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) <http://arxiv.org/abs/1411.0416>.

Author
Michael Hhle [aut, ths], Sebastian Meyer [aut, cre], Michaela Paul [aut], Leonhard Held [ctb, ths], 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 publication
2016-11-17 14:34:37
Maintainer
Sebastian Meyer <seb.meyer@fau.de>
License
GPL-2
Version
1.12.2
URLs

View on CRAN

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
algo.call
Query Transmission to Specified Surveillance Algorithm
algo.cdc
The CDC Algorithm
algo.compare
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 Test for Poisson or Negative Binomial Predictions
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
find.kh
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_calibration
Test Calibration of a 'hhh4' Model
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
Summarize 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
make.design
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
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 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 Incidence During a Given Period
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
surveillance-package
\Sexpr[stage=build]{(meta <-...
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

Files in this package

surveillance
surveillance/inst
surveillance/inst/jags
surveillance/inst/jags/bhpm.bugs
surveillance/inst/CITATION
surveillance/inst/NEWS.Rd
surveillance/inst/shapes
surveillance/inst/shapes/berlin.dbf
surveillance/inst/shapes/berlin.shx
surveillance/inst/shapes/berlin.sbx
surveillance/inst/shapes/berlin.shp
surveillance/inst/shapes/berlin.sbn
surveillance/inst/shapes/districtsD.RData
surveillance/inst/THANKS
surveillance/inst/extdata
surveillance/inst/extdata/h1_nrwrp.txt
surveillance/inst/extdata/n1.txt
surveillance/inst/extdata/salmonella.agona.txt
surveillance/inst/extdata/m5.txt
surveillance/inst/extdata/m2.txt
surveillance/inst/extdata/m3.txt
surveillance/inst/extdata/neighbourhood_BYBW.txt
surveillance/inst/extdata/s3.txt
surveillance/inst/extdata/s1.txt
surveillance/inst/extdata/q1_nrwh.txt
surveillance/inst/extdata/k1.txt
surveillance/inst/extdata/m4.txt
surveillance/inst/extdata/s2.txt
surveillance/inst/extdata/counts_flu_BYBW.txt
surveillance/inst/extdata/n2.txt
surveillance/inst/extdata/q2.txt
surveillance/inst/extdata/m1.txt
surveillance/inst/extdata/population_2001-12-31_BYBW.txt
surveillance/inst/doc
surveillance/inst/doc/twinstim.Rnw
surveillance/inst/doc/twinstim.pdf
surveillance/inst/doc/hhh4.Rnw
surveillance/inst/doc/hhh4.R
surveillance/inst/doc/twinstim.R
surveillance/inst/doc/monitoringCounts.R
surveillance/inst/doc/hhh4_spacetime.pdf
surveillance/inst/doc/glrnb.Rnw
surveillance/inst/doc/hhh4_spacetime.Rnw
surveillance/inst/doc/glrnb.R
surveillance/inst/doc/twinSIR.pdf
surveillance/inst/doc/surveillance.Rnw
surveillance/inst/doc/twinSIR.R
surveillance/inst/doc/monitoringCounts.pdf
surveillance/inst/doc/surveillance.pdf
surveillance/inst/doc/twinSIR.Rnw
surveillance/inst/doc/hhh4_spacetime.R
