These packages have been developed following RECON’s standards, are fully functional, documented and tested, and have been released on CRAN.
Collection of outbreak data.
Handling, visualisation and analysis of epidemiological contacts.
Computation, handling, visualisation and simple modelling of incidence.
The RECON packages listed below are still in development. They may be functional already, but a stable version has yet to be released.
R Estimation from Cluster Sizes
Rationalised and reproducible data cleaning.
Investigation of food-borne disease outbreaks.
Discretized probability distributions.
Docker images for RECON packages
Estimation of infectiousness in the early stage of an outbreak
Graphical user interface for epicontacts
Finding matching patient records across tabular data sets.
Small utilitary functions for epidemiology
Graphical user interface for incidence
Inferring transmission chains by integrating epidemiological and genetic data.
Projections of future incidence
Template shiny GUI for RECON packages
Tools to develop RECON packages
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.
Quantifying transmissibility throughout an epidemic from incidence time series.
Basic analysis and visualisation of complex line-list data (to be replaced by incidence and epicontacts).
Implementation of a generic json format for case outbreak data.
R package implementing EpiJSON format.
Inferring transmission chains using temporal and genetic information.
Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
Dynamical Systems Approach to Infectious Disease Epidemiology - a Shiny/R based teaching tool.