Other packages > Find by keyword >

surveillance  

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
View on CRAN: Click here


Download and install surveillance package within the R console
Install from CRAN:
install.packages("surveillance")

Install from Github:
library("remotes")
install_github("cran/surveillance")

Install by package version:
library("remotes")
install_version("surveillance", "1.25.0")



Attach the package and use:
library("surveillance")
Maintained by
Sebastian Meyer
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2005-11-18
Latest Update: 2025-06-25
Description:
Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.
How to cite:
Sebastian Meyer (2005). surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena. R package version 1.25.0, https://cran.r-project.org/web/packages/surveillance. Accessed 06 Mar. 2026.
Previous versions and publish date:
0.9-1 (2005-11-21 21:42), 0.9-2 (2006-09-05 20:45), 0.9-6 (2007-06-25 20:09), 0.9-7 (2007-11-18 09:52), 0.9-8 (2008-01-19 10:00), 0.9-9 (2008-01-21 20:34), 0.9 (2005-11-18 20:07), 1.0-2 (2009-03-06 08:30), 1.1-2 (2009-10-15 12:30), 1.1-6 (2010-05-25 17:58), 1.2-1 (2012-01-15 11:44), 1.4-1 (2012-07-26 09:07), 1.4-2 (2012-08-20 06:37), 1.5-0 (2012-12-12 09:14), 1.5-1 (2012-12-14 09:54), 1.5-2 (2013-03-19 07:24), 1.5-4 (2013-04-21 17:54), 1.6-0 (2013-09-09 19:50), 1.7-0 (2013-11-19 16:58), 1.8-0 (2014-06-17 12:30), 1.8-1 (2014-10-30 15:54), 1.8-2 (2014-12-20 14:12), 1.8-3 (2015-01-06 07:28), 1.9-0 (2015-06-11 12:04), 1.9-1 (2015-06-12 23:34), 1.10-0 (2015-11-06 11:51), 1.11.0 (2016-02-09 09:47), 1.12.0 (2016-04-03 16:40), 1.12.1 (2016-05-18 06:53), 1.12.2 (2016-11-17 14:34), 1.13.0 (2016-12-20 18:31), 1.13.1 (2017-04-29 00:25), 1.14.0 (2017-06-30 00:14), 1.15.0 (2017-10-06 22:34), 1.16.0 (2018-01-23 22:48), 1.16.1 (2018-05-29 00:16), 1.16.2 (2018-07-25 00:20), 1.17.0 (2019-02-22 15:30), 1.17.1 (2019-09-13 17:00), 1.17.2 (2019-11-12 07:50), 1.17.3 (2019-12-16 15:30), 1.18.0 (2020-03-19 16:50), 1.19.0 (2021-01-30 07:20), 1.19.1 (2021-03-31 07:10), 1.20.0 (2022-02-16 11:20), 1.20.1 (2022-07-19 13:50), 1.20.3 (2022-11-16 13:10), 1.21.0 (2023-03-15 14:10), 1.21.1 (2023-05-19 12:00), 1.22.0 (2023-10-30 21:40), 1.22.1 (2023-11-28 11:10), 1.23.0 (2024-05-04 07:50), 1.23.1 (2024-09-02 19:00), 1.24.0 (2024-10-01 20:10), 1.24.1 (2024-11-05 15:10)
Other packages that cited surveillance R package
View surveillance citation profile
Other R packages that surveillance depends, imports, suggests or enhances
Complete documentation for surveillance
Functions, R codes and Examples using the surveillance R package
Some associated functions: LRCUSUM.runlength . MMRcoverageDE . R0 . abattoir . addFormattedXAxis . addSeason2formula . aggregate.disProg . algo.bayes . algo.call . algo.cdc . algo.compare . algo.cusum . algo.farrington.assign.weights . algo.farrington.fitGLM . algo.farrington . algo.farrington.threshold . algo.glrnb . algo.hmm . algo.outbreakP . algo.quality . algo.rki . algo.rogerson . algo.summary . algo.twins . all.equal . animate . anscombe.residuals . arlCusum . backprojNP . bestCombination . boda . bodaDelay . calibration . campyDE . categoricalCUSUM . checkResidualProcess . clapply . coeflist . create.disProg . deleval . disProg2sts . discpoly . earsC . epidata . epidataCS . epidataCS_aggregate . epidataCS_animate . epidataCS_permute . epidataCS_plot . epidataCS_update . epidata_animate . epidata_intersperse . epidata_plot . epidata_summary . estimateGLRNbHook . fanplot . farringtonFlexible . find.kh . findH . findK . fluBYBW . formatDate . formatPval . glm_epidataCS . ha . hagelloch . hcl.colors . hepatitisA . hhh4 . hhh4_W . hhh4_W_utils . hhh4_formula . hhh4_internals . hhh4_methods . hhh4_plot . hhh4_predict . hhh4_simulate . hhh4_simulate_plot . hhh4_simulate_scores . hhh4_update . hhh4_validation . husO104Hosp . imdepi . imdepifit . influMen . intensityplot . intersectPolyCircle . isScalar . isoWeekYear . knox . ks.plot.unif . layout.labels . linelist2sts . m1 . magic.dim . makeControl . marks . measles.weser . measlesDE . meningo.age . momo . multiplicity.Spatial . multiplicity . nbOrder . nowcast . pairedbinCUSUM . permutationTest . pit . plapply . plot.atwins . plot.disProg . plot.survRes . poly2adjmat . polyAtBorder . primeFactors . print.algoQV . ranef . refvalIdxByDate . residualsCT . rotaBB . runifdisc . salmAllOnset . salmHospitalized . salmNewport . salmonella.agona . scores . shadar . sim.pointSource . sim.seasonalNoise . stK . stcd . sts-class . stsAggregate . stsBP-class . stsNC-class . stsNClist_animate . stsNewport . stsSlots . stsXtrct . sts_animate . sts_creation . sts_ggplot . sts_observation . sts_tidy . stsplot . stsplot_space . stsplot_spacetime . stsplot_time . surveillance-defunct . surveillance-package . surveillance.options . toLatex.sts . twinSIR . twinSIR_cox . twinSIR_exData . twinSIR_intensityplot . twinSIR_methods . twinSIR_profile . twinSIR_simulation . twinstim . twinstim_epitest . twinstim_iaf . twinstim_iafplot . twinstim_intensity . twinstim_methods . twinstim_plot . twinstim_profile . twinstim_siaf . twinstim_siaf_simulatePC . twinstim_simEndemicEvents . twinstim_simulation . twinstim_step . twinstim_tiaf . twinstim_update . unionSpatialPolygons . untie . wrap.algo . zetaweights . 
Some associated R codes: AllClass.R . AllGeneric.R . LRCUSUM.runlength.R . addSeason2formula.R . algo_bayes.R . algo_call.R . algo_cdc.R . algo_cusum.R . algo_farrington.R . algo_glrnb.R . algo_hmm.R . algo_outbreakP.R . algo_rki.R . algo_rogerson.R . algo_twins.R . backprojNP.R . boda.R . bodaDelay.R . calibration.R . calibration_null.R . catCUSUM.R . checkDerivatives.R . clapply.R . disProg.R . earsC.R . epidata.R . epidataCS.R . epidataCS_aggregate.R . epidataCS_animate.R . epidataCS_methods.R . epidataCS_plot.R . epidata_animate.R . epidata_plot.R . fanplot.R . farringtonFlexible.R . formatPval.R . functionTable.R . gd.R . glm_epidataCS.R . graphs.R . hcl.colors.R . hhh4.R . hhh4_W.R . hhh4_W_np.R . hhh4_W_powerlaw.R . hhh4_amplitudeShift.R . hhh4_calibration.R . hhh4_methods.R . hhh4_oneStepAhead.R . hhh4_plot.R . hhh4_simulate.R . hhh4_simulate_plot.R . hhh4_simulate_scores.R . intersectPolyCircle.R . isScalar.R . isoWeekYear.R . knox.R . ks.plot.unif.R . linelist2sts.R . magic.dim.R . makeControl.R . nowcast.R . options.R . pairedbinCUSUM.R . permutationTest.R . pit.R . plapply.R . plot.survRes.R . scores.R . sim_background.R . sim_pointSource.R . spatial_tools.R . stK.R . stcd.R . sts.R . stsBP.R . stsNC.R . stsNClist_animate.R . sts_animate.R . sts_coerce.R . sts_creation.R . sts_ggplot.R . sts_observation.R . sts_toLatex.R . stsplot_space.R . stsplot_spacetime.R . stsplot_time.R . twinSIR.R . twinSIR_helper.R . twinSIR_intensity.R . twinSIR_methods.R . twinSIR_profile.R . twinSIR_simulation.R . twinstim.R . twinstim_epitest.R . twinstim_helper.R . twinstim_iafplot.R . twinstim_intensity.R . twinstim_methods.R . twinstim_siaf.R . twinstim_siaf_exponential.R . twinstim_siaf_gaussian.R . twinstim_siaf_polyCub_iso.R . twinstim_siaf_powerlaw.R . twinstim_siaf_powerlaw1.R . twinstim_siaf_powerlawL.R . twinstim_siaf_step.R . twinstim_siaf_student.R . twinstim_simulation.R . twinstim_step.R . twinstim_tiaf.R . twinstim_tiaf_exponential.R . twinstim_tiaf_step.R . untie.R . wrap_univariate.R . zzz.R .  Full surveillance package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

lbfgs  
Limited-memory BFGS Optimization
A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implem ...
Download / Learn more Package Citations See dependency  
mlr3viz  
Visualizations for 'mlr3'
Visualization package of the 'mlr3' ecosystem. It features plots for mlr3 objects such as tasks, le ...
Download / Learn more Package Citations See dependency  
DatabionicSwarm  
Swarm Intelligence for Self-Organized Clustering
Algorithms implementing populations of agents that interact with one another and sense their environ ...
Download / Learn more Package Citations See dependency  
openxlsx  
Read, Write and Edit xlsx Files
Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, stylin ...
Download / Learn more Package Citations See dependency  
EMVS  
The Expectation-Maximization Approach to Bayesian Variable Selection
An efficient expectation-maximization algorithm for fitting Bayesian spike-and-slab regularization p ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  

26,264

R Packages

223,360

Dependencies

70,244

Author Associations

26,265

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA