@Article{newport2011,
  author = {C Bayer and H Bernard and R Prager and W Rabsch and P Hiller and B Malorny and B Pfefferkorn and C Frank and A de Jong and I Friesema and {others}},
  title = {An Outbreak of Salmonella Newport Associated with Mung  Bean Sprouts in Germany and the Netherlands, October to  November 2011},
  journal = {Eurosurveillance},
  year = {2014},
  volume = {19},
  number = {1},
  doi = {10.2807/1560-7917.es2014.19.1.20665},
}

@Article{becker_marschner93,
  author = {N. G. Becker and I. C. Marschner},
  title = {A Method for Estimating the Age-Specific Relative Risk of  {HIV} Infection from {AIDS} Incidence Data},
  journal = {Biometrika},
  year = {1993},
  volume = {80},
  number = {1},
  doi = {10.1093/biomet/80.1.165},
}

@ARTICLE{hoehle-heiden,
author = {{H{\"o}hle}, Michael and an der Heiden, Matthias},
title = {{B}ayesian {N}owcasting during the {STEC} {O104:H4} {O}utbreak in {G}ermany, 2011},
journal = {Biometrics},
volume = {70},
number = {4},
issn = {1541-0420},
doi = {10.1111/biom.12194},
pages = {993--1002},
year = {2014},
}

@Article{bernard_etal2014,
  author = {H. Bernard and D. Werber and M. H{\"o}hle},
  title = {Estimating the Under-Reporting of Norovirus Illness in {G}ermany Utilizing Enhanced Awareness of Diarrhoea during  a Large Outbreak of {S}higa Toxin-Producing {E. Coli  O104:H4} in 2011},
  journal = {BMC Infectious Diseases},
  year = {2014},
  volume = {14},
  number = {1},
  pages = {1--6},
  doi = {10.1186/1471-2334-14-116},
}

@Book{sp2,
  title = {Applied Spatial Data Analysis With \proglang{R}},
  edition = {2nd},
  publisher = {Springer-Verlag},
  year = {2013},
  author = {Roger S. Bivand and Edzer Pebesma and Virgilio Gomez-Rubio},
  doi = {10.1007/978-1-4614-7618-4},
}

@Article{brook_evans1972,
  author = {D. Brook and D. A. Evans},
  title = {An Approach to the Probability Distribution of Cusum Run  Length},
  journal = {Biometrika},
  year = {1972},
  volume = {59},
  pages = {539--549},
  number = {3},
  doi = {10.1093/biomet/59.3.539},
}

@Article{buckeridge2007,
  author = {David L. Buckeridge},
  title = {Outbreak Detection through Automated Surveillance: A  Review of the Determinants of Detection},
  journal = {Journal of Biomedical Informatics},
  year = {2007},
  volume = {40},
  pages = {370--379},
  number = {4},
}

@Article{chen1978,
  author = {Rina Chen},
  title = {A Surveillance System for Congenital Malformations},
  journal = {Journal of the American Statistical Association},
  year = {1978},
  volume = {73},
  pages = {323-327},
  number = {362},
  doi = {10.2307/2286660},
}

@Manual{epiestim,
  title = {\pkg{EpiEstim}: A Package to Estimate Time Varying  Reproduction Numbers from Epidemic Curves},
  author = {Anne Cori},
  year = {2013},
  note = {\proglang{R} package version 1.1-2},
  url = {https://CRAN.R-project.org/package=EpiEstim},
}

@Manual{datatable2013,
  title = {\pkg{data.table}: Extension of \pkg{data.frame} for Fast  Indexing, Fast Ordered Joins, Fast Assignment, Fast  Grouping and List Columns},
  author = {M Dowle and A Srinivasan and T Short and S Lianoglou},
  year = {2015},
  note = {\proglang{R} package version 1.9.6},
  url = {https://CRAN.R-project.org/package=data.table},
}

