surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hhle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. 'hhh4' estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. 'twinSIR' models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hhle (2009) <doi:10.1002/bimj.200900050>. 'twinstim' estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2015) <>.

AuthorMichael Hhle [aut, ths], Sebastian Meyer [aut, cre], Michaela Paul [aut], Leonhard Held [ctb, ths], Howard Burkom [ctb], Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb], Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabans Bov [ctb], Malle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb], Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)
Date of publication2017-03-28 14:37:16
MaintainerSebastian Meyer <>

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Man pages

abattoir: Abattoir Data

addFormattedXAxis: Formatted Time Axis for '"sts"' Objects

addSeason2formula: Function that adds a sine-/cosine formula to an existing...

aggregate.disProg: Aggregate the observed counts

algo.bayes: The Bayes System Query Transmission to Specified Surveillance Algorithm

algo.cdc: The CDC Algorithm Comparison of Specified Surveillance Systems using Quality...

algo.cusum: CUSUM method

algo.farrington: Surveillance for a count data time series using the...

algo.farrington.assign.weights: Assign weights to base counts

algo.farrington.fitGLM: Fit the Poisson GLM of the Farrington procedure for a single...

algo.farrington.threshold: Compute prediction interval for a new observation

algo.glrnb: Count Data Regression Charts

algo.hhh: Fit a Classical HHH Model (DEPRECATED)

algo.hhh.grid: Fit a Classical HHH Model (DEPRECATED) with Varying Start...

algo.hmm: Hidden Markov Model (HMM) method

algo.outbreakP: Semiparametric surveillance of outbreaks

algo.quality: Computation of Quality Values for a Surveillance System...

algo.rki: The system used at the RKI

algo.rogerson: Modified CUSUM method as proposed by Rogerson and Yamada...

algo.summary: Summary Table Generation for Several Disease Chains

algo.twins: Model fit based on a two-component epidemic model

all.equal: Test if Two Model Fits are (Nearly) Equal

animate: Generic animation of spatio-temporal objects

anscombe.residuals: Compute Anscombe Residuals

arlCusum: Calculation of Average Run Length for discrete CUSUM schemes

backprojNP: Non-parametric back-projection of incidence cases to exposure...

bestCombination: Partition of a number into two factors

boda: Surveillance for an univariate count data time series using...

bodaDelay: Bayesian Outbreak Detection in the Presence of Reporting...

calibration: Calibration Tests for Poisson or Negative Binomial...

campyDE: Cases of Campylobacteriosis and Absolute Humidity in Germany...

categoricalCUSUM: CUSUM detector for time-varying categorical time series

checkResidualProcess: Check the residual process of a fitted 'twinSIR' or...

coeflist: List Coefficients by Model Component

compMatrix.writeTable: Latex Table Generation

correct53to52: Data Correction from 53 to 52 weeks

create.disProg: Creating an object of class disProg

create.grid: Create a Matrix of Initial Values for 'algo.hhh.grid'

deleval: Surgical failures data

discpoly: Polygonal Approximation of a Disc/Circle

disProg2sts: Convert disProg object to sts and vice versa

earsC: Surveillance for a count data time series using the EARS C1,...

enlargeData: Data Enlargement

epidata: Continuous-Time SIR Event History of a Fixed Population

epidata_animate: Spatio-Temporal Animation of an Epidemic

epidataCS: Continuous Space-Time Marked Point Patterns with Grid-Based...

epidataCS_aggregate: Conversion (aggregation) of '"epidataCS"' to '"epidata"' or...

epidataCS_animate: Spatio-Temporal Animation of a Continuous-Time...

epidataCS_permute: Randomly Permute Time Points or Locations of '"epidataCS"'

epidataCS_plot: Plotting the Events of an Epidemic over Time and Space

epidataCS_update: Update method for '"epidataCS"'

epidata_intersperse: Impute Blocks for Extra Stops in '"epidata"' Objects

epidata_plot: Plotting the Evolution of an Epidemic

epidata_summary: Summarizing an Epidemic

estimateGLRNbHook: Hook function for in-control mean estimation

farringtonFlexible: Surveillance for an univariate count data time series using...

findH: Find decision interval for given in-control ARL and reference...

