Epidemiology Python Packages

epiweeks

Epidemiological weeks calculation based on CDC (MMWR) and ISO week numbering systems

amr

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

covasim

COVID-19 Agent-based Simulator (Covasim): a model for exploring coronavirus dynamics and interventions

causalestimate

Lightweight causal inference from precomputed propensity scores and outcome predictions: IPW, AIPW, TMLE, matching, bootstrap CIs. Pandas-native.

zepid

Epidemiology analysis package

covsirphy

CovsirPhy: Python library for COVID-19 analysis with phase-dependent SIR-derived ODE models.

metawards

MetaWards disease metapopulation analysis and modelling software. Professional geographical SIR model with a flexible plugin architecture to support complex scenario modelling

ehrapy

Electronic Health Record Analysis with Python.

pyseqtarget

Estimation of the observational analogs of the intention-to-treat and per-protocol effects of hypothetical treatment strategies

epispot-nightly

A tool for modeling infectious diseases.

bio-epidemiology-ner

Recognize bio-medical entities from a text corpus

seirsplus

Models of SEIRS epidemic dynamics with extensions, including network-structured populations, testing, contact tracing, and social distancing.

epidemik

Compartmental Epidemic Models in Python

saudeemdado-mcp

Servidor MCP do Saúde em Dado — a saúde do Brasil (DataSUS + IBGE) consultável por IA

opqua

Epidemiological modeling framework for pathogen population genetics and evolution.

emod-malaria

Source files for building the IDM EMOD disease transmission model.

epitator

EpiTator annotates epidemiological information in text documents. It is the natural language processing framework that powers GRITS and EIDR Connect.

patchsim

PatchSim is a modular metapopulation simulation framework for multi-disease epidemiological modelling.

june

June is a framework for agent based modelling in an epidemiological and geographical context.

emod-common

Source files for building the IDM EMOD disease transmission model.

emod-hiv

Source files for building the IDM EMOD disease transmission model.

dii-calculator

A Python package for calculating the Dietary Inflammatory Index (DII) from nutrient intake data

epymorph

EpiMoRPH spatial disease modeling

pyvoa

Python Virus Open Analysis: unified access to open epidemiological databases, with a standardised data format and built-in visualisation.