Man pages for surveillance
Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

abattoirAbattoir Data
addFormattedXAxisFormatted Time Axis for '"sts"' Objects
addSeason2formulaAdd Harmonics to an Existing Formula
aggregate.disProgAggregate a 'disProg' Object
algo.bayesThe Bayes System
algo.callQuery Transmission to Specified Surveillance Algorithm
algo.cdcThe CDC Algorithm
algo.compareComparison of Specified Surveillance Systems using Quality...
algo.cusumCUSUM method
algo.farringtonSurveillance for Count Time Series Using the Classic...
algo.farrington.assign.weightsAssign weights to base counts
algo.farrington.fitGLMFit Poisson GLM of the Farrington procedure for a single time...
algo.farrington.thresholdCompute prediction interval for a new observation
algo.glrnbCount Data Regression Charts
algo.hmmHidden Markov Model (HMM) method
algo.outbreakPSemiparametric surveillance of outbreaks
algo.qualityComputation of Quality Values for a Surveillance System...
algo.rkiThe system used at the RKI
algo.rogersonModified CUSUM method as proposed by Rogerson and Yamada...
algo.summarySummary Table Generation for Several Disease Chains
algo.twinsFit a Two-Component Epidemic Model using MCMC
all.equalTest if Two Model Fits are (Nearly) Equal
animateGeneric animation of spatio-temporal objects
anscombe.residualsCompute Anscombe Residuals
arlCusumCalculation of Average Run Length for discrete CUSUM schemes
backprojNPNon-parametric back-projection of incidence cases to exposure...
bestCombinationPartition of a number into two factors
bodaBayesian Outbreak Detection Algorithm (BODA)
bodaDelayBayesian Outbreak Detection in the Presence of Reporting...
calibrationCalibration Tests for Poisson or Negative Binomial...
campyDECampylobacteriosis and Absolute Humidity in Germany 2002-2011
categoricalCUSUMCUSUM detector for time-varying categorical time series
checkResidualProcessCheck the residual process of a fitted 'twinSIR' or...
clapplyConditional 'lapply'
coeflistList Coefficients by Model Component
create.disProgCreating an object of class 'disProg' (DEPRECATED)
delevalSurgical Failures Data
discpolyPolygonal Approximation of a Disc/Circle
disProg2stsConvert disProg object to sts and vice versa
earsCSurveillance for a count data time series using the EARS C1,...
epidataContinuous-Time SIR Event History of a Fixed Population
epidata_animateSpatio-Temporal Animation of an Epidemic
epidataCSContinuous Space-Time Marked Point Patterns with Grid-Based...
epidataCS_aggregateConversion (aggregation) of '"epidataCS"' to '"epidata"' or...
epidataCS_animateSpatio-Temporal Animation of a Continuous-Time...
epidataCS_permuteRandomly Permute Time Points or Locations of '"epidataCS"'
epidataCS_plotPlotting the Events of an Epidemic over Time and Space
epidataCS_updateUpdate method for '"epidataCS"'
epidata_intersperseImpute Blocks for Extra Stops in '"epidata"' Objects
epidata_plotPlotting the Evolution of an Epidemic
epidata_summarySummarizing an Epidemic
estimateGLRNbHookHook function for in-control mean estimation
fanplotFan Plot of Forecast Distributions
farringtonFlexibleSurveillance for Univariate Count Time Series Using an...
findHFind decision interval for given in-control ARL and reference...
findKFind Reference Value
find.khDetermine the k and h values in a standard normal setting
fluBYBWInfluenza in Southern Germany
formatDateConvert Dates to Character (Including Quarter Strings)
formatPvalPretty p-Value Formatting
glm_epidataCSFit an Endemic-Only 'twinstim' as a Poisson-'glm'
haHepatitis A in Berlin
hagelloch1861 Measles Epidemic in the City of Hagelloch, Germany
hcl.colorsHCL-based Heat Colors from the 'colorspace' Package
hepatitisAHepatitis A in Germany
hhh4Fitting HHH Models with Random Effects and Neighbourhood...
hhh4_formulaSpecify Formulae in a Random Effects HHH Model
hhh4_internalsInternal Functions Dealing with 'hhh4' Models
hhh4_methodsPrint, Summary and other Standard Methods for '"hhh4"'...
hhh4_plotPlots for Fitted 'hhh4'-models
hhh4_predictPredictions from a 'hhh4' Model
hhh4_simulateSimulate '"hhh4"' Count Time Series
hhh4_simulate_plotPlot Simulations from '"hhh4"' Models
hhh4_simulate_scoresProper Scoring Rules for Simulations from 'hhh4' Models
hhh4_update'update' a fitted '"hhh4"' model
hhh4_validationPredictive Model Assessment for 'hhh4' Models
hhh4_WPower-Law and Nonparametric Neighbourhood Weights for...
hhh4_W_utilsExtract Neighbourhood Weights from a Fitted 'hhh4' Model
husO104HospHospitalization date for HUS cases of the STEC outbreak in...
imdepiOccurrence of Invasive Meningococcal Disease in Germany
influMenInfluenza and meningococcal infections in Germany, 2001-2006
intensityplotPlot Paths of Point Process Intensities
intersectPolyCircleIntersection of a Polygonal and a Circular Domain
isoWeekYearFind ISO Week and Year of Date Objects
isScalarChecks if the Argument is Scalar
knoxKnox Test for Space-Time Interaction
ks.plot.unifPlot the ECDF of a uniform sample with Kolmogorov-Smirnov...
layout.labelsLayout Items for 'spplot'
linelist2stsConvert Dates of Individual Case Reports into a Time Series...
