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

abattoirAbattoir Data
addFormattedXAxisFormatted Time Axis for '"sts"' Objects
addSeason2formulaFunction that adds a sine-/cosine formula to an existing...
aggregate.disProgAggregate the observed counts
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 a count data time series using the...
algo.farrington.assign.weightsAssign weights to base counts
algo.farrington.fitGLMFit the Poisson GLM of the Farrington procedure for a single...
algo.farrington.thresholdCompute prediction interval for a new observation
algo.glrnbCount Data Regression Charts
algo.glrpoisPoisson regression charts
algo.hhhModel fit based on the Held, Hoehle, Hofman paper
algo.hhh.gridFunction to try multiple starting values
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.twinsModel fit based on a two-component epidemic model
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
bodaSurveillance for an univariate count data time series using...
bodaDelayBayesian aberration detection in presence of reporting...
calibrationCalibration Test for Poisson or Negative Binomial Predictions
campyDECases of Campylobacteriosis and Absolute Humidity in Germany...
categoricalCUSUMCUSUM detector for time-varying categorical time series
checkResidualProcessCheck the residual process of a fitted 'twinSIR' or...
coeflistList Coefficients by Model Component
compMatrix.writeTableLatex Table Generation
correct53to52Data Correction from 53 to 52 weeks
create.disProgCreating an object of class disProg
create.gridComputes a matrix of initial values
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,...
enlargeDataData Enlargement
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
estimateGLRPoisHookHook function for in-control mean estimation
farringtonFlexibleSurveillance for an univariate count data time series using...
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
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
hepatitisAHepatitis A in Germany
hhh4Fitting HHH Models with Random Effects and Neighbourhood...
hhh4_calibrationTest Calibration of a 'hhh4' Model
hhh4_formulaSpecify Formulae in a Random Effects HHH Model
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_plotSummarize 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...
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
inside.gpc.polyTest Whether Points are Inside a '"gpc.poly"' Polygon
intensityplotPlot Paths of Point Process Intensities
intersectPolyCircleIntersection of a Polygonal and a Circular Domain
isoWeekYearFind ISO week and ISO year of a vector of Date objects on...
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 individual case information based on dates into an...
loglikelihoodCalculation of the loglikelihood needed in algo.hhh
LRCUSUM.runlengthRun length computation of a CUSUM detector
m1RKI SurvStat Data
magic.dimReturns a suitable k1 x k2 for plotting the disProgObj
make.designCreate the design matrices
makePlotPlot Generation
marksImport from package 'spatstat'
meanResponseCalculate mean response needed in algo.hhh
measlesDEMeasles in the 16 states of Germany
measles.weserMeasles in the Weser-Ems region of Lower Saxony, Germany,...
meningo.ageMeningococcal infections in France 1985-1995
MMRcoverageDEMMR coverage levels in the 16 states of Germany
momoDanish 1994-2008 all cause mortality data for six age groups
multiplicityImport from package 'spatstat'
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.atwinsPlot results of a twins model fit
plot.disProgPlot Generation of the Observed and the defined Outbreak...
plot.survResPlot a survRes object
poly2adjmatDerive Adjacency Structure of '"SpatialPolygons"'
polyAtBorderIndicate Polygons at the Border
predict.ahPredictions from a HHH model
primeFactorsPrime number factorization
print.algoQVPrint quality value object
qlomaxQuantile Function of the Lomax Distribution
R0Computes reproduction numbers from fitted models
readDataReading of Disease Data
refvalIdxByDateCompute indices of reference value using Date class
residuals.ahResiduals from a HHH model
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
salmNewportTruncatedSalmonella Newport cases in Germany 2001-2011 by data of...
salmonella.agonaSalmonella Agona cases in the UK 1990-1995
scale.gpc.polyCentering and Scaling a '"gpc.poly"' Polygon
shadarSalmonella Hadar cases in Germany 2001-2006
simHHHSimulates data based on the model proposed by Held et. al...
sim.pointSourceGeneration of Simulated Point Source Epidemy
sim.seasonalNoiseGeneration of Background Noise for Simulated Timeseries
stcdSpatio-temporal cluster detection
stKDiggle et al (1995) K-function test for space-time clustering
stsAggregateAggregate the the series of an sts object
sts_animateAnimated Maps and Time Series of Disease Incidence
stsBP-classClass "stsBP" - a class inheriting from class 'sts' which...
sts-classClass '"sts"' - surveillance time series
sts_creationFunction for simulating a time series
stsNC-classClass "stsNC" - a class inheriting from class 'sts' which...
sts_observationFunction for creating a sts-object with a given observation...
stsplotPlot-Methods for Surveillance Time-Series Objects
stsplot_spaceMap of Disease Incidence During a Given Period
stsplot_spacetimeMap of Disease Incidence
stsplot_timeTime-Series Plots for '"sts"' Objects
stsSlotsGeneric functions to access '"sts"' slots
stsXtrctExtraction and Subsetting of 'sts' objects
sumNeighboursCalculates the sum of counts of adjacent areas
surveillance.optionsOptions of the 'surveillance' Package
testPrint xtable for several diseases and the summary
testSimPrint xtable for a Simulated Disease and the Summary
toFileDisProgWriting of Disease Data
toLatex.sts'toLatex'-Method for (lists of) '"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_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
jimhester/surveillance documentation built on May 19, 2019, 10:33 a.m.