@Article{sim:sim3197,
  author = {Ronald D. Fricker and Benjamin L. Hegler and David A. Dunfee},
  title = {Comparing Syndromic Surveillance Detection Methods: EARS'  versus a CUSUM-Based Methodology},
  journal = {Statistics in Medicine},
  year = {2008},
  volume = {27},
  pages = {3407--3429},
  number = {17},
  doi = {10.1002/sim.3197},
}

@Book{frisen2008financial,
  title = {Financial Surveillance},
  publisher = {John Wiley \& Sons},
  year = {2008},
  author = {Marianne Fris{\'e}n},
}

@Article{fri2009,
  author = {Marianne Fris{\'e}n and Eva Andersson},
  title = {Semiparametric Surveillance of Monotonic Changes},
  journal = {Sequential Analysis},
  year = {2009},
  volume = {28},
  pages = {434-454},
  number = {4},
  doi = {10.1080/07474940903238029},
}

@Article{frisen_etal2009,
  author = {M. Fris{\'e}n and E. Andersson and L. Schi{\"o}ler},
  title = {Robust Outbreak Surveillance of Epidemics in Sweden},
  journal = {Statistics in Medicine},
  year = {2009},
  volume = {28},
  pages = {476-493},
  doi = {10.1002/sim.3483},
}

@InCollection{hoehle2010,
  author = {Michael H\"{o}hle},
  title = {Online Change-Point Detection in Categorical Time Series},
  booktitle = {Statistical Modelling and Regression Structures},
  publisher = {Physica-Verlag HD},
  year = {2010},
  editor = {Thomas Kneib and Gerhard Tutz},
  pages = {377-397},
}

@Article{held_etal2006,
  author = {L. Held and M. Hofmann and M. H{\"o}hle and V. Schmid},
  title = {A Two Component Model for Counts of Infectious Diseases},
  journal = {Biostatistics},
  year = {2006},
  volume = {7},
  pages = {422--437},
  doi = {10.1093/biostatistics/kxj016},
}

@Article{hulth_etal2010,
  author = {A. Hulth and N. Andrews and S. Ethelberg and J. Dreesman and D. Faensen and W. {van Pelt} and J. Schnitzler},
  title = {Practical Usage of Computer-Supported Outbreak Detection  in Five European Countries},
  journal = {Eurosurveillance},
  year = {2010},
  volume = {15},
  number = {36},
}

@Article{outbreaker,
  author = {Thibaut Jombart and Anne Cori and Xavier Didelot and Simon Cauchemez and Christophe Fraser and Neil Ferguson},
  title = {Bayesian Reconstruction of Disease Outbreaks by Combining  Epidemiologic and Genomic Data},
  journal = {PLoS Computional Biology},
  year = {2014},
  volume = {10},
  pages = {e1003457},
  number = {1},
  doi = {10.1371/journal.pcbi.1003457},
}

@Manual{spc,
  title = {\pkg{spc}: Statistical Process Control -- Collection of  Some Useful Functions},
  author = {Sven Knoth},
  year = {2016},
  note = {\proglang{R} package version 0.5.3},
  url = {https://CRAN.R-project.org/package=spc},
}

@Manual{satscan,
  title = {\pkg{SaTScan}: Software for the Spatial, Temporal and  Space-Time Scan Statistics},
  author = {Martin Kulldorff},
  address = {Boston},
  year = {1997},
  url = {https://www.satscan.org/},
}

@Article{lawless1987,
  author = {Jerald F Lawless},
  title = {Negative Binomial and Mixed Poisson Regression},
  journal = {Canadian Journal of Statistics},
  year = {1987},
  volume = {15},
  pages = {209--225},
  number = {3},
  publisher = {John Wiley \& Sons},
  doi = {10.2307/3314912},
}

