LRCUSUM.runlength       Run length computation of a CUSUM detector
MMRcoverageDE           MMR coverage levels in the 16 states of Germany
R0                      Computes reproduction numbers from fitted
                        models
W_powerlaw              Power-Law and Nonparametric Neighbourhood
                        Weights for 'hhh4'-Models
[,sts-method            Subsetting '"sts"' Objects
abattoir                Abattoir Data
addFormattedXAxis       Formatted Time Axis for '"sts"' Objects
addSeason2formula       Add Harmonics to an Existing Formula
aggregate.sts           Aggregate an '"sts"' Object Over Time or Across
                        Units
alarms                  Generic Functions to Access '"sts"' Slots
algo.bayes              The Bayes System
algo.call               Query Transmission to Specified Surveillance
                        Algorithm
algo.cdc                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.threshold
                        Compute prediction interval for a new
                        observation
algo.glrnb              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.rogerson           Modified CUSUM method as proposed by Rogerson
                        and Yamada (2004)
algo.summary            Summary Table Generation for Several Disease
                        Chains
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
anscombe.residuals      Compute Anscombe Residuals
arlCusum                Calculation of Average Run Length for discrete
                        CUSUM schemes
as.ts.sts               Convert an '"sts"' Object to '"ts"' or '"xts"'
autoplot.sts            Time-Series Plots for '"sts"' Objects Using
                        'ggplot2'
backprojNP              Non-parametric back-projection of incidence
                        cases to exposure cases using a known
                        incubation time as in Becker et al (1991)
bestCombination         Partition of a number into two factors
boda                    Bayesian Outbreak Detection Algorithm (BODA)
bodaDelay               Bayesian Outbreak Detection in the Presence of
                        Reporting Delays
calibrationTest         Calibration Tests for Poisson or Negative
                        Binomial Predictions
campyDE                 Campylobacteriosis and Absolute Humidity in
                        Germany 2002-2011
categoricalCUSUM        CUSUM detector for time-varying categorical
                        time series
checkResidualProcess    Check the residual process of a fitted
                        'twinSIR' or 'twinstim'
clapply                 Conditional 'lapply'
coeflist                List Coefficients by Model Component
cox                     Identify Endemic Components in an Intensity
                        Model
deleval                 Surgical Failures Data
disProg2sts             Convert disProg object to sts and vice versa
discpoly                Polygonal Approximation of a Disc/Circle
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"'
epitest                 Permutation Test for Space-Time Interaction in
                        '"twinstim"'
fanplot                 Fan Plot of Forecast Distributions
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
fluBYBW                 Influenza in Southern Germany
formatDate              Convert Dates to Character (Including Quarter
                        Strings)
formatPval              Pretty p-Value Formatting
getNEweights            Extract Neighbourhood Weights from a Fitted
                        'hhh4' Model
glm_epidataCS           Fit an Endemic-Only 'twinstim' as a
                        Poisson-'glm'
ha                      Hepatitis A in Berlin
hagelloch               1861 Measles Epidemic in the City of Hagelloch,
                        Germany
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
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
intensityplot           Plot Paths of Point Process Intensities
intensityplot.twinstim
                        Plotting Intensities of Infection over Time or
                        Space
intersectPolyCircle     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
knox                    Knox Test for Space-Time Interaction
ks.plot.unif            Plot the ECDF of a uniform sample with
                        Kolmogorov-Smirnov bounds
layout.labels           Layout Items for 'spplot'
linelist2sts            Convert Dates of Individual Case Reports into a
                        Time Series of Counts
m1                      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'
measles.weser           Measles in the Weser-Ems region of Lower
                        Saxony, Germany, 2001-2002
measlesDE               Measles in the 16 states of Germany
meningo.age             Meningococcal infections in France 1985-1997
momo                    Danish 1994-2008 all-cause mortality data for
                        eight age groups
multiplicity            Import from package 'spatstat.geom'
multiplicity.Spatial    Count Number of Instances of Points
nbOrder                 Determine Neighbourhood Order Matrix from
                        Binary Adjacency Matrix
nowcast                 Adjust a univariate time series of counts for
                        observed but-not-yet-reported events
oneStepAhead            Predictive Model Assessment for 'hhh4' Models
pairedbinCUSUM          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)
plapply                 Verbose and Parallel 'lapply'
plot.epidata            Plotting the Evolution of an Epidemic
plot.epidataCS          Plotting the Events of an Epidemic over Time
                        and Space
plot.hhh4               Plots for Fitted 'hhh4'-models
plot.hhh4sims           Plot Simulations from '"hhh4"' Models
plot.twinSIR            Plotting Paths of Infection Intensities for
                        'twinSIR' Models
plot.twinstim           Plots for a Fitted 'twinstim'
poly2adjmat             Derive Adjacency Structure of
                        '"SpatialPolygons"'
polyAtBorder            Indicate Polygons at the Border
predict.hhh4            Predictions from a 'hhh4' Model
primeFactors            Prime Number Factorization
print.algoQV            Print Quality Value Object
print.hhh4              Print, Summary and other Standard Methods for
                        '"hhh4"' 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
ranef                   Import from package 'nlme'
refvalIdxByDate         Compute indices of reference value using Date
                        class
residuals.twinSIR       Extract Cox-Snell-like Residuals of a Fitted
                        Point Process
rotaBB                  Rotavirus cases in Brandenburg, Germany, during
                        2002-2013 stratified by 5 age categories
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
scores                  Proper Scoring Rules for Poisson or Negative
                        Binomial Predictions
scores.hhh4sims         Proper Scoring Rules for Simulations from
                        'hhh4' Models
shadar                  Salmonella Hadar cases in Germany 2001-2006
siaf                    Spatial Interaction Function Objects
siaf.constant           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
simulate.hhh4           Simulate '"hhh4"' Count Time Series
stKtest                 Diggle et al (1995) K-function test for
                        space-time clustering
stcd                    Spatio-temporal cluster detection
stepComponent           Stepwise Model Selection by AIC
sts-class               Class '"sts"' - surveillance time series
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
sts_creation            Simulate Count Time Series with Outbreaks
sts_observation         Create an 'sts' object with a given observation
                        date
stsplot                 Plot Methods for Surveillance Time-Series
                        Objects
stsplot_space           Map of Disease Counts/Incidence accumulated
                        over a Given Period
stsplot_time            Time-Series Plots for '"sts"' Objects
summary.epidata         Summarizing an Epidemic
surveillance-package    'surveillance': Temporal and Spatio-Temporal
                        Modeling and Monitoring of Epidemic Phenomena
surveillance.options    Options of the 'surveillance' Package
tiaf                    Temporal Interaction Function Objects
tidy.sts                Convert an '"sts"' Object to a Data Frame in
                        Long (Tidy) Format
toLatex.sts             'toLatex'-Method for '"sts"' Objects
twinSIR                 Fit an Additive-Multiplicative Intensity Model
                        for SIR Data
twinstim                Fit a Two-Component Spatio-Temporal Point
                        Process Model
unionSpatialPolygons    Compute the Unary Union of '"SpatialPolygons"'
untie                   Randomly Break Ties in Data
update.epidataCS        Update method for '"epidataCS"'
update.hhh4             'update' a fitted '"hhh4"' model
update.twinstim         'update'-method for '"twinstim"'
wrap.algo               Multivariate Surveillance through independent
                        univariate algorithms
zetaweights             Power-Law Weights According to Neighbourhood
                        Order
