# Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

## Documentation for package ‘surveillance’ version 1.26.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P Q R S T U V W X Y Z misc

surveillance-package | 'surveillance': 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 | Add Harmonics to an Existing Formula
aggregate-method | Aggregate an '"sts"' Object Over Time or Across Units
aggregate.hhh4sims | Plot Simulations from '"hhh4"' Models
aggregate.hhh4simslist | Plot Simulations from '"hhh4"' Models
aggregate.sts | Aggregate an '"sts"' Object Over Time or Across Units
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 Count Time Series Using the Classic Farrington Method
algo.farrington.assign.weights | Assign weights to base counts
algo.farrington.fitGLM | Fit Poisson GLM of the Farrington procedure for a single time point
algo.farrington.fitGLM.fast | Fit Poisson GLM of the Farrington procedure for a single time point
algo.farrington.fitGLM.populationOffset | Fit 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 | Count Data Regression Charts
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
all.equal.hhh4 | Test if Two Model Fits are (Nearly) Equal
all.equal.twinstim | Test if Two Model Fits are (Nearly) Equal
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 Counts or Incidence
animate.summary.epidata | Spatio-Temporal Animation of an Epidemic
animate_nowcasts | Animate a Sequence of Nowcasts
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.data.frame.sts | 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 | Plot Simulations from '"hhh4"' Models
as.stepfun.epidataCS | Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
as.ts.sts | Class '"sts"' - surveillance time series
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
autoplot.sts | Time-Series Plots for '"sts"' Objects Using 'ggplot2'

## -- B --

backprojNP | 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 | Bayesian Outbreak Detection Algorithm (BODA)
bodaDelay | Bayesian Outbreak Detection in the Presence of Reporting Delays

## -- C --

calc.outbreakP.statistic | Semiparametric surveillance of outbreaks
calibrationTest | Calibration Tests for Poisson or Negative Binomial Predictions
calibrationTest.default | Calibration Tests for Poisson or Negative Binomial Predictions
calibrationTest.hhh4 | Predictive Model Assessment for 'hhh4' Models
calibrationTest.oneStepAhead | Predictive Model Assessment for 'hhh4' Models
campyDE | 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'
clapply | Conditional 'lapply'
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
coefW | Extract Neighbourhood Weights from a Fitted 'hhh4' Model
coerce-method | Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
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
confint.hhh4 | Print, Summary and other Standard Methods for '"hhh4"' Objects
confint.oneStepAhead | Predictive Model Assessment for 'hhh4' Models
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
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
drop1.twinstim | Stepwise Model Selection by AIC
dss | Proper Scoring Rules for Poisson or Negative Binomial Predictions

## -- E --

earsC | Surveillance for a count data time series using the EARS C1, C2 or C3 method and its extensions
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
extractAIC.twinSIR | Print, Summary and Extraction Methods for '"twinSIR"' Objects

## -- F --

fanplot | Fan Plot of Forecast Distributions
farrington | Surveillance for Count Time Series Using the Classic Farrington Method
farringtonFlexible | Surveillance for Univariate Count Time Series Using an Improved Farrington Method
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 | Import from package 'nlme'
fixef.hhh4 | Print, Summary and other Standard Methods for '"hhh4"' Objects
fluBYBW | Influenza in Southern Germany
formatDate | Convert Dates to Character (Including Quarter Strings)
formatPval | Pretty p-Value Formatting
formula.hhh4 | Print, Summary and other Standard Methods for '"hhh4"' Objects
frequency-method | Class '"sts"' - surveillance time series

## -- G --

getMaxEV | Plots for Fitted 'hhh4'-models
getMaxEV_season | Plots for Fitted 'hhh4'-models
getNEweights | Extract Neighbourhood Weights from a Fitted 'hhh4' Model
getSourceDists | Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
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 | Example 'twinstim' Fit for the 'imdepi' Data
influMen | Influenza and meningococcal infections in Germany, 2001-2006
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.owin | Intersection of a Polygonal and a Circular Domain
intersperse | Impute Blocks for Extra Stops in '"epidata"' Objects
isoWeekYear | Find ISO Week and Year of Date Objects

## -- 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 Dates of Individual Case Reports into a Time Series of Counts
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 | Proper Scoring Rules 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 | Compute Suitable k1 x k2 Layout for Plotting
makeControl | Generate 'control' Settings for an 'hhh4' Model
marks | Import from package 'spatstat.geom'
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 1985-1997
MMRcoverageDE | MMR coverage levels in the 16 states of Germany
momo | Danish 1994-2008 all-cause mortality data for eight 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.geom'
multiplicity.Spatial | Count Number of Instances of Points

