Epidemiology Python Packages

epiweeks

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

156K 20 6

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.

30K 111 24

pyseqtarget

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

2K 2 1

covasim

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

2K 289 239

zepid

Epidemiology analysis package

2K 155 33

epymorph

EpiMoRPH spatial disease modeling

2K 9 3

emod-malaria

Source files for building the IDM EMOD disease transmission model.

2K 106 53

emod-hiv

Source files for building the IDM EMOD disease transmission model.

2K 106 53

metawards

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

2K 14 6

covsirphy

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

2K 112 44

emod-common

Source files for building the IDM EMOD disease transmission model.

1K 106 53

pysofra

Python equivalent of R's gtsummary and tableone — publication-ready Table 1, regression, and survival tables with survey weights and multiple imputation

1K 1 0

bio-epidemiology-ner

Recognize bio-medical entities from a text corpus

1K 133 9

epispot-nightly

A tool for modeling infectious diseases.

1K 18 6

episia

Python toolkit for epidemiological modelling and reporting. SIR/SEIR/SEIRD compartmental models, sensitivity analysis, interactive visualisations, and automated HTML/Markdown/JSON reports, built for low-resource health contexts.

911 6 1

opqua

Epidemiological modeling framework for pathogen population genetics and evolution.

820 19 7

seirsplus

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

803 678 220

vahtian-epinet

Transparent network/feature-space toolkit for graph-shaped data: honest evaluation (calibration, permutation nulls, model cards), closed-form contestability, and federated governed aggregates. Research demonstrator, not clinical decision support.

734 1 0