surveillance/inst/doc/hhh4.pdf
surveillance/inst/doc/surveillance.R
surveillance/inst/doc/monitoringCounts.Rnw
surveillance/inst/doc/glrnb.pdf
surveillance/tests
surveillance/tests/testthat.R
surveillance/tests/testthat
surveillance/tests/testthat/test-calibration.R
surveillance/tests/testthat/test-determineSources.R
surveillance/tests/testthat/test-bodaDelay.R
surveillance/tests/testthat/test-plapply.R
surveillance/tests/testthat/test-farringtonFlexible.R
surveillance/tests/testthat/test-hhh4_NegBinGrouped.R
surveillance/tests/testthat/test-hhh4_ARasNE.R
surveillance/tests/testthat/test-toLatex.sts.R
surveillance/tests/testthat/test-siafs.R
surveillance/tests/testthat/test-tiafs.R
surveillance/tests/testthat/test-formatDate.R
surveillance/tests/testthat/test-hhh4+algo.hhh.R
surveillance/tests/testthat/test-hhh4+derivatives.R
surveillance/tests/testthat/test-nbOrder.R
surveillance/tests/testthat/test-sts.R
surveillance/tests/testthat/test-twinstim_score.R
surveillance/tests/testthat/test-algo.glrnb.R
surveillance/src
surveillance/src/stcd-assuncaocorrea.cc
surveillance/src/ks.c
surveillance/src/twins.cc
surveillance/src/determineSources.cc
surveillance/src/surveillance.c
surveillance/src/stcd-assuncaocorrea.h
surveillance/src/backproj.cc
surveillance/src/RcppExports.cpp
surveillance/src/gsl_wrappers.h
surveillance/NAMESPACE
surveillance/demo
surveillance/demo/cost.R
surveillance/demo/biosurvbook.R
surveillance/demo/00Index
surveillance/demo/fluBYBW.R
surveillance/data
surveillance/data/m4.RData
surveillance/data/foodata.RData
surveillance/data/n2.RData
surveillance/data/imdepifit.RData
surveillance/data/m2.RData
surveillance/data/MMRcoverageDE.RData
surveillance/data/abattoir.RData
surveillance/data/q2.RData
surveillance/data/salmonella.agona.RData
surveillance/data/momo.RData
surveillance/data/hepatitisA.RData
surveillance/data/n1.RData
surveillance/data/ha.sts.RData
surveillance/data/salmAllOnset.RData
surveillance/data/fooepidata.RData
surveillance/data/hagelloch.RData
surveillance/data/q1_nrwh.RData
surveillance/data/influMen.RData
surveillance/data/m5.RData
surveillance/data/s2.RData
surveillance/data/imdepi.RData
surveillance/data/k1.RData
surveillance/data/campyDE.RData
surveillance/data/fluBYBW.RData
surveillance/data/measlesDE.RData
surveillance/data/foofit.RData
surveillance/data/stsNewport.RData
surveillance/data/salmNewport.RData
surveillance/data/salmHospitalized.RData
surveillance/data/rotaBB.RData
surveillance/data/shadar.RData
surveillance/data/meningo.age.RData
surveillance/data/measlesWeserEms.RData
surveillance/data/s1.RData
surveillance/data/s3.RData
surveillance/data/m3.RData
surveillance/data/husO104Hosp.RData
surveillance/data/ha.RData
surveillance/data/deleval.RData
surveillance/data/m1.RData
surveillance/data/h1_nrwrp.RData
surveillance/data/measles.weser.RData
surveillance/R
surveillance/R/twinSIR_intensity.R
surveillance/R/epidataCS.R
surveillance/R/wrap_univariate.R
surveillance/R/boda.R
surveillance/R/modifyListcall.R
surveillance/R/twinstim_iafplot.R