findK: Find reference value Determine the k and h values in a standard normal setting

fluBYBW: Influenza in Southern Germany

formatPval: Pretty p-Value Formatting

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...

hhh4_formula: Specify Formulae in a Random Effects HHH Model

hhh4_methods: Print, Summary and other Standard Methods for '"hhh4"'...

hhh4_plot: Plots for Fitted 'hhh4'-models

hhh4_predict: Predictions from a 'hhh4' Model

hhh4_simulate: Simulate '"hhh4"' Count Time Series

hhh4_simulate_plot: Plot Simulations from '"hhh4"' Models

hhh4_simulate_scores: Proper Scoring Rules for Simulations from 'hhh4' Models

hhh4_update: 'update' a fitted '"hhh4"' model

hhh4_validation: Predictive Model Assessment for 'hhh4' Models

hhh4_W: Power-Law and Nonparametric Neighbourhood Weights for...

husO104Hosp: Hospitalization date for HUS cases of the STEC outbreak in...

imdepi: Occurrence of Invasive Meningococcal Disease in Germany

influMen: Influenza and meningococcal infections in Germany, 2001-2006

inside.gpc.poly: Test Whether Points are Inside a '"gpc.poly"' Polygon

intensityplot: Plot Paths of Point Process Intensities

intersectPolyCircle: Intersection of a Polygonal and a Circular Domain

isoWeekYear: Find ISO week and ISO year of a vector of Date objects on...

isScalar: Checks if the Argument is Scalar

knox: Knox Test for Space-Time Interaction

ks.plot.unif: Plot the ECDF of a uniform sample with Kolmogorov-Smirnov...

layout.labels: Layout Items for 'spplot'

linelist2sts: Convert individual case information based on dates into an...

loglikelihood: Calculation of the loglikelihood needed in algo.hhh

LRCUSUM.runlength: Run length computation of a CUSUM detector

m1: RKI SurvStat Data

magic.dim: Returns a suitable k1 x k2 for plotting the disProgObj Create the design matrices

makePlot: Plot Generation

marks: Import from package 'spatstat'

meanResponse: Calculate mean response needed in algo.hhh

measlesDE: Measles in the 16 states of Germany

measles.weser: Measles in the Weser-Ems region of Lower Saxony, Germany,...

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

multiplicity: Import from package 'spatstat'

multiplicity.Spatial: Count Number of Instances of Points

nbOrder: Determine Neighbourhood Order Matrix from Binary Adjacency...

nowcast: Adjust a univariate time series of counts for observed...

pairedbinCUSUM: Paired binary CUSUM and its run-length computation

permutationTest: Monte Carlo Permutation Test for Paired Individual Scores

pit: Non-Randomized Version of the PIT Histogram (for Count Data)

plapply: Verbose and Parallel 'lapply'

plot.atwins: Plot results of a twins model fit

plot.disProg: Plot Generation of the Observed and the defined Outbreak...

plot.survRes: Plot a survRes object

poly2adjmat: Derive Adjacency Structure of '"SpatialPolygons"'

polyAtBorder: Indicate Polygons at the Border

predict.ah: Predictions from a HHH model

primeFactors: Prime number factorization

print.algoQV: Print quality value object

qlomax: Quantile Function of the Lomax Distribution

R0: Computes reproduction numbers from fitted models

ranef: Import from package 'nlme'

readData: Reading of Disease Data

refvalIdxByDate: Compute indices of reference value using Date class

residuals.ah: Residuals from a HHH model

residualsCT: Extract Cox-Snell-like Residuals of a Fitted Point Process

rotaBB: Rotavirus cases in Brandenburg, Germany, during 2002-2013...

runifdisc: Sample Points Uniformly on a Disc

salmAllOnset: Salmonella cases in Germany 2001-2014 by data of symptoms...

