Data Wrangling and Automated Reports from 'SIVIGILA' source

R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parameters for infectious diseases

Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies

R package with tools for estimating vaccine effectiveness and vaccine related metrics

R package to estimate disease severity and under-reporting in real-time, accounting for reporting delays in epidemic time-series

R package for statistical and spatiotemporal modeling of epidemiological data for vector-borne diseases in Colombia

R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility

R package to clean and standardize epidemiological data

A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.

An R package for simulating line lists

[RETIRED. Use the epichains package instead]. Methods for simulating and analysing the sizes and lengths of chains from branching process models

R package for handling linelist data

An R package for importing epi data into R.

R-universe for the epiverse-trace GitHub organisation

[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates

Estimation of individual level variation in transmission

Tutorials to learn real-time analysis that includes accessing epidemiological delays, estimating transmission metrics, forecasting, and severity from aggregated incidence data, superspreading from line list and contact data, and simulating transmission chains.

Software development blueprints for epiverse-trace

Tutorials to learn reading, cleaning and validating case data, and converting line list data to incidence for visualizing epidemic curves.

Database of epidemiological parameters