LRCUSUM.runlengthRun length computation of a CUSUM detector
m1RKI SurvStat Data
magic.dimCompute Suitable k1 x k2 Layout for Plotting
makeControlGenerate 'control' Settings for an 'hhh4' Model
marksImport from package 'spatstat.geom'
measlesDEMeasles in the 16 states of Germany
measles.weserMeasles in the Weser-Ems region of Lower Saxony, Germany,...
meningo.ageMeningococcal infections in France 1985-1997
MMRcoverageDEMMR coverage levels in the 16 states of Germany
momoDanish 1994-2008 all-cause mortality data for eight age...
multiplicityImport from package 'spatstat.geom'
multiplicity.SpatialCount Number of Instances of Points
nbOrderDetermine Neighbourhood Order Matrix from Binary Adjacency...
nowcastAdjust a univariate time series of counts for observed...
pairedbinCUSUMPaired binary CUSUM and its run-length computation
permutationTestMonte Carlo Permutation Test for Paired Individual Scores
pitNon-Randomized Version of the PIT Histogram (for Count Data)
plapplyVerbose and Parallel 'lapply'
plot.atwinsPlots for Fitted 'algo.twins' Models
plot.disProgPlot Observed Counts and Defined Outbreak States of a...
plot.survResPlot a 'survRes' object
poly2adjmatDerive Adjacency Structure of '"SpatialPolygons"'
polyAtBorderIndicate Polygons at the Border
primeFactorsPrime Number Factorization
print.algoQVPrint Quality Value Object
R0Computes reproduction numbers from fitted models
ranefImport from package 'nlme'
refvalIdxByDateCompute indices of reference value using Date class
residualsCTExtract Cox-Snell-like Residuals of a Fitted Point Process
rotaBBRotavirus cases in Brandenburg, Germany, during 2002-2013...
runifdiscSample Points Uniformly on a Disc
salmAllOnsetSalmonella cases in Germany 2001-2014 by data of symptoms...
salmHospitalizedHospitalized Salmonella cases in Germany 2004-2014
salmNewportSalmonella Newport cases in Germany 2004-2013
salmonella.agonaSalmonella Agona cases in the UK 1990-1995
scoresProper Scoring Rules for Poisson or Negative Binomial...
shadarSalmonella Hadar cases in Germany 2001-2006
sim.pointSourceSimulate Point-Source Epidemics
sim.seasonalNoiseGeneration of Background Noise for Simulated Timeseries
stcdSpatio-temporal cluster detection
stKDiggle et al (1995) K-function test for space-time clustering
stsAggregateAggregate an '"sts"' Object Over Time or Across Units
sts_animateAnimated Maps and Time Series of Disease Counts or Incidence
stsBP-classClass "stsBP" - a class inheriting from class 'sts' which...
sts-classClass '"sts"' - surveillance time series
sts_creationSimulate Count Time Series with Outbreaks
sts_ggplotTime-Series Plots for '"sts"' Objects Using 'ggplot2'
stsNC-classClass "stsNC" - a class inheriting from class 'sts' which...
stsNClist_animateAnimate a Sequence of Nowcasts
stsNewportSalmonella Newport cases in Germany 2001-2015
sts_observationCreate an 'sts' object with a given observation date
stsplotPlot Methods for Surveillance Time-Series Objects
stsplot_spaceMap of Disease Counts/Incidence accumulated over a Given...
stsplot_spacetimeAnimated Map of Disease Incidence (DEPRECATED)
stsplot_timeTime-Series Plots for '"sts"' Objects
stsSlotsGeneric Functions to Access '"sts"' Slots
sts_tidyConvert an '"sts"' Object to a Data Frame in Long (Tidy)...
stsXtrctSubsetting '"sts"' Objects
surveillance-defunctDefunct Functions in Package 'surveillance'
surveillance.optionsOptions of the 'surveillance' Package
toLatex.sts'toLatex'-Method for '"sts"' Objects
twinSIRFit an Additive-Multiplicative Intensity Model for SIR Data
twinSIR_coxIdentify Endemic Components in an Intensity Model
twinSIR_exDataToy Data for 'twinSIR'
twinSIR_intensityplotPlotting Paths of Infection Intensities for 'twinSIR' Models
twinSIR_methodsPrint, Summary and Extraction Methods for '"twinSIR"' Objects
twinSIR_profileProfile Likelihood Computation and Confidence Intervals
twinSIR_simulationSimulation of Epidemic Data
twinstimFit a Two-Component Spatio-Temporal Point Process Model
twinstim_epitestPermutation Test for Space-Time Interaction in '"twinstim"'
twinstim_iafTemporal and Spatial Interaction Functions for 'twinstim'
twinstim_iafplotPlot the Spatial or Temporal Interaction Function of a...
twinstim_intensityPlotting Intensities of Infection over Time or Space
twinstim_methodsPrint, Summary and Extraction Methods for '"twinstim"'...
twinstim_plotPlot methods for fitted 'twinstim"s
twinstim_profileProfile Likelihood Computation and Confidence Intervals for...
twinstim_siafSpatial Interaction Function Objects
twinstim_siaf_simulatePCSimulation from an Isotropic Spatial Kernel via Polar...
twinstim_simEndemicEventsQuick Simulation from an Endemic-Only 'twinstim'
twinstim_simulationSimulation of a Self-Exciting Spatio-Temporal Point Process
twinstim_stepStepwise Model Selection by AIC
twinstim_tiafTemporal Interaction Function Objects
twinstim_update'update'-method for '"twinstim"'
unionSpatialPolygonsCompute the Unary Union of '"SpatialPolygons"'
untieRandomly Break Ties in Data
wrap.algoMultivariate Surveillance through independent univariate...
xtable.algoQVXtable quality value object
zetaweightsPower-Law Weights According to Neighbourhood Order
surveillance documentation built on Nov. 2, 2023, 6:05 p.m.