Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena


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Documentation for package ‘surveillance’ version 1.10-0

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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
addFormattedXAxis Formatted Time Axis for '"sts"' Objects
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.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 Algorithm
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 Count 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.sts Animated Maps and Time Series of Disease Incidence
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 Continuous-Time SIR Event History of a Fixed Population
as.epidata.data.frame Continuous-Time SIR Event History of a Fixed Population
as.epidata.default Continuous-Time SIR Event History of a Fixed Population
as.epidata.epidataCS Conversion (aggregation) of '"epidataCS"' to '"epidata"' or '"sts"'
as.epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
as.hhh4simslist Summarize Simulations from '"hhh4"' Models
as.stepfun.epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
as.xts.sts Class '"sts"' - surveillance time series
at2ndChange Formatted Time Axis for '"sts"' Objects
atChange Formatted Time Axis for '"sts"' Objects
atMedian Formatted Time Axis for '"sts"' Objects

-- 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
boda Surveillance for an univariate count data time series using the Bayesian Outbreak Detection Algorithm (BODA) described in Manitz and Hoehle (2013)
bodaDelay Bayesian aberration detection in presence of reporting delays.

-- C --

calc.outbreakP.statistic Semiparametric surveillance of outbreaks
calibrationTest Calibration Test for Poisson or Negative Binomial Predictions
calibrationTest.default Calibration Test for Poisson or Negative Binomial Predictions
calibrationTest.hhh4 Test Calibration of a 'hhh4' Model
calibrationTest.oneStepAhead Predictive Model Assessment for 'hhh4' Models
campyDE Cases of Campylobacteriosis and Absolute Humidity in Germany 2002-2011
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.ahg Function to try multiple starting values
coef.epitest Permutation Test for Space-Time Interaction in '"twinstim"'
coef.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
coeflist List Coefficients by Model Component
coeflist.default List Coefficients by Model Component
coeflist.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
coeflist.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
coerce-method Class '"sts"' - surveillance time series
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
coerce-method Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
compMatrix.writeTable Latex Table Generation
confint.hhh4 Print, Summary and other Standard Methods for '"hhh4"' 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 --

delayCDF Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
delayCDF-method Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
deleval Surgical failures data
dim-method Class '"sts"' - surveillance time series
dimnames-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 a univariate time series of counts for observed but-not-yet-reported events
drop1.twinstim Stepwise Model Selection by AIC
dss Calibration Test for Poisson or Negative Binomial Predictions

-- 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 Continuous-Time SIR Event History of a Fixed Population
epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
epidataCS2sts Conversion (aggregation) of '"epidataCS"' to '"epidata"' or '"sts"'
epidataCSplot_space Plotting the Events of an Epidemic over Time and Space
epidataCSplot_time Plotting the Events of an Epidemic over Time and Space
epitest Permutation Test for Space-Time Interaction in '"twinstim"'
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 other Standard Methods for '"hhh4"' Objects
fixef.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
fluBYBW Influenza in Southern Germany
formatDate Find ISO week and ISO year of a vector of Date objects on Windows
formatPval Pretty p-Value Formatting
formula.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects

-- G --

getMaxEV Plots for Fitted 'hhh4'-models
getMaxEV_season Plots for Fitted 'hhh4'-models
glm_epidataCS Fit an Endemic-Only 'twinstim' as a Poisson-'glm'
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 Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
hepatitisA Hepatitis A in Germany
hhh4 Fitting HHH Models with Random Effects and Neighbourhood Structure
husO104Hosp Hospitalization date for HUS cases of the STEC outbreak in Germany, 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 on Windows

-- K --

k1 RKI SurvStat Data
knox Knox Test for Space-Time Interaction
ks.plot.unif Plot the ECDF of a uniform sample with Kolmogorov-Smirnov bounds

-- L --

layout.labels Layout Items for 'spplot'
layout.scalebar Layout Items for 'spplot'
linelist2sts Convert individual case information based on dates into an aggregated time series of counts
LLR.fun Run length computation of a CUSUM detector
logLik.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
logLik.twinSIR Print, Summary and Extraction Methods for '"twinSIR"' Objects
logLik.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
logS Adjust a univariate time series of counts for observed but-not-yet-reported events
logs Calibration Test for Poisson or Negative Binomial Predictions
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 Import from package 'spatstat'
marks.epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
measles.weser Measles in the Weser-Ems region of Lower Saxony, Germany, 2001-2002
measlesDE Measles in the 16 states of Germany
measlesWeserEms Measles in the Weser-Ems region of Lower Saxony, Germany, 2001-2002
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 Import from package 'spatstat'
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
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 Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
nobs.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
nobs.twinstim Print, Summary and Extraction Methods for '"twinstim"' Objects
nowcast Adjust a univariate time series of counts for observed but-not-yet-reported events
nowcast.fit Adjust a univariate time series of counts for observed but-not-yet-reported events

-- 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 a univariate time series of counts for observed but-not-yet-reported events