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

scale.gpc.poly: Centering and Scaling a '"gpc.poly"' Polygon

scores: Proper Scoring Rules for Poisson or Negative Binomial...

shadar: Salmonella Hadar cases in Germany 2001-2006

simHHH: Simulates data based on the model proposed by Held et. al...

sim.pointSource: Simulate Point-Source Epidemics

sim.seasonalNoise: Generation of Background Noise for Simulated Timeseries

stcd: Spatio-temporal cluster detection

stK: Diggle et al (1995) K-function test for space-time clustering

stsAggregate: Aggregate an '"sts"' Object Over Time or Across Units

sts_animate: Animated Maps and Time Series of Disease Counts or Incidence

stsBP-class: Class "stsBP" - a class inheriting from class 'sts' which...

sts-class: Class '"sts"' - surveillance time series

sts_creation: Function for simulating a time series

stsNC-class: Class "stsNC" - a class inheriting from class 'sts' which...

stsNClist_animate: Animate a sequence of nowcasts

stsNewport: Salmonella Newport cases in Germany 2004-2013

sts_observation: Function for creating a sts-object with a given observation...

stsplot: Plot-Methods for Surveillance Time-Series Objects

stsplot_space: Map of Disease Counts/Incidence accumulated over a Given...

stsplot_spacetime: Map of Disease Incidence

stsplot_time: Time-Series Plots for '"sts"' Objects

stsSlots: Generic functions to access '"sts"' slots

stsXtrct: Extraction and Subsetting of '"sts"' Objects

sumNeighbours: Calculates the sum of counts of adjacent areas

surveillance.options: Options of the 'surveillance' Package

test: Print xtable for several diseases and the summary

testSim: Print xtable for a Simulated Disease and the Summary

toFileDisProg: Writing of Disease Data

toLatex.sts: 'toLatex'-Method for '"sts"' Objects

twinSIR: Fit an Additive-Multiplicative Intensity Model for SIR Data

twinSIR_cox: Identify Endemic Components in an Intensity Model

twinSIR_exData: Toy Data for 'twinSIR'

twinSIR_intensityplot: Plotting Paths of Infection Intensities for 'twinSIR' Models

twinSIR_methods: Print, Summary and Extraction Methods for '"twinSIR"' Objects

twinSIR_profile: Profile Likelihood Computation and Confidence Intervals

twinSIR_simulation: Simulation of Epidemic Data

twinstim: Fit a Two-Component Spatio-Temporal Point Process Model

twinstim_epitest: Permutation Test for Space-Time Interaction in '"twinstim"'

twinstim_iaf: Temporal and Spatial Interaction Functions for 'twinstim'

twinstim_iafplot: Plot the Spatial or Temporal Interaction Function of a...

twinstim_intensity: Plotting Intensities of Infection over Time or Space

twinstim_methods: Print, Summary and Extraction Methods for '"twinstim"'...

twinstim_plot: Plot methods for fitted 'twinstim"s

twinstim_profile: Profile Likelihood Computation and Confidence Intervals for...

twinstim_siaf: Spatial Interaction Function Objects

twinstim_siaf_simulatePC: Simulation from an Isotropic Spatial Kernel via Polar...

twinstim_simulation: Simulation of a Self-Exciting Spatio-Temporal Point Process

twinstim_step: Stepwise Model Selection by AIC

twinstim_tiaf: Temporal Interaction Function Objects

twinstim_update: 'update'-method for '"twinstim"'

unionSpatialPolygons: Compute the Unary Union of '"SpatialPolygons"'

untie: Randomly Break Ties in Data

wrap.algo: Multivariate Surveillance through independent univariate...

