Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena


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Documentation for package ‘surveillance’ version 1.7-0

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surveillance-package Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

-- A --

abattoir Abattoir Data
add1.twinstim Stepwise Model Selection by AIC
addSeason2formula Function that adds a sine-/cosine formula to an existing formula.
aggregate-method Aggregate the the series of an sts object
aggregate.disProg Aggregate the observed counts
AIC.ah4 Print, Summary and Extraction Methods for '"ah4"' Objects
AIC.twinSIR Print, Summary and Extraction Methods for '"twinSIR"' Objects
alarms Generic functions to access '"sts"' slots
alarms-method Class '"sts"' - surveillance time series
alarms<- Generic functions to access '"sts"' slots
alarms<--method Class '"sts"' - surveillance time series
algo.bayes The Bayes System
algo.bayes1 The Bayes System
algo.bayes2 The Bayes System
algo.bayes3 The Bayes System
algo.bayesLatestTimepoint The Bayes System
algo.call Query Transmission to Specified Surveillance Systems
algo.cdc The CDC Algorithm
algo.cdcLatestTimepoint The CDC Algorithm
algo.compare Comparison of Specified Surveillance Systems using Quality Values
algo.cusum CUSUM method
algo.farrington Surveillance for a count data time series using the Farrington method.
algo.farrington.assign.weights Assign weights to base counts
algo.farrington.fitGLM Fit the Poisson GLM of the Farrington procedure for a single time point
algo.farrington.fitGLM.fast Fit the Poisson GLM of the Farrington procedure for a single time point
algo.farrington.fitGLM.populationOffset Fit the Poisson GLM of the Farrington procedure for a single time point
algo.farrington.threshold Compute prediction interval for a new observation
algo.glrnb Cound data regression charts
algo.glrpois Poisson regression charts
algo.hhh Model fit based on the Held, Hoehle, Hofman paper
algo.hhh.grid Function to try multiple starting values
algo.hmm Hidden Markov Model (HMM) method
algo.outbreakP Semiparametric surveillance of outbreaks
algo.quality Computation of Quality Values for a Surveillance System Result
algo.rki The system used at the RKI
algo.rki1 The system used at the RKI
algo.rki2 The system used at the RKI
algo.rki3 The system used at the RKI
algo.rkiLatestTimepoint The system used at the RKI
algo.rogerson Modified CUSUM method as proposed by Rogerson and Yamada (2004)
algo.summary Summary Table Generation for Several Disease Chains
algo.twins Model fit based on a two-component epidemic model
animate Generic animation of spatio-temporal objects
animate.epidata Spatio-Temporal Animation of an Epidemic
animate.epidataCS Spatio-Temporal Animation of a Continuous-Time Continuous-Space Epidemic
animate.summary.epidata Spatio-Temporal Animation of an Epidemic
anscombe.residuals Compute Anscombe residuals
arlCusum Calculation of Average Run Length for discrete CUSUM schemes
as.data.frame-method Class '"sts"' - surveillance time series
as.epidata Class for Epidemic Data Discrete in Space and Continuous in Time
as.epidata.default Class for Epidemic Data Discrete in Space and Continuous in Time
as.epidata.epidataCS Conversion (aggregation) of '"epidataCS"' to '"epidata"' or '"sts"'
as.epidataCS Class for Representing Continuous Space-Time Point Process Data

-- B --

backprojNP Non-parametric back-projection of incidence cases to exposure cases using a known incubation time as in Becker et al (1991).
backprojNP.fit Non-parametric back-projection of incidence cases to exposure cases using a known incubation time as in Becker et al (1991).
bayes Multivariate Surveillance through independent univariate algorithms
bestCombination Partition of a number into two factors

