Some guidelines for citing package ‘surveillance’ in publications:
The seminal paper introducing the hhh4() modeling framework:
Held L, Höhle M and Hofmann M (2005). “A statistical framework for the analysis of multivariate infectious disease surveillance counts.” Statistical Modelling, 5(3), pp. 187–199. ISSN 1471-082X, doi: 10.1191/1471082X05st098oa.
For multivariate hhh4() models *without* random effects, cite:
Paul M, Held L and Toschke AM (2008). “Multivariate modelling of infectious disease surveillance data.” Statistics in Medicine, 27(29), pp. 6250–6267. ISSN 0277-6715, doi: 10.1002/sim.3440.
For multivariate hhh4() models *with* random effects, cite:
Paul M and Held L (2011). “Predictive assessment of a non-linear random effects model for multivariate time series of infectious disease counts.” Statistics in Medicine, 30(10), pp. 1118–1136. ISSN 0277-6715, doi: 10.1002/sim.4177.
For spatial power-law models with hhh4() or twinstim(), cite:
Meyer S and Held L (2014). “Power-law models for infectious disease spread.” The Annals of Applied Statistics, 8(3), pp. 1612–1639. ISSN 1932-6157, doi: 10.1214/14-AOAS743.
If twinSIR() is used, cite:
Höhle M (2009). “Additive-multiplicative regression models for spatio-temporal epidemics.” Biometrical Journal, 51(6), pp. 961–978. ISSN 0323-3847, doi: 10.1002/bimj.200900050.
If twinstim() is used, cite:
Meyer S, Elias J and Höhle M (2012). “A space-time conditional intensity model for invasive meningococcal disease occurrence.” Biometrics, 68(2), pp. 607–616. ISSN 0006-341X, doi: 10.1111/j.1541-0420.2011.01684.x.
If knox() or epitest() is used, cite:
Meyer S, Warnke I, Rössler W and Held L (2016). “Model-based testing for space-time interaction using point processes: An application to psychiatric hospital admissions in an urban area.” Spatial and Spatio-temporal Epidemiology, 17, pp. 15–25. ISSN 1877-5845, doi: 10.1016/j.sste.2016.03.002.
For many of the algo.* functions, the appropriate citation is:
Höhle M (2007). “surveillance: An R package for the monitoring of infectious diseases.” Computational Statistics, 22(4), pp. 571–582. doi: 10.1007/s00180-007-0074-8.
If boda() is used, cite:
Manitz J and Höhle M (2013). “Bayesian outbreak detection algorithm for monitoring reported cases of campylobacteriosis in Germany.” Biometrical Journal, 55(4), pp. 509–526. ISSN 0323-3847, doi: 10.1002/bimj.201200141.
For the nowcast()ing functionality, the appropriate citation is:
Höhle M and an der Heiden M (2014). “Bayesian Nowcasting during the STEC O104:H4 Outbreak in Germany, 2011.” Biometrics, 70(4), pp. 993–1002. doi: 10.1111/biom.12194.
As a general software reference for the monitoring functionality, please cite:
Salmon M, Schumacher D and Höhle M (2016). “Monitoring Count Time Series in R: Aberration Detection in Public Health Surveillance.” Journal of Statistical Software, 70(10), pp. 1–35. doi: 10.18637/jss.v070.i10.
As a general reference for the spatio-temporal modeling frameworks, please cite:
Meyer S, Held L and Höhle M (2016). “Spatio-Temporal Analysis of Epidemic Phenomena Using the R Package surveillance.” Journal of Statistical Software. Preprint available at http://arxiv.org/abs/1411.0416.
To cite the software package ‘surveillance’ itself, use:
Michael Höhle, Sebastian Meyer and Michaela Paul (2016). surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena. R package version 1.13.0. https://CRAN.R-project.org/package=surveillance
In general, the references given in the help pages of the respective main functions should be used.