@InProceedings{sweave,
  author = {Friedrich Leisch},
  title = {\texttt{Sweave} and Beyond: Computations on Text Documents},
  booktitle = {Proceedings of the 3rd International Workshop on  Distributed Statistical Computing, Vienna, Austria},
  year = {2003},
  editor = {Kurt Hornik and Friedrich Leisch and Achim Zeileis},
  note = {{ISSN 1609-395X}},
  url = {https://www.R-project.org/conferences/DSC-2003/Proceedings/},
}

@Manual{tscount,
  title = {\pkg{tscount}: Analysis of Count Time Series},
  author = {Tobias Liboschik and Roland Fried and Konstantinos Fokianos and Philipp Probst},
  year = {2015},
  note = {\proglang{R} package version 1.0.0},
  url = {https://CRAN.R-project.org/package=tscount},
}

@article{liboschik_tscount_2015,
  title = {{tscount}: An R Package for Analysis of Count Time Series
Following Generalized Linear Models},
  volume = {06/15},
  doi = {10.17877/DE290R-7239},
  language = {en},
  journal = {TU Dortmund, SFB 823 Discussion Paper},
  author = {Liboschik, Tobias and Fokianos, Konstantinos and Fried,
Roland},
  year = {2015}
}

@Article{lucas1982fast,
  author = {James M Lucas and Ronald B Crosier},
  title = {Fast Initial Response for CUSUM Quality-Control Schemes:  Give Your CUSUM a Head Start},
  journal = {Technometrics},
  year = {1982},
  volume = {24},
  pages = {199--205},
  number = {3},
  doi = {10.2307/1268679},
}

@Article{radio,
  author = {Peng Luo and Timothy A DeVol and Julia L Sharp},
  title = {CUSUM Analyses of Time-Interval Data for Online Radiation  Monitoring},
  journal = {Health Physics},
  year = {2012},
  volume = {102},
  pages = {637--645},
  number = {6},
  publisher = {LWW},
  doi = {10.1097/hp.0b013e3182430106},
}

@Article{manitz2013,
  author = {Juliane Manitz and Michael H\"{o}hle},
  title = {Bayesian Outbreak Detection Algorithm for Monitoring  Reported Cases of Campylobacteriosis in Germany},
  journal = {Biometrical Journal},
  year = {2013},
  volume = {55},
  pages = {509--526},
  number = {4},
  issn = {1521-4036},
  doi = {10.1002/bimj.201200141},
}

@Manual{ssas,
  title = {Microsoft SQL Server Analysis Services, Version~2012},
  author = {{Microsoft Corp.}},
  year = {2012},
  url = {https://www.microsoft.com/},
}

@Manual{ssrs,
  title = {Microsoft SQL Server Reporting Services, Version~2012},
  author = {{Microsoft Corp.}},
  year = {2012},
  url = {https://www.microsoft.com/},
}

@Article{noufaily2012,
  author = {A. Noufaily and D. G. Enki and P. Farrington and P. Garthwaite and N. Andrews and A. Charlett},
  title = {An Improved Algorithm for Outbreak Detection in Multiple  Surveillance Systems},
  journal = {Statistics in Medicine},
  year = {2012},
  volume = {32},
  pages = {1206--1222},
  number = {7},
  doi = {10.1002/sim.5595},
}

@Article{sp1,
  author = {Edzer J. Pebesma and Roger S. Bivand},
  title = {Classes and Methods for Spatial Data in \proglang{R}},
  journal = {\proglang{R} News},
  year = {2005},
  volume = {5},
  pages = {9--13},
  number = {2},
  url = {https://CRAN.R-project.org/doc/Rnews/},
}

@Article{pierce_schafer86,
  author = {D. A. Pierce and D. W. Schafer},
  title = {Residuals in Generalized Linear Models},
  journal = {Journal of the American Statistical Association},
  year = {1986},
  volume = {81},
  pages = {977-986},
  number = {396},
  doi = {10.2307/2289071},
}