-- C --

calc.outbreakP.statistic Semiparametric surveillance of outbreaks
catcusum.LLRcompute CUSUM detector for time-varying categorical time series
categoricalCUSUM CUSUM detector for time-varying categorical time series
checkResidualProcess Check the residual process of a fitted 'twinSIR' or 'twinstim'
coef.ah Model fit based on the Held, Hoehle, Hofman paper
coef.ah4 Print, Summary and Extraction Methods for '"ah4"' Objects
coef.ahg Function to try multiple starting values
coerce-method Class "stsBP" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting or nowcasting surveillance time series
colnames-method Class '"sts"' - surveillance time series
compMatrix.writeTable Latex Table Generation
confint.ah4 Print, Summary and Extraction Methods for '"ah4"' Objects
control Generic functions to access '"sts"' slots
control-method Class '"sts"' - surveillance time series
control<- Generic functions to access '"sts"' slots
control<--method Class '"sts"' - surveillance time series
correct53to52 Data Correction from 53 to 52 weeks
create.disProg Creating an object of class disProg
create.grid Computes a matrix of initial values
cusum Multivariate Surveillance through independent univariate algorithms

-- D --

deleval Surgical failures data
dim-method Class '"sts"' - surveillance time series
discpoly Polygonal Approximation of a Disc/Circle
disProg2sts Convert disProg object to sts and vice versa
dist.median Adjust observed epidemic curve for reporting delay of cases
drop1.twinstim Stepwise Model Selection by AIC

-- E --

earsC Surveillance for a count data time series using the EARS C1, C2 or C3 method.
em.step.becker Non-parametric back-projection of incidence cases to exposure cases using a known incubation time as in Becker et al (1991).
enlargeData Data Enlargement
epidata Class for Epidemic Data Discrete in Space and Continuous in Time
epidataCS Class for Representing Continuous Space-Time Point Process Data
epidataCS2sts Conversion (aggregation) of '"epidataCS"' to '"epidata"' or '"sts"'
epoch Generic functions to access '"sts"' slots
epoch-method Class '"sts"' - surveillance time series
epoch<- Generic functions to access '"sts"' slots
epoch<--method Class '"sts"' - surveillance time series
epochInYear Class '"sts"' - surveillance time series
epochInYear-method Class '"sts"' - surveillance time series
estimateGLRNbHook Hook function for in-control mean estimation
estimateGLRPoisHook Hook function for in-control mean estimation
extractAIC.twinSIR Print, Summary and Extraction Methods for '"twinSIR"' Objects

-- F --

farrington Multivariate Surveillance through independent univariate algorithms
farringtonFlexible Surveillance for an univariate count data time series using the improved Farrington method described in Noufaily et al. (2012).
fe Specify Formulae in a Random Effects HHH Model
find.kh Determine the k and h values in a standard normal setting
findH Find decision interval for given in-control ARL and reference value
findK Find reference value
fixef Print, Summary and Extraction Methods for '"ah4"' Objects
fixef.ah4 Print, Summary and Extraction Methods for '"ah4"' Objects
fluBYBW Influenza in Southern Germany
formatPval Pretty p-Value Formatting

-- G --

glrnb Multivariate Surveillance through independent univariate algorithms
glrpois Multivariate Surveillance through independent univariate algorithms

-- H --

h1_nrwrp RKI SurvStat Data
ha Hepatitis A in Berlin
ha.sts Hepatitis A in Berlin
hagelloch 1861 measles epidemic in the city of Hagelloch, Germany
hagelloch.df 1861 measles epidemic in the city of Hagelloch, Germany
head.epidataCS Class for Representing Continuous Space-Time Point Process Data
hepatitisA Hepatitis A in Germany
hhh4 Random effects HHH model fit as described in Paul and Held (2011)
hValues Find decision interval for given in-control ARL and reference value