## -- N --

n1 | RKI SurvStat Data
n2 | RKI SurvStat Data
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

## -- 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

## -- 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.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 | Plot Simulations from '"hhh4"' Models
plot.hhh4simslist | Plot Simulations from '"hhh4"' Models
plot.knox | Knox Test for Space-Time Interaction
plot.oneStepAhead | Predictive Model Assessment for 'hhh4' Models
plot.profile.twinSIR | Profile Likelihood Computation and Confidence Intervals
plot.stKtest | Diggle et al (1995) K-function test for space-time clustering
plot.sts | Plot Methods for Surveillance Time-Series Objects
plot.summary.epidata | Plotting the Evolution of an Epidemic
plot.twinSIR | Plotting Paths of Infection Intensities for 'twinSIR' Models
plot.twinstim | Plots for a Fitted 'twinstim'
plotHHH4sims_fan | Plot Simulations from '"hhh4"' Models
plotHHH4sims_size | Plot Simulations from '"hhh4"' Models
plotHHH4sims_time | Plot 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.hhh4 | Predictions from a 'hhh4' Model
predint | Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
predint-method | Class "stsNC" - a class inheriting from class 'sts' which allows the user to store the results of back-projecting surveillance time series
primeFactors | Prime Number Factorization
print.algoQV | Print Quality Value Object
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
quantile.oneStepAhead | Predictive Model Assessment for 'hhh4' Models

## -- 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 | Import from package 'nlme'
ranef.hhh4 | Print, Summary and other Standard Methods for '"hhh4"' Objects
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.hhh4 | Print, Summary and other Standard Methods for '"hhh4"' Objects
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 | Proper Scoring Rules for Poisson or Negative Binomial Predictions

## -- 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
salmonella.agona | Salmonella Agona cases in the UK 1990-1995
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 | Proper Scoring Rules for Poisson or Negative Binomial Predictions
scores.default | Proper Scoring Rules for Poisson or Negative Binomial Predictions
scores.hhh4 | Predictive Model Assessment for 'hhh4' Models
scores.hhh4sims | Proper Scoring Rules for Simulations from 'hhh4' Models
scores.hhh4simslist | Proper Scoring Rules for Simulations from 'hhh4' Models
scores.oneStepAhead | Predictive Model Assessment for 'hhh4' Models
ses | Proper Scoring Rules for Poisson or Negative Binomial Predictions
shadar | Salmonella Hadar cases in Germany 2001-2006
siaf | Spatial Interaction Function Objects
siaf.constant | Temporal and Spatial Interaction Functions for 'twinstim'
siaf.exponential | 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.powerlaw1 | 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 | Simulate Point-Source Epidemics
sim.seasonalNoise | Generation of Background Noise for Simulated Timeseries
simEndemicEvents | Quick Simulation from an Endemic-Only 'twinstim'
simEpidata | Simulation of Epidemic Data
simEpidataCS | Simulation of a Self-Exciting Spatio-Temporal Point Process
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
start-method | Class '"sts"' - surveillance time series
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
stsNClist_animate | Animate a Sequence of Nowcasts
stsNewport | Salmonella Newport cases in Germany 2001-2015
stsplot | Plot Methods for Surveillance Time-Series Objects
stsplot_alarm | Time-Series Plots for '"sts"' Objects
stsplot_space | Map of Disease Counts/Incidence accumulated over a Given Period
stsplot_time | Time-Series Plots for '"sts"' Objects
stsplot_time1 | Time-Series Plots for '"sts"' Objects
sts_creation | Simulate Count Time Series with Outbreaks
sts_observation | Create an '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 | '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
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'
tidy.sts | Convert an '"sts"' Object to a Data Frame in Long (Tidy) Format
toLatex-method | 'toLatex'-Method for '"sts"' Objects
toLatex.knox | Knox Test for Space-Time Interaction
toLatex.sts | 'toLatex'-Method for '"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 | Computation of Quality Values for a Surveillance System Result
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 | Subsetting '"sts"' Objects
[.epidata | Continuous-Time SIR Event History of a Fixed Population
[.epidataCS | Continuous Space-Time Marked Point Patterns with Grid-Based Covariates