xtable.algoQV: Xtable quality value object

zetaweights: Power-Law Weights According to Neighbourhood Order


abattoir Man page
add1.twinstim Man page
addFormattedXAxis Man page
addSeason2formula Man page
aggregate.disProg Man page
aggregate,sts,ANY,ANY-method Man page
aggregate,stsBP-method Man page
aggregate,sts-method Man page
AIC.twinSIR Man page
alarms Man page
alarms<- Man page
alarms<-,stsBP-method Man page
alarms,stsBP-method Man page
alarms<-,sts-method Man page
alarms,sts-method Man page
algo.bayes Man page
algo.bayes1 Man page
algo.bayes2 Man page
algo.bayes3 Man page
algo.bayesLatestTimepoint Man page Man page
algo.cdc Man page
algo.cdcLatestTimepoint Man page Man page
algo.cusum Man page
algo.farrington Man page
algo.farrington.assign.weights Man page
algo.farrington.fitGLM Man page Man page
algo.farrington.fitGLM.populationOffset Man page
algo.farrington.threshold Man page
algo.glrnb Man page
algo.glrpois Man page
algo.hhh Man page
algo.hhh.grid Man page
algo.hmm Man page
algo.outbreakP Man page
algo.quality Man page
algo.rki Man page
algo.rki1 Man page
algo.rki2 Man page
algo.rki3 Man page
algo.rkiLatestTimepoint Man page
algo.rogerson Man page
algo.summary Man page
algo.twins Man page
all.equal.hhh4 Man page
all.equal.twinstim Man page
animate Man page
animate.epidata Man page
animate.epidataCS Man page
animate_nowcasts Man page
animate.sts Man page
animate.summary.epidata Man page
anscombe.residuals Man page
arlCusum Man page,stsBP-method Man page,sts-method Man page
as.epidata Man page
as.epidataCS Man page Man page
as.epidata.default Man page
as.epidata.epidataCS Man page
as.hhh4simslist Man page
as.stepfun.epidataCS Man page
as.xts.sts Man page
at2ndChange Man page
atChange Man page
atMedian Man page
backprojNP Man page Man page
bayes Man page
bestCombination Man page
boda Man page
bodaDelay Man page
calc.outbreakP.statistic Man page
calibrationTest Man page
calibrationTest.default Man page
calibrationTest.hhh4 Man page
calibrationTest.oneStepAhead Man page
campyDE Man page
catcusum.LLRcompute Man page
categoricalCUSUM Man page
checkResidualProcess Man page
coef.ah Man page
coef.ahg Man page
coef.epitest Man page
coef.hhh4 Man page
coeflist Man page
coeflist.default Man page
coeflist.hhh4 Man page
coeflist.twinstim Man page
coerce,sts,stsBP-method Man page
coerce,sts,stsNC-method Man page
coerce,sts,ts-method Man page
coerce,ts,sts-method Man page
colnames,stsBP,missing,missing-method Man page
compMatrix.writeTable Man page
confint.hhh4 Man page
control Man page
control<- Man page
control<-,stsBP-method Man page
control,stsBP-method Man page
control<-,sts-method Man page
control,sts-method Man page
correct53to52 Man page
cox Man page
create.disProg Man page
create.grid Man page
cusum Man page
delayCDF Man page
delayCDF,stsNC-method Man page
deleval Man page
dimnames,sts-method Man page
dim,stsBP-method Man page
dim,sts-method Man page
discpoly Man page
disProg2sts Man page
dist.median Man page
drop1.twinstim Man page
dss Man page
earsC Man page
em.step.becker Man page
enlargeData Man page
epidata Man page
[.epidata Man page
epidataCS Man page
[.epidataCS Man page
epidataCS2sts Man page
epidataCSplot_space Man page
epidataCSplot_time Man page
epitest Man page
epoch Man page
epoch<- Man page
epochInYear Man page
epochInYear,stsBP-method Man page
epochInYear,sts-method Man page
epoch<-,stsBP-method Man page
epoch,stsBP-method Man page
epoch<-,sts-method Man page
epoch,sts-method Man page
estimateGLRNbHook Man page
extractAIC.twinSIR Man page
farrington Man page
farringtonFlexible Man page
fe Man page
findH Man page