surveillance/R/epidataCS_animate.R
surveillance/R/catCUSUM.R
surveillance/R/twinstim_siaf_step.R
surveillance/R/sts_creation.R
surveillance/R/twinSIR_methods.R
surveillance/R/twinstim_tiaf_exponential.R
surveillance/R/hhh4_simulate_plot.R
surveillance/R/twinstim_intensity.R
surveillance/R/checkDerivatives.R
surveillance/R/stsNC.R
surveillance/R/permutationTest.R
surveillance/R/stcd.R
surveillance/R/sts.R
surveillance/R/twinstim_siaf_powerlaw.R
surveillance/R/qlomax.R
surveillance/R/twinstim_helper.R
surveillance/R/plapply.R
surveillance/R/stsNClist_animate.R
surveillance/R/twinSIR_profile.R
surveillance/R/bodaDelay.R
surveillance/R/sts_toLatex.R
surveillance/R/backprojNP.R
surveillance/R/addSeason2formula.R
surveillance/R/stsplot_time.R
surveillance/R/epidataCS_methods.R
surveillance/R/knox.R
surveillance/R/intersectPolyCircle.R
surveillance/R/algo_outbreakP.R
surveillance/R/epidata_animate.R
surveillance/R/misc_dataProcessing.R
surveillance/R/hhh4_oneStepAhead.R
surveillance/R/LRCUSUM.runlength.R
surveillance/R/pairedbinCUSUM.R
surveillance/R/graphs.R
surveillance/R/hhh4.R
surveillance/R/AllClass.R
surveillance/R/twinstim.R
surveillance/R/twinstim_tiaf_step.R
surveillance/R/twinstim_siaf.R
surveillance/R/hhh4_simulate_scores.R
surveillance/R/twinstim_tiaf.R
surveillance/R/scores.R
surveillance/R/epidataCS_plot.R
surveillance/R/sysdata.rda
surveillance/R/twinstim_simulation.R
surveillance/R/hhh4_calibration.R
surveillance/R/gd.R
surveillance/R/stsBP.R
surveillance/R/stK.R
surveillance/R/sts_observation.R
surveillance/R/twinstim_epitest.R
surveillance/R/algo_farrington.R
surveillance/R/epidata.R
surveillance/R/hhh4_W_powerlaw.R
surveillance/R/twinstim_siaf_student.R
surveillance/R/algo_rogerson.R
surveillance/R/earsC.R
surveillance/R/gpc.poly-methods.R
surveillance/R/options.R
surveillance/R/plot_multi.R
surveillance/R/twinstim_step.R
surveillance/R/farringtonFlexible.R
surveillance/R/RcppExports.R
surveillance/R/algo_call.R
surveillance/R/nowcast.R
surveillance/R/twinstim_methods.R
surveillance/R/algo_glrnb.R
surveillance/R/hhh4_plot.R
surveillance/R/sim_pointSource.R
surveillance/R/calibration_null.R
surveillance/R/plot_xtable.R
surveillance/R/twinSIR.R
surveillance/R/algo_rki.R
surveillance/R/linelist2sts.R
surveillance/R/twinstim_siaf_gaussian.R
surveillance/R/calibration.R
surveillance/R/untie.R
surveillance/R/twinSIR_simulation.R
surveillance/R/algo_bayes.R
surveillance/R/twinSIR_helper.R
surveillance/R/hhh4_simulate.R
surveillance/R/twinstim_siaf_powerlawL.R
surveillance/R/sts_coerce.R
surveillance/R/glm_epidataCS.R
surveillance/R/plot_graphics.R
surveillance/R/AllGeneric.R
surveillance/R/sim_HHH.R
surveillance/R/functionTable.R
surveillance/R/sim_background.R
surveillance/R/pit.R
surveillance/R/hhh4_W_np.R
surveillance/R/algo_twins.R
surveillance/R/algo_hmm.R
surveillance/R/newtonRaphson.R
surveillance/R/algo_cusum.R
surveillance/R/stsplot_space.R
surveillance/R/algo_cdc.R
surveillance/R/sts_animate.R
surveillance/R/spatial_tools.R
surveillance/R/isoWeekYear.R
surveillance/R/hhh4_W.R