@Article{reynolds2000,
  author = {{Reynolds, Jr.}, Marion R. and Zachary G. Stoumbos},
  title = {A General Approach to Modeling CUSUM Charts for a Proportion},
  journal = {IIE Transactions},
  year = {2000},
  volume = {32},
  pages = {515-535},
  number = {6},
  language = {English},
  publisher = {Kluwer Academic Publishers},
  doi = {10.1080/07408170008963928},
}

@Article{rigby2005,
  author = {R. A. Rigby and D. M. Stasinopoulos},
  title = {Generalized Additive Models for Location, Scale and Shape},
  journal = {Journal of the Royal Statistical Society C},
  year = {2005},
  volume = {54},
  pages = {507--554},
  number = {3},
  doi = {10.1111/j.1467-9876.2005.00510.x},
}

@Manual{rodbc2013,
  title = {\pkg{RODBC}: ODBC Database Access},
  author = {Brian Ripley and Michael Lapsley},
  year = {2016},
  note = {\proglang{R} package version 1.3-13},
  url = {https://CRAN.R-project.org/package=RODBC},
}

@Article{rogerson_yamada2004,
  author = {P. A. Rogerson and I. Yamada},
  title = {Approaches to Syndromic Surveillance When Data Consist of  Small Regional Counts},
  journal = {Morbidity and Mortality Weekly Report},
  year = {2004},
  volume = {53},
  pages = {79--85},
  doi = {10.1037/e307182005-016},
}

@Article{rossi_etal99,
  author = {G. Rossi and L. Lampugnani and M. Marchi},
  title = {An Approximate {CUSUM} Procedure for Surveillance of  Health Events},
  journal = {Statistics in Medicine},
  year = {1999},
  volume = {18},
  pages = {2111--2122},
  doi = {10.1002/(sici)1097-0258(19990830)18:16<2111::aid-sim171>3.0.co;2-q},
}

@Article{inla,
  title = {Approximate Bayesian Inference for Latent Gaussian Models Using Integrated Nested Laplace Approximations},
  author = {H. Rue and S. Martino and N. Chopin},
  journal = {Journal of the Royal Statistical Society B},
  year = {2009},
  volume = {71},
  number = {2},
  pages = {319--392},
  doi = {10.1111/j.1467-9868.2008.00700.x}
}

@Manual{xts,
  title = {\pkg{xts}: eXtensible Time Series},
  author = {Jeffrey A. Ryan and Joshua M. Ulrich},
  year = {2014},
  note = {\proglang{R} package version 0.9-7},
  url = {https://CRAN.R-project.org/package=xts},
}

@Article{dirk,
  author = {M. Salmon and D. Schumacher and H. Burmann and C. Frank and H. Claus and M. H{\"o}hle},
  title = {A system for automated outbreak detection of communicable diseases in {Germany}},
  journal = {Eurosurveillance},
  year = {2016},
  volume = {21},
  number = {13},
  doi = {10.2807/1560-7917.ES.2016.21.13.30180},
}

@Article{maelle,
  author = {M. Salmon and D. Schumacher and K. Stark and M. H{\"o}hle},
  title = {{B}ayesian Outbreak Detection in the Presence of Reporting  Delays},
  journal = {Biometrical Journal},
  year = {2015},
  volume = {57},
  number = {6},
  pages = {1051--1067},
  doi = {10.1002/bimj.201400159},
}

@Article{accident,
  author = {Anna Schuh and Jaime A. Camelio and William H. Woodall},
  title = {Control Charts for Accident Frequency: a Motivation for  Real-Time Occupational Safety Monitoring},
  journal = {International Journal of Injury Control and Safety  Promotion},
  year = {2014},
  volume = {21},
  number = {2},
  pages = {154--162},
  doi = {10.1080/17457300.2013.792285},
}

@Article{qcc,
  author = {Luca Scrucca},
  title = {\pkg{qcc}: An \proglang{R} Package for Quality Control  Charting and Statistical Process Control},
  journal = {\proglang{R} News},
  year = {2004},
  volume = {4},
  number = {1},
  pages = {11--17},
  url = {https://CRAN.R-project.org/doc/Rnews/},
}