findK Man page Man page
fixef Man page
fixef.hhh4 Man page
fluBYBW Man page
foodata Man page
fooepidata Man page
foofit Man page
formatDate Man page
formatPval Man page
formula.hhh4 Man page
getMaxEV Man page
getMaxEV_season Man page
getSourceDists Man page
glm_epidataCS Man page
glrnb Man page
glrpois Man page
h1_nrwrp Man page
ha Man page
hagelloch Man page
hagelloch.df Man page
ha.sts Man page
head.epidataCS Man page
hepatitisA Man page
hhh4 Man page
hmm Man page
husO104Hosp Man page
hValues Man page
iafplot Man page
imdepi Man page
imdepifit Man page
influMen Man page
initialize,stsBP-method Man page
initialize,sts-method Man page
inside.gpc.poly Man page
intensityplot Man page
intensityplot.simEpidata Man page
intensityplot.simEpidataCS Man page
intensityplot.twinSIR Man page
intensityplot.twinstim Man page
intensity.twinstim Man page
intersectPolyCircle Man page
intersectPolyCircle.gpc.poly Man page
intersectPolyCircle.owin Man page
intersectPolyCircle.SpatialPolygons Man page
intersperse Man page
isoWeekYear Man page
isScalar Man page
k1 Man page
knox Man page
ks.plot.unif Man page
layout.labels Man page
layout.scalebar Man page
linelist2sts Man page Man page
loglikelihood Man page
logLik.hhh4 Man page
logLik.twinSIR Man page
logLik.twinstim Man page
logs Man page
logS Man page
LRCUSUM.runlength Man page
m1 Man page
m2 Man page
m3 Man page
m4 Man page
m5 Man page
magic.dim Man page Man page
makePlot Man page
marks Man page
marks.epidataCS Man page
meanResponse Man page
measlesDE Man page
measles.weser Man page
measlesWeserEms Man page
meningo.age Man page
MMRcoverageDE Man page
momo Man page
multinomialTS Man page
multinomialTS<- Man page
multinomialTS<-,stsBP-method Man page
multinomialTS,stsBP-method Man page
multinomialTS<-,sts-method Man page
multinomialTS,sts-method Man page
multiplicity Man page
multiplicity.Spatial Man page
n1 Man page
n2 Man page
naninf2zero Man page
nbOrder Man page
ncol,stsBP-method Man page
neighbourhood Man page
neighbourhood<- Man page
neighbourhood<-,stsBP-method Man page
neighbourhood,stsBP-method Man page
neighbourhood<-,sts-method Man page
neighbourhood,sts-method Man page
nobs.epidataCS Man page
nobs.hhh4 Man page
nobs.twinstim Man page
nowcast Man page
nrow,stsBP-method Man page
observed Man page
observed<- Man page
observed<-,stsBP-method Man page
observed,stsBP-method Man page
observed<-,sts-method Man page
observed,sts-method Man page
oneStepAhead Man page
outbreakP Man page
outcomeFunStandard Man page Man page
pairedbinCUSUM Man page
pairedbinCUSUM.LLRcompute Man page
pairedbinCUSUM.runlength Man page
permutationTest Man page
permute.epidataCS Man page
pit Man page
pit.default Man page
pit.hhh4 Man page
pit.oneStepAhead Man page
plapply Man page
plot.atwins Man page
plot.disProg Man page Man page
plot.epidata Man page
plot.epidataCS Man page
plot.epitest Man page
plot.hhh4 Man page
plotHHH4_fitted Man page
plotHHH4_fitted1 Man page
plotHHH4_maps Man page
plotHHH4_maxEV Man page
plotHHH4_neweights Man page
plotHHH4_ri Man page
plotHHH4_season Man page
plot.hhh4sims Man page
plotHHH4sims_fan Man page
plot.hhh4simslist Man page
plotHHH4sims_size Man page
plotHHH4sims_time Man page
plot.knox Man page
plot.profile.twinSIR Man page
plot.stKtest Man page
plot,stsBP-method Man page
plot,stsBP,missing-method Man page
plot,sts,missing-method Man page
plot,stsNC,missing-method Man page
plot.summary.epidata Man page
plot.survRes Man page Man page
plot.twinSIR Man page
plot.twinstim Man page
poly2adjmat Man page
polyAtBorder Man page
population Man page
population<- Man page