surveillance/R/ks.plot.unif.R
surveillance/R/hhh4_methods.R
surveillance/R/zzz.R
surveillance/R/epidata_plot.R
surveillance/R/stsplot_spacetime.R
surveillance/R/testcalls.R
surveillance/R/epidataCS_aggregate.R
surveillance/R/algo_hhh.R
surveillance/vignettes
surveillance/vignettes/twinstim.Rnw
surveillance/vignettes/monitoringCounts-cache
surveillance/vignettes/monitoringCounts-cache/pMC.RData
surveillance/vignettes/monitoringCounts-cache/boda.covars.RData
surveillance/vignettes/monitoringCounts-cache/boda.RData
surveillance/vignettes/monitoringCounts-cache/pMarkovChain.RData
surveillance/vignettes/monitoringCounts-cache/rlsims-multinom.RData
surveillance/vignettes/surveillance-cache.RData
surveillance/vignettes/surveillance-hmm.pdf
surveillance/vignettes/hhh4.Rnw
surveillance/vignettes/glrnb.Rnw
surveillance/vignettes/hhh4_spacetime.Rnw
surveillance/vignettes/monitoringCounts.bib
surveillance/vignettes/twinstim-cache.RData
surveillance/vignettes/surveillance.Rnw
surveillance/vignettes/hhh4-cache.RData
surveillance/vignettes/hhh4_spacetime-cache.RData
surveillance/vignettes/twinSIR.Rnw
surveillance/vignettes/references.bib
surveillance/vignettes/twinSIR-cache.RData
surveillance/vignettes/monitoringCounts.Rnw
surveillance/MD5
surveillance/build
surveillance/build/vignette.rds
surveillance/build/partial.rdb
surveillance/DESCRIPTION
surveillance/man
surveillance/man/hhh4_methods.Rd
surveillance/man/twinSIR_intensityplot.Rd
surveillance/man/backprojNP.Rd
surveillance/man/epidata_intersperse.Rd
surveillance/man/addSeason2formula.Rd
surveillance/man/twinSIR_methods.Rd
surveillance/man/algo.hhh.grid.Rd
surveillance/man/epidata_animate.Rd
surveillance/man/estimateGLRNbHook.Rd
surveillance/man/arlCusum.Rd
surveillance/man/imdepi.Rd
surveillance/man/create.disProg.Rd
surveillance/man/epidataCS.Rd
surveillance/man/categoricalCUSUM.Rd
surveillance/man/fluBYBW.Rd
surveillance/man/husO104Hosp.Rd
surveillance/man/twinstim_plot.Rd
surveillance/man/runifdisc.Rd
surveillance/man/hhh4_simulate_plot.Rd
surveillance/man/twinSIR_exData.Rd
surveillance/man/plot.survRes.Rd
surveillance/man/twinSIR_simulation.Rd
surveillance/man/polyAtBorder.Rd
surveillance/man/stsplot.Rd
surveillance/man/epidataCS_plot.Rd
surveillance/man/primeFactors.Rd
surveillance/man/isoWeekYear.Rd
surveillance/man/campyDE.Rd
surveillance/man/coeflist.Rd
surveillance/man/twinstim_step.Rd
surveillance/man/stsSlots.Rd
surveillance/man/print.algoQV.Rd
surveillance/man/algo.bayes.Rd
surveillance/man/twinstim_siaf_simulatePC.Rd
surveillance/man/LRCUSUM.runlength.Rd
surveillance/man/simHHH.Rd
surveillance/man/earsC.Rd
surveillance/man/measlesDE.Rd
surveillance/man/epidata_summary.Rd
surveillance/man/refvalIdxByDate.Rd
surveillance/man/disProg2sts.Rd
surveillance/man/compMatrix.writeTable.Rd
surveillance/man/surveillance.options.Rd
surveillance/man/R0.Rd
surveillance/man/checkResidualProcess.Rd
surveillance/man/anscombe.residuals.Rd
surveillance/man/algo.farrington.assign.weights.Rd
surveillance/man/algo.compare.Rd
surveillance/man/influMen.Rd
