The R package surveillance implements statistical methods for the retrospective modeling and prospective monitoring of epidemic phenomena in temporal and spatio-temporal contexts. Focus is on (routinely collected) public health surveillance data, but the methods just as well apply to data from environmetrics, econometrics or the social sciences. As many of the monitoring methods rely on statistical process control methodology, the package is also relevant to quality control and reliability engineering.

Details

The package implements many typical outbreak detection procedures such as Stroup et al. (1989), Farrington et al. (1996), Rossi et al. (1999), Rogerson and Yamada (2001), a Bayesian approach (Höhle, 2007), negative binomial CUSUM methods (Höhle and Mazick, 2009), and a detector based on generalized likelihood ratios (Höhle and Paul, 2008), see wrap.algo. Also CUSUMs for the prospective change-point detection in binomial, beta-binomial and multinomial time series are covered based on generalized linear modeling, see categoricalCUSUM. This includes, e.g., paired comparison Bradley-Terry modeling described in Höhle (2010), or paired binary CUSUM (pairedbinCUSUM) described by Steiner et al. (1999). The package contains several real-world datasets, the ability to simulate outbreak data, visualize the results of the monitoring in temporal, spatial or spatio-temporal fashion. In dealing with time series data, the fundamental data structure of the package is the S4 class sts wrapping observations, monitoring results and date handling for multivariate time series. A recent overview of the available monitoring procedures is given by Salmon et al. (2016).

For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. The function hhh4 offers inference methods for the (multivariate) count time series models of Held et al. (2005), Paul et al. (2008), Paul and Held (2011), Held and Paul (2012), and Meyer and Held (2014). See vignette("hhh4") for a general introduction and vignette("hhh4_spacetime") for a discussion and illustration of spatial hhh4 models. Furthermore, the fully Bayesian approach for univariate time series of counts from Held et al. (2006) is implemented as function algo.twins. Self-exciting point processes are modeled through endemic-epidemic conditional intensity functions. twinSIR (Höhle, 2009) models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks; see vignette("twinSIR") for an illustration. twinstim (Meyer et al., 2012) fits spatio-temporal point process models to point patterns of infective events, e.g., time-stamped geo-referenced surveillance data on infectious disease occurrence; see vignette("twinstim") for an illustration. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017).

Author

Michael Höhle, Sebastian Meyer, Michaela Paul

Maintainer: Sebastian Meyer <seb.meyer@fau.de>

Acknowledgements

Substantial contributions of code by: Leonhard Held, Howard Burkom, Thais Correa, Mathias Hofmann, Christian Lang, Juliane Manitz, Andrea Riebler, Daniel Sabanés Bové, Maëlle Salmon, Dirk Schumacher, Stefan Steiner, Mikko Virtanen, Wei Wei, Valentin Wimmer .

Furthermore, the authors would like to thank the following people for ideas, discussions, testing and feedback: Doris Altmann, Johannes Bracher, Caterina De Bacco, Johannes Dreesman, Johannes Elias, Marc Geilhufe, Jim Hester, Kurt Hornik, Mayeul Kauffmann, Junyi Lu, Lore Merdrignac, Tim Pollington, Marcos Prates, Brian D. Ripley, Barry Rowlingson, Christopher W. Ryan, Klaus Stark, Yann Le Strat, André Michael Toschke, Wei Wei, George Wood, Achim Zeileis, Bing Zhang .

References

citation(package="surveillance") gives the two main software references for the modeling (Meyer et al., 2017) and the monitoring (Salmon et al., 2016) functionalities:

  • Meyer S, Held L, Höhle M (2017). “Spatio-Temporal Analysis of Epidemic Phenomena Using the R Package surveillance.” Journal of Statistical Software, 77(11), 1--55. doi: 10.18637/jss.v077.i11 .

  • Salmon M, Schumacher D, Höhle M (2016). “Monitoring Count Time Series in R: Aberration Detection in Public Health Surveillance.” Journal of Statistical Software, 70(10), 1--35. doi: 10.18637/jss.v070.i10 .

Further references are listed in surveillance:::REFERENCES.

If you use the surveillance package in your own work, please do cite the corresponding publications.

See also

Examples

## Additional documentation and illustrations of the methods are
## available in the form of package vignettes and demo scripts:
vignette(package = "surveillance")
demo(package = "surveillance")