population<-,stsBP-method Man page
population,stsBP-method Man page
population<-,sts-method Man page
population,sts-method Man page
predict.ah Man page
predict.ahg Man page
predict.hhh4 Man page
predint Man page
predint,stsNC-method Man page
primeFactors Man page
print.ah Man page
print.ahg Man page
print.algoQV Man page
print.disProg Man page
print.epidata Man page
print.epidataCS Man page
print.hhh4 Man page
print.summary.epidata Man page
print.summary.epidataCS Man page
print.summary.hhh4 Man page
print.summary.twinSIR Man page
print.summary.twinstim Man page
print.twinSIR Man page
print.twinstim Man page
profile.twinSIR Man page
profile.twinstim Man page
q1_nrwh Man page
q2 Man page
qlomax Man page
R0 Man page
R0.simEpidataCS Man page
R0.twinstim Man page
ranef Man page
ranef.hhh4 Man page
readData Man page
refvalIdxByDate Man page
reportingTriangle Man page
reportingTriangle,stsNC-method Man page
reset.surveillance.options Man page
residuals.ah Man page
residuals.ahg Man page
residuals.hhh4 Man page
residuals.simEpidataCS Man page
residuals.twinSIR Man page
residuals.twinstim Man page
ri Man page
rki Man page
rogerson Man page
rotaBB Man page
rps Man page
RPS Man page
runifdisc Man page
s1 Man page
s2 Man page
s3 Man page
salmAllOnset Man page
salmHospitalized Man page
salmNewport Man page
salmonella.agona Man page
scale.gpc.poly Man page
score Man page
scores Man page
scores.default Man page
scores.hhh4 Man page
scores.hhh4sims Man page
scores.hhh4simslist Man page
scores.oneStepAhead Man page
score,stsNC-method Man page
ses Man page
shadar Man page
siaf Man page
siaf.constant Man page
siaf.gaussian Man page
siaf.powerlaw Man page
siaf.powerlawL Man page
siaf.simulatePC Man page
siaf.step Man page
siaf.student Man page
simEpidata Man page
simEpidataCS Man page
simHHH Man page
simHHH.ah Man page
simHHH.default Man page
simpleR0 Man page
sim.pointSource Man page
sim.seasonalNoise Man page
simulate.hhh4 Man page
simulate.twinSIR Man page
simulate.twinstim Man page
stateplot Man page
stcd Man page
stepComponent Man page
stKtest Man page
sts Man page
sts2disProg Man page
[,sts,ANY,ANY,ANY-method Man page
stsBP-class Man page
sts-class Man page
sts_creation Man page
[,sts-method Man page
stsNC-class Man page
stsNClist_animate Man page
stsNewport Man page
sts_observation Man page
stsplot Man page
stsplot_alarm Man page
stsplot_space Man page
stsplot_spacetime Man page
stsplot_time Man page
stsplot_time1 Man page
subset.epidataCS Man page
summary.epidata Man page
summary.epidataCS Man page
summary.hhh4 Man page
summary.twinSIR Man page
summary.twinstim Man page
sumNeighbours Man page
surveillance.options Man page
tail.epidataCS Man page
terms.hhh4 Man page
test Man page
testSim Man page
tiaf Man page
tiaf.constant Man page
tiaf.exponential Man page
tiaf.step Man page
toFileDisProg Man page
toLatex.sts Man page
toLatex,sts-method Man page
toLatex.summary.twinstim Man page
twinSIR Man page
twinstim Man page
unionSpatialPolygons Man page
untie Man page
untie.default Man page
untie.epidataCS Man page
untie.matrix Man page
update.epidata Man page
update.epidataCS Man page
update.hhh4 Man page
update.twinstim Man page
upperbound Man page
upperbound<- Man page
upperbound<-,stsBP-method Man page
upperbound,stsBP-method Man page
upperbound<-,sts-method Man page
upperbound,sts-method Man page
vcov.hhh4 Man page
vcov.twinSIR Man page
vcov.twinstim Man page
W_np Man page
W_powerlaw Man page
wrap.algo Man page
xtable.algoQV Man page
xtable.summary.twinstim Man page
xtable.twinstim Man page
year Man page
year,sts-method Man page
zetaweights Man page


