This is a curated list of resourses for the R programming language on Epidemiology and Public Health. The aim is to provide a Task View-like list of resourses together with some installation script.

The list below include purpose-specific packages. However, some more general packages can be used to buld models for data analysis. Other interesting Task Views include Clinical Trials, Genetics, Medical Imaging, Meta-Analysis, Pharmacokinetics and Survival.

Epidemiology and Public Health

  • Epi includes functions for demographic and epidemiological analysis in the Lexis diagram

  • epibasix contains elementary tools for analysis of common epidemiological problems (sample size estimation, analysis of 2x2 tables, measures of agreement, etc.).

  • epiDisplay is a package for data exploration and results representation related to the
    epicalc package (off-CRAN now).

  • epiR implements a wide range of methods for the analysis of epidemiological data, including rate standardization, measures of association, analysis of contigency tables, risk estimates and many others.

  • epiReport includes a number of functions for the creation of epidemiological reports similar to the ECDC Annual Epidemiological Report (AER).

  • epitools is another package for the analysis oftwo-way and multi-way contingency tables.

  • pubh is a toolbox with a number of functions on general methods in epidemiology and public health methods, inclusing reporting of coefficients and confidence intervals for regression models.

Disease mapping

  • DCluster implements some methods for assessing spatial autocorrealtion in the relative risks and the detection of clusters of disease.

  • DClusterm implements model-based detection of disease clusters using GLMs, GLMMs and zero-inflated models.

  • sp provides a set of classes and methods for the analysis of spatial data that also includes plotting functions to create cloropeth maps.

  • surveillance includes methods for the modeling and monitoring time series of counts, proportions, categorical data and continuous-time point processes. This package implements many typical outbreak detection procedure.

Infectuous Diseases

  • DSAIDE includes functions to simulate different scenarios for infectious disease epidemiology using dynamical systems models.

  • EpiModel implements a number of mathematical models of infectious diseases dynamics. These models include deterministic compartmental models, stochastic agent-based models and stochastic network models.

  • shinySIR provides a number of interactive Shiny Apps for mathematical models of infectious disease spread.

Other resources

  • Epicalc book shows how to conduct an analysis of epidemiological data using R and Epicalc.

  • R Epidemics Consortium (RECON) is an international not-for-profit, non-governmental organisation gathering experts in data science, modelling methodology, public health, and software development to create the next generation of analytics tools for informing the response to disease outbreaks, health emergencies and humanitarian crises, using the R software and other free, open-source resources.