Released packages

These packages have been developed following RECON’s standards, are fully functional, documented and tested, and have been released on CRAN.

outbreaks

Collection of outbreak data.

epicontacts

Handling, visualisation and analysis of epidemiological contacts.

incidence

Computation, handling, visualisation and simple modelling of incidence.


Up-and-coming packages

The RECON packages listed below are still in development. They may be functional already, but a stable version has yet to be released.

branchr

R Estimation from Cluster Sizes

cleanr

Rationalised and reproducible data cleaning.

dibbler

Investigation of food-borne disease outbreaks.

distcrete

Discretized probability distributions.

docker

Docker images for RECON packages

earlyR

Estimation of infectiousness in the early stage of an outbreak

epicontacts.ui

Graphical user interface for epicontacts

epimatch

Finding matching patient records across tabular data sets.

epitrix

Small utilitary functions for epidemiology

incidence.ui

Graphical user interface for incidence

outbreaker2

Inferring transmission chains by integrating epidemiological and genetic data.

projections

Projections of future incidence

recon.ui

Template shiny GUI for RECON packages

recontools

Tools to develop RECON packages

vimes

Visualisation and Monitoring of Epidemics, including some outbreak detection algorithms.


The packages listed below mostly predate RECON, but have been authored by RECON members and are relevant for infectious disease epidemiology.

EpiEstim

Quantifying transmissibility throughout an epidemic from incidence time series.

OutbreakTools

Basic analysis and visualisation of complex line-list data (to be replaced by incidence and epicontacts).

EpiJSON

Implementation of a generic json format for case outbreak data.

repijson

R package implementing EpiJSON format.

outbreaker

Inferring transmission chains using temporal and genetic information.

surveillance

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

DSAIDE

Dynamical Systems Approach to Infectious Disease Epidemiology - a Shiny/R based teaching tool.