Released projects and packages

These projects are in a usable form. Packages have been developed following RECON’s standards, are fully functional, documented and tested, and have been released on CRAN.

distcrete

Discretized probability distributions.

epicontacts

Handling, visualisation and analysis of epidemiological contacts.

epitrix

Small helpers and tricks for epidemics analysis

incidence

Computation, handling, visualisation and simple modelling of incidence.

outbreaker2

Modular framework for outbreak reconstruction.

outbreaks

Collection of outbreak data.

RECON learn

Open training platform for epidemics analysis


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.

deployer

Portable environment for epidemics analysis

dibbler

Investigation of food-borne disease outbreaks.

docker

Docker images for RECON packages

earlyR

Estimation of infectiousness in the early stage of an outbreak

epicontacts.ui

Graphical user interface for epicontacts

epiflows

Visualisation and analysis of passenger flows

epimaps

Helpers and wrappers for mapping diseases

epimatch

Finding matching patient records across tabular data sets.

gisfirstaid

Tutorials and code gists for mapping infectious diseases

incidence.ui

Graphical user interface for incidence

nomad

Pack up R to take away

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.

EpiModel

Mathematical Modeling of Infectious Disease Dynamics