## Use meta data extracted from the DESCRIPTION file to get author names
## (the variable 'meta' is defined in readCitationFile())
authors <- utils:::.read_authors_at_R_field(meta$"Authors@R")


### Outer header

citHeader("Some guidelines for citing package",
          sQuote("surveillance"), "in publications:")



############
### hhh4 ###
############

bibentry(
    bibtype = "Article",
    header = "The seminal paper introducing the hhh4() modeling framework:",
    author = c(authors[c("LH","MH")], person("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"
)

bibentry(
    bibtype = "Article",
    header = "For multivariate hhh4() models *without* random effects, cite:",
    author = c(authors[c("MP","LH")], person(c("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"
)

bibentry(
    bibtype = "Article",
    header = "For multivariate hhh4() models *with* random effects, cite:",
    author = authors[c("MP","LH")],
    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"
)

bibentry(
    bibtype = "Article",
    header = "For spatial power-law models with hhh4() or twinstim(), cite:",
    author = authors[c("SM", "LH")],
    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"
)


###############
### twinSIR ###
###############

bibentry(
    bibtype = "Article",
    header = "If twinSIR() is used, cite:",
    author = authors["MH"],
    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"
)


################
### twinstim ###
################

bibentry(
    bibtype = "Article",
    header = "If twinstim() is used, cite:",
    author = c(authors["SM"], person("Johannes", "Elias"), authors["MH"]),
    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"
)

bibentry(
    bibtype = "Article",
    header = "If knox() or epitest() is used, cite:",
    author = c(authors["SM"], person("Ingeborg", "Warnke"),
               person("Wulf", "Rössler"), authors["LH"]),
    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"
)


##############
### algo.* ###
##############

bibentry(
    bibtype = "Article",
    header = "For many of the algo.* functions, the appropriate citation is:",
    title = "surveillance: An {R} package for the monitoring of infectious diseases",
    author = authors["MH"],
    journal = "Computational Statistics",
    year = "2007",
    volume = "22",
    number = "4",
    pages = "571--582",
    doi = "10.1007/s00180-007-0074-8"
)


############
### boda ###
############

bibentry(
    bibtype = "Article",
    header = "If boda() is used, cite:",
    author = c(person("Juliane", "Manitz"), authors["MH"]),
    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"
)


###############
### nowcast ###
###############

bibentry(
    bibtype = "Article",
    header = "For the nowcast()ing functionality, the appropriate citation is:",
    title = "Bayesian Nowcasting during the STEC O104:H4 Outbreak in Germany, 2011", 
    author = c(authors["MH"],person("Matthias", "an der Heiden")),
    journal = "Biometrics",
    year = "2014",
    volume = "70",
    number = "4",
    pages = "993--1002",
    doi = "10.1111/biom.12194"
)


##################
### JSS papers ###
##################

bibentry(
    bibtype = "Article",
    header = "As a general software reference for the monitoring functionality, please cite:",
    author = authors[c("MS", "DS", "MH")],
    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"
)

bibentry(
    bibtype = "Article",
    header = "As a general reference for the spatio-temporal modeling frameworks, please cite:",
    author = authors[c("SM", "LH", "MH")],
    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}"
)


################################
### basic software reference ###
################################

{
    softwareRef <- citation(auto = meta)
    softwareRef$key <- "R:surveillance"
    softwareRef$header <- paste("To cite the software package",
                                sQuote("surveillance"), "itself, use:")
    softwareRef
}



### Outer footer

citFooter("In general, the references given in the help pages",
          "of the respective main functions should be used.")