-- 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 Monte Carlo Permutation Test for Paired Individual Scores
permute.epidataCS Randomly Permute Time Points or Locations of '"epidataCS"'
pit Non-Randomized Version of the PIT Histogram (for Count Data)
pit.default Non-Randomized Version of the PIT Histogram (for Count Data)
pit.hhh4 Predictive Model Assessment for 'hhh4' Models
pit.oneStepAhead Predictive Model Assessment for 'hhh4' Models
plapply Verbose and Parallel 'lapply'
plot-method Plot-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.epitest Permutation Test for Space-Time Interaction in '"twinstim"'
plot.hhh4 Plots for Fitted 'hhh4'-models
plot.hhh4sims Summarize Simulations from '"hhh4"' Models
plot.hhh4simslist Summarize Simulations from '"hhh4"' Models
plot.knox Knox Test for Space-Time Interaction
plot.profile.twinSIR Profile Likelihood Computation and Confidence Intervals
plot.stKtest Diggle et al (1995) K-function test for space-time clustering
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
plotHHH4sims_size Summarize Simulations from '"hhh4"' Models
plotHHH4sims_time Summarize Simulations from '"hhh4"' Models
plotHHH4_fitted Plots for Fitted 'hhh4'-models
plotHHH4_fitted1 Plots for Fitted 'hhh4'-models
plotHHH4_maps Plots for Fitted 'hhh4'-models
plotHHH4_maxEV Plots for Fitted 'hhh4'-models
plotHHH4_neweights Plots for Fitted 'hhh4'-models
plotHHH4_ri Plots for Fitted 'hhh4'-models
plotHHH4_season Plots for Fitted 'hhh4'-models
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
predict.ah Predictions from a HHH model
predict.ahg Predictions from a HHH model
predict.hhh4 Predictions from a 'hhh4' Model
primeFactors Prime number factorization
print.ah Model fit based on the Held, Hoehle, Hofman paper
print.ahg Function to try multiple starting values
print.algoQV Print quality value object
print.disProg Creating an object of class disProg
print.epidata Continuous-Time SIR Event History of a Fixed Population
print.epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
print.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
print.summary.epidata Summarizing an Epidemic
print.summary.epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
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 reproduction numbers from fitted models
R0.simEpidataCS Computes reproduction numbers from fitted models
R0.twinstim Computes reproduction numbers from fitted models
ranef Print, Summary and other Standard Methods for '"hhh4"' Objects
ranef.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
readData Reading of Disease Data
refvalIdxByDate Compute indices of reference value using Date class
reportingTriangle Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
reportingTriangle-method Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
reset.surveillance.options Options of the 'surveillance' Package
residuals.ah Residuals from a HHH model
residuals.ahg Residuals from a HHH model
residuals.simEpidataCS Extract Cox-Snell-like Residuals of a Fitted Point Process
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
rotaBB Rotavirus cases in Brandenburg, Germany, during 2002-2013 stratified by 5 age categories
RPS Adjust a univariate time series of counts for observed but-not-yet-reported events
rps Calibration Test for Poisson or Negative Binomial Predictions
runifdisc Sample Points Uniformly on a Disc

-- S --

s1 RKI SurvStat Data
s2 RKI SurvStat Data
s3 RKI SurvStat Data
salmAllOnset Salmonella cases in Germany 2001-2014 by data of symptoms onset
salmHospitalized Hospitalized Salmonella cases in Germany 2004-2014
salmNewport Salmonella Newport cases in Germany 2004-2013
salmNewportTruncated Salmonella Newport cases in Germany 2001-2011 by data of symptoms onset
salmonella.agona Salmonella Agona cases in the UK 1990-1995
scale.gpc.poly Centering and Scaling a '"gpc.poly"' Polygon
score Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
score-method Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
scores Predictive Model Assessment for 'hhh4' Models
scores.hhh4 Predictive Model Assessment for 'hhh4' Models
scores.hhh4sims Summarize Simulations from '"hhh4"' Models
scores.hhh4simslist Summarize Simulations from '"hhh4"' Models
scores.oneStepAhead Predictive Model Assessment for 'hhh4' Models
shadar Salmonella Hadar cases in Germany 2001-2006
siaf Spatial Interaction Function Objects
siaf.constant Temporal and Spatial Interaction Functions for 'twinstim'
siaf.gaussian 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'
siaf.step Temporal and Spatial Interaction Functions for 'twinstim'
siaf.student 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)
simpleR0 Computes reproduction numbers from fitted models
simulate.hhh4 Simulate '"hhh4"' Count Time Series
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
stKtest Diggle et al (1995) K-function test for space-time clustering
sts Class '"sts"' - surveillance time series
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
stsNC-class Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
stsplot Plot-Methods for Surveillance Time-Series Objects
stsplot_alarm Time-Series Plots for '"sts"' Objects
stsplot_space Map of Disease Incidence During a Given Period
stsplot_spacetime Map of Disease Incidence
stsplot_time Time-Series Plots for '"sts"' Objects
stsplot_time1 Time-Series Plots for '"sts"' Objects
sts_creation Function for simulating a time series
sts_observation Function for creating a sts-object with a given observation date
subset.epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
summary.epidata Summarizing an Epidemic
summary.epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
summary.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
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 Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
test Print xtable for several diseases and the summary
testSim Print xtable for a Simulated Disease and the Summary
tiaf Temporal Interaction Function Objects
tiaf.constant Temporal and Spatial Interaction Functions for 'twinstim'
tiaf.exponential Temporal and Spatial Interaction Functions for 'twinstim'
tiaf.step Temporal and Spatial Interaction Functions for 'twinstim'
toFileDisProg Writing of Disease Data
toLatex-method 'toLatex'-Method for (lists of) '"sts"' Objects
toLatex.sts 'toLatex'-Method for (lists of) '"sts"' Objects
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.epidata Continuous-Time SIR Event History of a Fixed Population
update.epidataCS Update method for '"epidataCS"'
update.hhh4 'update' a fitted '"hhh4"' model
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.hhh4 Print, Summary and other Standard Methods for '"hhh4"' Objects
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
W_np Power-Law and Nonparametric Neighbourhood Weights for 'hhh4'-Models
W_powerlaw Power-Law and Nonparametric Neighbourhood Weights for 'hhh4'-Models

-- 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 Continuous-Time SIR Event History of a Fixed Population
[.epidataCS Continuous Space-Time Marked Point Patterns with Grid-Based Covariates