-- I --

iafplot Plot the spatial or temporal interaction function of a twimstim
imdepi Occurrence of Invasive Meningococcal Disease in Germany
imdepifit Occurrence of Invasive Meningococcal Disease in Germany
influMen Influenza and meningococcal infections in Germany, 2001-2006
initialize-method Class '"sts"' - surveillance time series
inside.gpc.poly Test Whether Points are Inside a '"gpc.poly"' Polygon
intensity.twinstim Plotting Intensities of Infection over Time or Space
intensityplot Plot Paths of Point Process Intensities
intensityplot.simEpidata Plotting Paths of Infection Intensities for 'twinSIR' Models
intensityplot.simEpidataCS Plotting Intensities of Infection over Time or Space
intensityplot.twinSIR Plotting Paths of Infection Intensities for 'twinSIR' Models
intensityplot.twinstim Plotting Intensities of Infection over Time or Space
intersectPolyCircle Intersection of a Polygonal and a Circular Domain
intersectPolyCircle.gpc.poly Intersection of a Polygonal and a Circular Domain
intersectPolyCircle.owin Intersection of a Polygonal and a Circular Domain
intersectPolyCircle.SpatialPolygons Intersection of a Polygonal and a Circular Domain
intersperse Impute Blocks for Extra Stops in '"epidata"' Objects
isoWeekYear Find ISO week and ISO year of a vector of Date objects

-- K --

k1 RKI SurvStat Data
ks.plot.unif Plot the ECDF of a uniform sample with Kolmogorov-Smirnov bounds

-- L --

linelist2sts Convert individual case information based on dates into an aggregated time series
LLR.fun Run length computation of a CUSUM detector
logLik.ah4 Print, Summary and Extraction Methods for '"ah4"' Objects
logLik.twinSIR Print, Summary and Extraction Methods for '"twinSIR"' Objects
logLik.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
logS Adjust observed epidemic curve for reporting delay of cases
LRCUSUM.runlength Run length computation of a CUSUM detector

-- M --

m1 RKI SurvStat Data
m2 RKI SurvStat Data
m3 RKI SurvStat Data
m4 RKI SurvStat Data
m5 RKI SurvStat Data
magic.dim Returns a suitable k1 x k2 for plotting the disProgObj
makePlot Plot Generation
marks Class for Representing Continuous Space-Time Point Process Data
marks.epidataCS Class for Representing Continuous Space-Time Point Process Data
measles.weser Measles epidemics in Lower Saxony in 2001-2002
measlesDE Measles in the 16 states of Germany
meningo.age Meningococcal infections in France 1985-1995
MMRcoverageDE MMR coverage levels in the 16 states of Germany
momo Danish 1994-2008 all cause mortality data for six age groups
multinomialTS Generic functions to access '"sts"' slots
multinomialTS-method Class '"sts"' - surveillance time series
multinomialTS<- Generic functions to access '"sts"' slots
multinomialTS<--method Class '"sts"' - surveillance time series
multiplicity Count Number of Instances of Points
multiplicity.default Count Number of Instances of Points
multiplicity.Spatial Count Number of Instances of Points

-- N --

n1 RKI SurvStat Data
n2 RKI SurvStat Data
naninf2zero Non-parametric back-projection of incidence cases to exposure cases using a known incubation time as in Becker et al (1991).
nbOrder Determine Neighbourhood Order Matrix from Binary Adjacency Matrix
ncol-method Class '"sts"' - surveillance time series
neighbourhood Generic functions to access '"sts"' slots
neighbourhood-method Class '"sts"' - surveillance time series
neighbourhood<- Generic functions to access '"sts"' slots
neighbourhood<--method Class '"sts"' - surveillance time series
nobs.epidataCS Class for Representing Continuous Space-Time Point Process Data
nobs.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
nowcast Adjust observed epidemic curve for reporting delay of cases
nowcast.fit Adjust observed epidemic curve for reporting delay of cases
nrow-method Class '"sts"' - surveillance time series

-- O --

observed Generic functions to access '"sts"' slots
observed-method Class '"sts"' - surveillance time series
observed<- Generic functions to access '"sts"' slots
observed<--method Class '"sts"' - surveillance time series
oneStepAhead Predictive Model Assessment for HHH4 models
outbreakP Multivariate Surveillance through independent univariate algorithms
outcomeFunStandard Run length computation of a CUSUM detector
outside.ci Adjust observed epidemic curve for reporting delay of cases