R/AllClass.R R/AllGeneric.R R/LRCUSUM.runlength.R R/RcppExports.R R/addSeason2formula.R R/algo_bayes.R R/algo_call.R R/algo_cdc.R R/algo_cusum.R R/algo_farrington.R R/algo_glrnb.R R/algo_hhh.R R/algo_hmm.R R/algo_outbreakP.R R/algo_rki.R R/algo_rogerson.R R/algo_twins.R R/backprojNP.R R/boda.R R/bodaDelay.R R/calibration.R R/calibration_null.R R/catCUSUM.R R/checkDerivatives.R R/earsC.R R/epidata.R R/epidataCS.R R/epidataCS_aggregate.R R/epidataCS_animate.R R/epidataCS_methods.R R/epidataCS_plot.R R/epidata_animate.R R/epidata_plot.R R/farringtonFlexible.R R/functionTable.R R/gd.R R/glm_epidataCS.R R/gpc.poly-methods.R R/graphs.R R/hhh4.R R/hhh4_W.R R/hhh4_W_np.R R/hhh4_W_powerlaw.R R/hhh4_calibration.R R/hhh4_methods.R R/hhh4_oneStepAhead.R R/hhh4_plot.R R/hhh4_simulate.R R/hhh4_simulate_plot.R R/hhh4_simulate_scores.R R/intersectPolyCircle.R R/isoWeekYear.R R/knox.R R/ks.plot.unif.R R/linelist2sts.R R/misc_dataProcessing.R R/modifyListcall.R R/newtonRaphson.R R/nowcast.R R/options.R R/pairedbinCUSUM.R R/permutationTest.R R/pit.R R/plapply.R R/plot_graphics.R R/plot_multi.R R/plot_xtable.R R/qlomax.R R/scores.R R/sim_HHH.R R/sim_background.R R/sim_pointSource.R R/spatial_tools.R R/stK.R R/stcd.R R/sts.R R/stsBP.R R/stsNC.R R/stsNClist_animate.R R/sts_animate.R R/sts_coerce.R R/sts_creation.R R/sts_observation.R R/sts_toLatex.R R/stsplot_space.R R/stsplot_spacetime.R R/stsplot_time.R
R/testcalls.R R/twinSIR.R R/twinSIR_helper.R R/twinSIR_intensity.R R/twinSIR_methods.R R/twinSIR_profile.R R/twinSIR_simulation.R R/twinstim.R R/twinstim_epitest.R R/twinstim_helper.R R/twinstim_iafplot.R R/twinstim_intensity.R R/twinstim_methods.R R/twinstim_siaf.R R/twinstim_siaf_gaussian.R R/twinstim_siaf_powerlaw.R R/twinstim_siaf_powerlawL.R R/twinstim_siaf_step.R R/twinstim_siaf_student.R R/twinstim_simulation.R R/twinstim_step.R R/twinstim_tiaf.R R/twinstim_tiaf_exponential.R R/twinstim_tiaf_step.R R/untie.R R/wrap_univariate.R R/zzz.R
demo/biosurvbook.R demo/cost.R demo/fluBYBW.R
man/LRCUSUM.runlength.Rd man/MMRcoverageDE.Rd man/R0.Rd man/abattoir.Rd man/addFormattedXAxis.Rd man/addSeason2formula.Rd man/aggregate.disProg.Rd man/algo.bayes.Rd man/ man/algo.cdc.Rd man/ man/algo.cusum.Rd man/algo.farrington.Rd man/algo.farrington.assign.weights.Rd man/algo.farrington.fitGLM.Rd man/algo.farrington.threshold.Rd man/algo.glrnb.Rd man/algo.hhh.Rd man/algo.hhh.grid.Rd man/algo.hmm.Rd man/algo.outbreakP.Rd man/algo.quality.Rd man/algo.rki.Rd man/algo.rogerson.Rd man/algo.summary.Rd man/algo.twins.Rd man/all.equal.Rd man/animate.Rd man/anscombe.residuals.Rd man/arlCusum.Rd man/backprojNP.Rd man/bestCombination.Rd man/boda.Rd man/bodaDelay.Rd man/calibration.Rd man/campyDE.Rd man/categoricalCUSUM.Rd man/checkResidualProcess.Rd man/coeflist.Rd man/compMatrix.writeTable.Rd man/correct53to52.Rd man/create.disProg.Rd man/create.grid.Rd man/deleval.Rd man/disProg2sts.Rd man/discpoly.Rd man/earsC.Rd man/enlargeData.Rd man/epidata.Rd man/epidataCS.Rd man/epidataCS_aggregate.Rd man/epidataCS_animate.Rd man/epidataCS_permute.Rd man/epidataCS_plot.Rd man/epidataCS_update.Rd man/epidata_animate.Rd man/epidata_intersperse.Rd man/epidata_plot.Rd