Corresponding BibTeX entries:
@Article{,
author = {Leonhard Held and Michael Höhle and Mathias Hofmann},
title = {A statistical framework for the analysis of multivariate
infectious disease surveillance counts},
journal = {Statistical Modelling},
issn = {1471-082X},
year = {2005},
volume = {5},
number = {3},
pages = {187--199},
doi = {10.1191/1471082X05st098oa},
}
@Article{,
author = {Michaela Paul and Leonhard Held and André Michael
Toschke},
title = {Multivariate modelling of infectious disease surveillance
data},
journal = {Statistics in Medicine},
issn = {0277-6715},
year = {2008},
volume = {27},
number = {29},
pages = {6250--6267},
doi = {10.1002/sim.3440},
}
@Article{,
author = {Michaela Paul and Leonhard Held},
title = {Predictive assessment of a non-linear random effects model
for multivariate time series of infectious disease counts},
journal = {Statistics in Medicine},
issn = {0277-6715},
year = {2011},
volume = {30},
number = {10},
pages = {1118--1136},
doi = {10.1002/sim.4177},
}
@Article{,
author = {Sebastian Meyer and Leonhard Held},
title = {Power-law models for infectious disease spread},
journal = {The Annals of Applied Statistics},
issn = {1932-6157},
year = {2014},
volume = {8},
number = {3},
pages = {1612--1639},
doi = {10.1214/14-AOAS743},
}
@Article{,
author = {Michael Höhle},
title = {Additive-multiplicative regression models for
spatio-temporal epidemics},
journal = {Biometrical Journal},
issn = {0323-3847},
year = {2009},
volume = {51},
number = {6},
pages = {961--978},
doi = {10.1002/bimj.200900050},
}
@Article{,
author = {Sebastian Meyer and Johannes Elias and Michael Höhle},
title = {A space-time conditional intensity model for invasive
meningococcal disease occurrence},
journal = {Biometrics},
issn = {0006-341X},
year = {2012},
volume = {68},
number = {2},
pages = {607--616},
doi = {10.1111/j.1541-0420.2011.01684.x},
}
@Article{,
author = {Sebastian Meyer and Ingeborg Warnke and Wulf Rössler and
Leonhard Held},
title = {Model-based testing for space-time interaction using point
processes: An application to psychiatric hospital admissions in
an urban area},
journal = {Spatial and Spatio-temporal Epidemiology},
issn = {1877-5845},
year = {2016},
volume = {17},
pages = {15--25},
doi = {10.1016/j.sste.2016.03.002},
}
@Article{,
title = {surveillance: An {R} package for the monitoring of
infectious diseases},
author = {Michael Höhle},
journal = {Computational Statistics},
year = {2007},
volume = {22},
number = {4},
pages = {571--582},
doi = {10.1007/s00180-007-0074-8},
}
@Article{,
author = {Juliane Manitz and Michael Höhle},
title = {Bayesian outbreak detection algorithm for monitoring
reported cases of campylobacteriosis in Germany},
journal = {Biometrical Journal},
issn = {0323-3847},
year = {2013},
volume = {55},
number = {4},
pages = {509--526},
doi = {10.1002/bimj.201200141},
}
@Article{,
title = {Bayesian Nowcasting during the STEC O104:H4 Outbreak in
Germany, 2011},
author = {Michael Höhle and Matthias {an der Heiden}},
journal = {Biometrics},
year = {2014},
volume = {70},
number = {4},
pages = {993--1002},
doi = {10.1111/biom.12194},
}
@Article{,
author = {Maëlle Salmon and Dirk Schumacher and Michael Höhle},
title = {Monitoring Count Time Series in {R}: Aberration Detection
in Public Health Surveillance},
journal = {Journal of Statistical Software},
year = {2016},
volume = {70},
number = {10},
pages = {1--35},
doi = {10.18637/jss.v070.i10},
}
@Article{,
author = {Sebastian Meyer and Leonhard Held and Michael Höhle},
title = {Spatio-Temporal Analysis of Epidemic Phenomena Using the R
Package surveillance},
journal = {Journal of Statistical Software},
year = {2016},
note = {Preprint available at
\url{http://arxiv.org/abs/1411.0416}},
}
@Manual{R:surveillance,
title = {surveillance: Temporal and Spatio-Temporal Modeling and
Monitoring of Epidemic Phenomena},
author = {Michael Höhle and Sebastian Meyer and Michaela Paul},
year = {2016},
note = {R package version 1.13.0},
url = {https://CRAN.R-project.org/package=surveillance},
}