-- P --

pairedbinCUSUM Paired binary CUSUM and its run-length computation
pairedbinCUSUM.LLRcompute Paired binary CUSUM and its run-length computation
pairedbinCUSUM.runlength Paired binary CUSUM and its run-length computation
permutationTest Random effects HHH model fit as described in Paul and Held (2011)
pit Random effects HHH model fit as described in Paul and Held (2011)
plot-method Display Methods for Surveillance Time-Series Objects
plot.atwins Plot results of a twins model fit
plot.disProg Plot Generation of the Observed and the defined Outbreak States of a (multivariate) time series
plot.disProg.one Plot Generation of the Observed and the defined Outbreak States of a (multivariate) time series
plot.epidata Plotting the Evolution of an Epidemic
plot.epidataCS Plotting the Events of an Epidemic over Time and Space
plot.sts.alarm Display Methods for Surveillance Time-Series Objects
plot.sts.spacetime Display Methods for Surveillance Time-Series Objects
plot.sts.time Display Methods for Surveillance Time-Series Objects
plot.sts.time.one Display Methods for Surveillance Time-Series Objects
plot.summary.epidata Plotting the Evolution of an Epidemic
plot.survRes Plot a survRes object
plot.survRes.one Plot a survRes object
plot.twinSIR Plotting Paths of Infection Intensities for 'twinSIR' Models
plot.twinstim Plot methods for fitted 'twinstim"s
poly2adjmat Derive Adjacency Structure of '"SpatialPolygons"'
polyAtBorder Indicate Polygons at the Border
population Generic functions to access '"sts"' slots
population-method Class '"sts"' - surveillance time series
population<- Generic functions to access '"sts"' slots
population<--method Class '"sts"' - surveillance time series
powerlaw Power-Law Neighbourhood Weights for 'hhh4' Models
predict.ah Predictions from a HHH model
predict.ah4 Predictions from a 'hhh4' Model
predict.ahg Predictions from a HHH model
primeFactors Prime number factorization
print.ah Model fit based on the Held, Hoehle, Hofman paper
print.ah4 Print, Summary and Extraction Methods for '"ah4"' Objects
print.ahg Function to try multiple starting values
print.algoQV Print quality value object
print.disProg Creating an object of class disProg
print.epidata Class for Epidemic Data Discrete in Space and Continuous in Time
print.epidataCS Class for Representing Continuous Space-Time Point Process Data
print.summary.epidata Summarizing an Epidemic
print.summary.epidataCS Class for Representing Continuous Space-Time Point Process Data
print.summary.twinSIR Print, Summary and Extraction Methods for '"twinSIR"' Objects
print.summary.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
print.twinSIR Print, Summary and Extraction Methods for '"twinSIR"' Objects
print.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
profile.twinSIR Profile Likelihood Computation and Confidence Intervals
profile.twinstim Profile Likelihood Computation and Confidence Intervals for 'twinstim' objects

-- Q --

q1_nrwh RKI SurvStat Data
q2 RKI SurvStat Data
qlomax Quantile Function of the Lomax Distribution

-- R --

R0 Computes basic reproduction numbers from fitted models
R0.simEpidataCS Computes basic reproduction numbers from fitted models
R0.twinstim Computes basic reproduction numbers from fitted models
ranef Print, Summary and Extraction Methods for '"ah4"' Objects
ranef.ah4 Print, Summary and Extraction Methods for '"ah4"' Objects
readData Reading of Disease Data
refvalIdxByDate Compute indices of reference value using Date class
reset.surveillance.options Options of the 'surveillance' Package
residuals.ah Residuals from a HHH model
residuals.ahg Residuals from a HHH model
residuals.twinSIR Extract Cox-Snell-like Residuals of a Fitted Point Process
residuals.twinstim Extract Cox-Snell-like Residuals of a Fitted Point Process
ri Specify Formulae in a Random Effects HHH Model
rki Multivariate Surveillance through independent univariate algorithms
RPS Adjust observed epidemic curve for reporting delay of cases
runifdisc Sample Points Uniformly on a Disc

