe containing the population allocated to the ISRM grid geometry
• incidence: a geodataframe containing the raw incidence data from BenMAP
• pop_inc: a geodataframe containing the combined population and incidence data based on the requested geographies

Internal Functions

• load_data: reads in the population and incidence data from feather files
• update_pop: updates the population dataset by melting (unpivot) and renaming columns
• update_inc: updates the incidence dataset by pivoting columns around endpoints and renaming columns
• get_incidence_lookup: creates a small incidence lookup table based on the name and age ranges
• get_incidence_pop: helper function that returns the incidence for a given name, race, age range, and endpoint
• make_incidence_lookup: creates a lookup dictionary using the get_incidence_pop function for each endpoint
• incidence_by_age: creates a smaller incidence table for merging by calling get_incidence_lookup for each endpoint
• combine_pop_inc: creates the pop_inc dataframe by doing a spatial merge on the population and incidence data and then using lookup tables to determine the appropriate values