@Article{shmueli2010,
  author = {Galit Shmueli and Howard Burkom},
  title = {Statistical Challenges Facing Early Outbreak Detection in  Biosurveillance},
  journal = {Technometrics},
  year = {2010},
  volume = {52},
  pages = {39-51},
  number = {1},
  doi = {10.1198/tech.2010.06134},
}

@Article{sonesson2003,
  author = {Christian Sonesson and David Bock},
  title = {A Review and Discussion of Prospective Statistical  Surveillance in Public Health},
  journal = {Journal of the Royal Statistical Society A},
  year = {2003},
  volume = {166},
  pages = {5--21},
  number = {1},
  doi = {10.1111/1467-985x.00256},
}

@Article{stasjss,
  author = {D. Mikis Stasinopoulos and Robert A. Rigby},
  title = {Generalized Additive Models for Location Scale and Shape (GAMLSS) in \proglang{R}},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {23},
  pages = {1--46},
  number = {7},
  doi = {10.18637/jss.v023.i07},
}

@Article{steiner1999,
  author = {S. H. Steiner and R. J. Cook and V. T. Farewell},
  title = {Monitoring Paired Binary Surgical Outcomes Using  Cumulative Sum Charts},
  journal = {Statistics in Medicine},
  year = {1999},
  volume = {18},
  pages = {69--86},
  doi = {10.1002/(sici)1097-0258(19990115)18:1<69::aid-sim966>3.0.co;2-l},
}

@Manual{outbreaktools,
  title = {\pkg{OutbreakTools}: Basic Tools for the Analysis of  Disease Outbreaks},
  author = {{The Hackout Team}},
  year = {2016},
  note = {\proglang{R} package version 0.1-14},
  url = {https://CRAN.R-project.org/package=OutbreakTools},
}

@Article{unkel2012,
  author = {Steffen Unkel and C. Paddy Farrington and Paul H. Garthwaite and Chris Robertson and Nick Andrews},
  title = {Statistical Methods for the Prospective Detection of  Infectious Disease Outbreaks: A Review},
  journal = {Journal of the Royal Statistical Society A},
  year = {2012},
  volume = {175},
  pages = {49--82},
  number = {1},
  doi = {10.1111/j.1467-985x.2011.00714.x},
}

@Manual{testthat2013,
  title = {\pkg{testthat}: Unit Testing for \proglang{R}},
  author = {Hadley Wickham},
  year = {2016},
  note = {\proglang{R} package version 1.0.2},
  url = {https://CRAN.R-project.org/package=testthat},
}

@InCollection{knitr,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {\pkg{knitr}: A Comprehensive Tool for Reproducible Research in \proglang{R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
}

@Article{zoo,
  author = {Achim Zeileis and Gabor Grothendieck},
  title = {\pkg{zoo}: S3 Infrastructure for Regular and Irregular Time Series},
  journal = {Journal of Statistical Software},
  year = {2005},
  volume = {14},
  pages = {1--27},
  number = {6},
  doi = {10.18637/jss.v014.i06},
}

@Article{strucchange,
  author = {Achim Zeileis and Friedrich Leisch and Kurt Hornik and Christian Kleiber},
  title = {\pkg{strucchange}: An \proglang{R} Package for Testing for  Structural Change in Linear Regression Models},
  journal = {Journal of Statistical Software},
  year = {2002},
  volume = {7},
  pages = {1--38},
  number = {2},
  doi = {10.18637/jss.v007.i02},
}

@Manual{mglm,
  title = {\pkg{MGLM}: Multivariate Response Generalized Linear  Models},
  author = {Yiwen Zhang and Hua Zhou},
  year = {2016},
  note = {\proglang{R} package version 0.0.7},
  url = {https://CRAN.R-project.org/package=MGLM},
}