-- S --

s1 RKI SurvStat Data
s2 RKI SurvStat Data
s3 RKI SurvStat Data
salmonella.agona Salmonella Agona cases in the UK 1990-1995
scale.gpc.poly Centering and Scaling a '"gpc.poly"' Polygon
scores Predictive Model Assessment for HHH4 models
shadar Salmonella Hadar cases in Germany 2001-2006
show-method Display Methods for Surveillance Time-Series Objects
siaf.constant Temporal and Spatial Interaction Functions for 'twinstim'
siaf.gaussian Temporal and Spatial Interaction Functions for 'twinstim'
siaf.lomax Temporal and Spatial Interaction Functions for 'twinstim'
siaf.powerlaw Temporal and Spatial Interaction Functions for 'twinstim'
siaf.powerlawL Temporal and Spatial Interaction Functions for 'twinstim'
sim.pointSource Generation of Simulated Point Source Epidemy
sim.seasonalNoise Generation of Background Noise for Simulated Timeseries
simEpidata Simulation of Epidemic Data
simEpidataCS Simulation of a Self-Exciting Spatio-Temporal Point Process
simHHH Simulates data based on the model proposed by Held et. al (2005)
simHHH.ah Simulates data based on the model proposed by Held et. al (2005)
simHHH.default Simulates data based on the model proposed by Held et. al (2005)
simulate.ah4 Simulates data based on the model proposed by Paul and Held (2011)
simulate.twinSIR Simulation of Epidemic Data
simulate.twinstim Simulation of a Self-Exciting Spatio-Temporal Point Process
stateplot Plotting the Evolution of an Epidemic
stcd Spatio-temporal cluster detection
stepComponent Stepwise Model Selection by AIC
sts-class Class '"sts"' - surveillance time series
sts2disProg Convert disProg object to sts and vice versa
stsBP-class Class "stsBP" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting or nowcasting surveillance time series
subset.epidataCS Class for Representing Continuous Space-Time Point Process Data
summary.ah4 Print, Summary and Extraction Methods for '"ah4"' Objects
summary.epidata Summarizing an Epidemic
summary.epidataCS Class for Representing Continuous Space-Time Point Process Data
summary.twinSIR Print, Summary and Extraction Methods for '"twinSIR"' Objects
summary.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
surveillance Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
surveillance.options Options of the 'surveillance' Package

-- T --

tail.epidataCS Class for Representing Continuous Space-Time Point Process Data
test Print xtable for several diseases and the summary
testSim Print xtable for a Simulated Disease and the Summary
tiaf.constant Temporal and Spatial Interaction Functions for 'twinstim'
tiaf.exponential Temporal and Spatial Interaction Functions for 'twinstim'
toFileDisProg Writing of Disease Data
toLatex.summary.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
twinSIR Fit an Additive-Multiplicative Intensity Model for SIR Data
twinstim Fit a Two-Component Spatio-Temporal Point Process Model

-- U --

unionSpatialPolygons Compute the Unary Union of '"SpatialPolygons"'
untie Randomly Break Ties in Data
untie.default Randomly Break Ties in Data
untie.epidataCS Randomly Break Ties in Data
untie.matrix Randomly Break Ties in Data
update.epidataCS Update method for '"epidataCS"'
update.twinstim 'update'-method for '"twinstim"'
upperbound Generic functions to access '"sts"' slots
upperbound-method Class '"sts"' - surveillance time series
upperbound<- Generic functions to access '"sts"' slots
upperbound<--method Class '"sts"' - surveillance time series

-- V --

vcov.twinSIR Print, Summary and Extraction Methods for '"twinSIR"' Objects
vcov.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects

-- W --

wrap.algo Multivariate Surveillance through independent univariate algorithms

-- X --

xtable.algoQV Xtable quality value object
xtable.summary.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
xtable.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects

-- Y --

year Class '"sts"' - surveillance time series
year-method Class '"sts"' - surveillance time series

-- Z --

zetaweights Power-Law Weights According to Neighbourhood Order

-- misc --

[-method Extraction and Subsetting of 'sts' objects
[.epidata Class for Epidemic Data Discrete in Space and Continuous in Time
[.epidataCS Class for Representing Continuous Space-Time Point Process Data