man/epidata_summary.Rd man/estimateGLRNbHook.Rd man/farringtonFlexible.Rd man/ man/findH.Rd man/findK.Rd man/fluBYBW.Rd man/formatPval.Rd man/glm_epidataCS.Rd man/ha.Rd man/hagelloch.Rd man/hepatitisA.Rd man/hhh4.Rd man/hhh4_W.Rd man/hhh4_formula.Rd man/hhh4_methods.Rd man/hhh4_plot.Rd man/hhh4_predict.Rd man/hhh4_simulate.Rd man/hhh4_simulate_plot.Rd man/hhh4_simulate_scores.Rd man/hhh4_update.Rd man/hhh4_validation.Rd man/husO104Hosp.Rd man/imdepi.Rd man/influMen.Rd man/inside.gpc.poly.Rd man/intensityplot.Rd man/intersectPolyCircle.Rd man/isScalar.Rd man/isoWeekYear.Rd man/knox.Rd man/ks.plot.unif.Rd man/layout.labels.Rd man/linelist2sts.Rd man/loglikelihood.Rd man/m1.Rd man/magic.dim.Rd man/ man/makePlot.Rd man/marks.Rd man/meanResponse.Rd man/measles.weser.Rd man/measlesDE.Rd man/meningo.age.Rd man/momo.Rd man/multiplicity.Rd man/multiplicity.Spatial.Rd man/nbOrder.Rd man/nowcast.Rd man/pairedbinCUSUM.Rd man/permutationTest.Rd man/pit.Rd man/plapply.Rd man/plot.atwins.Rd man/plot.disProg.Rd man/plot.survRes.Rd man/poly2adjmat.Rd man/polyAtBorder.Rd man/predict.ah.Rd man/primeFactors.Rd man/print.algoQV.Rd man/qlomax.Rd man/ranef.Rd man/readData.Rd man/refvalIdxByDate.Rd man/residuals.ah.Rd man/residualsCT.Rd man/rotaBB.Rd man/runifdisc.Rd man/salmAllOnset.Rd man/salmHospitalized.Rd man/salmNewport.Rd man/salmonella.agona.Rd man/scale.gpc.poly.Rd man/scores.Rd man/shadar.Rd man/sim.pointSource.Rd man/sim.seasonalNoise.Rd man/simHHH.Rd man/stK.Rd man/stcd.Rd man/sts-class.Rd man/stsAggregate.Rd man/stsBP-class.Rd man/stsNC-class.Rd man/stsNClist_animate.Rd man/stsNewport.Rd man/stsSlots.Rd man/stsXtrct.Rd man/sts_animate.Rd man/sts_creation.Rd man/sts_observation.Rd man/stsplot.Rd man/stsplot_space.Rd man/stsplot_spacetime.Rd man/stsplot_time.Rd man/sumNeighbours.Rd
man/surveillance.options.Rd man/test.Rd man/testSim.Rd man/toFileDisProg.Rd man/toLatex.sts.Rd man/twinSIR.Rd man/twinSIR_cox.Rd man/twinSIR_exData.Rd man/twinSIR_intensityplot.Rd man/twinSIR_methods.Rd man/twinSIR_profile.Rd man/twinSIR_simulation.Rd man/twinstim.Rd man/twinstim_epitest.Rd man/twinstim_iaf.Rd man/twinstim_iafplot.Rd man/twinstim_intensity.Rd man/twinstim_methods.Rd man/twinstim_plot.Rd man/twinstim_profile.Rd man/twinstim_siaf.Rd man/twinstim_siaf_simulatePC.Rd man/twinstim_simulation.Rd man/twinstim_step.Rd man/twinstim_tiaf.Rd man/twinstim_update.Rd man/unionSpatialPolygons.Rd man/untie.Rd man/wrap.algo.Rd man/xtable.algoQV.Rd man/zetaweights.Rd
tests/testthat.R tests/testthat/test-algo.glrnb.R tests/testthat/test-bodaDelay.R tests/testthat/test-calibration.R tests/testthat/test-createLambda.R tests/testthat/test-determineSources.R tests/testthat/test-earsc.R tests/testthat/test-farringtonFlexible.R tests/testthat/test-formatDate.R tests/testthat/test-hhh4+algo.hhh.R tests/testthat/test-hhh4+derivatives.R tests/testthat/test-hhh4_ARasNE.R tests/testthat/test-hhh4_NegBinGrouped.R tests/testthat/test-nbOrder.R tests/testthat/test-plapply.R tests/testthat/test-siafs.R tests/testthat/test-sts.R tests/testthat/test-tiafs.R tests/testthat/test-toLatex.sts.R tests/testthat/test-twinstim_score.R

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