synthetic-health-population

An algorithm to use publicly available health statistics in order to generate a synthetic health population of an area.

Settings

File config.ini contains setting for the application. Currently, a country to be used can be specified as well as population size to be produced

[generate]
# default country
country = NZ
# default size of population to produce
population_size = 5

Input

Input for the application consists of a number of files referring to the country/area.

In order to add a new area, two new sections need to be added to file config.ini, for example:
New Zealand requires section [NZ] with locations for demographics and deprivation input files as well as [NZ_modules] section with location of lifestyle and disease modules input files

[NZ]
# input filed for NZ
demographics = input/nz/demographic/nz_demographics.csv
deprivation = input/nz/demographic/nz_deprivation.csv

[NZ_modules]
# lifestyle modules for NZ
smoking = input/nz/lifestyle/smoking.csv
physical_activity = input/nz/lifestyle/physical_activity.csv
body_size = input/nz/lifestyle/body_size.csv
# disease modules for NZ
diabetes_1 = input/nz/disease/diabetes_1.csv
diabetes_2 = input/nz/disease/diabetes_2.csv
CVD = input/nz/disease/CVD.csv

Output

The applications saves the results to two csv files named patients.csv and timelines.csv located in the outputs folder.

Installation

git clone https://github.com/maciejtarsa/synthetic-health-population
cd synthetic-health-population
python3 -m venv env
source env/bin/activate
python3 -m pip install --editable .

Running

Move to the folder and run

cd synthetic-health-population
source env/bin/activate
generate_patients

Possible options for running

Specify number of patients

generate_patients -p 2

or

generate_patients --population 2

print detailed information about probabilities and transitions for each state

generate_patients --prob

print information about each patient

generate_patients --display