surveillance/man/wrap.algo.Rd
surveillance/man/findH.Rd
surveillance/man/multiplicity.Rd
surveillance/man/twinstim_profile.Rd
surveillance/man/salmHospitalized.Rd
surveillance/man/algo.farrington.Rd
surveillance/man/animate.Rd
surveillance/man/loglikelihood.Rd
surveillance/man/twinstim_intensity.Rd
surveillance/man/ranef.Rd
surveillance/man/epidataCS_permute.Rd
surveillance/man/addFormattedXAxis.Rd
surveillance/man/linelist2sts.Rd
surveillance/man/residualsCT.Rd
surveillance/man/all.equal.Rd
surveillance/man/testSim.Rd
surveillance/man/readData.Rd
surveillance/man/makePlot.Rd
surveillance/man/permutationTest.Rd
surveillance/man/calibration.Rd
surveillance/man/ks.plot.unif.Rd
surveillance/man/algo.call.Rd
surveillance/man/shadar.Rd
surveillance/man/hhh4_calibration.Rd
surveillance/man/hhh4_simulate.Rd
surveillance/man/residuals.ah.Rd
surveillance/man/sts_observation.Rd
surveillance/man/hagelloch.Rd
surveillance/man/hhh4_validation.Rd
surveillance/man/twinstim_epitest.Rd
surveillance/man/stcd.Rd
surveillance/man/algo.outbreakP.Rd
surveillance/man/toLatex.sts.Rd
surveillance/man/hhh4.Rd
surveillance/man/unionSpatialPolygons.Rd
surveillance/man/algo.cdc.Rd
surveillance/man/stsXtrct.Rd
surveillance/man/predict.ah.Rd
surveillance/man/untie.Rd
surveillance/man/magic.dim.Rd
surveillance/man/algo.farrington.fitGLM.Rd
surveillance/man/m1.Rd
surveillance/man/twinSIR_cox.Rd
surveillance/man/intensityplot.Rd
surveillance/man/xtable.algoQV.Rd
surveillance/man/twinstim_methods.Rd
surveillance/man/formatPval.Rd
surveillance/man/create.grid.Rd
surveillance/man/knox.Rd
surveillance/man/pairedbinCUSUM.Rd
surveillance/man/epidataCS_animate.Rd
surveillance/man/twinSIR.Rd
surveillance/man/algo.hhh.Rd
surveillance/man/algo.farrington.threshold.Rd
surveillance/man/discpoly.Rd
surveillance/man/stsNC-class.Rd
surveillance/man/intersectPolyCircle.Rd
surveillance/man/salmAllOnset.Rd
surveillance/man/sts-class.Rd
surveillance/man/plapply.Rd
surveillance/man/test.Rd
surveillance/man/nowcast.Rd
surveillance/man/hhh4_predict.Rd
surveillance/man/stsAggregate.Rd
surveillance/man/stsNewport.Rd
surveillance/man/algo.rogerson.Rd
surveillance/man/epidata_plot.Rd
surveillance/man/meningo.age.Rd
surveillance/man/marks.Rd
surveillance/man/correct53to52.Rd
surveillance/man/find.kh.Rd
surveillance/man/scale.gpc.poly.Rd
surveillance/man/twinstim_siaf.Rd
surveillance/man/stsNClist_animate.Rd
surveillance/man/epidataCS_aggregate.Rd
surveillance/man/glm_epidataCS.Rd
surveillance/man/twinstim_iaf.Rd
surveillance/man/momo.Rd
surveillance/man/hepatitisA.Rd
surveillance/man/twinstim_tiaf.Rd
surveillance/man/sumNeighbours.Rd
surveillance/man/epidata.Rd
surveillance/man/inside.gpc.poly.Rd
surveillance/man/toFileDisProg.Rd
surveillance/man/twinSIR_profile.Rd
surveillance/man/twinstim_update.Rd
surveillance/man/algo.hmm.Rd
surveillance/man/algo.twins.Rd
surveillance/man/measles.weser.Rd
surveillance/man/pit.Rd
surveillance/man/layout.labels.Rd
surveillance/man/surveillance-package.Rd
surveillance/man/rotaBB.Rd
surveillance/man/stsplot_time.Rd
surveillance/man/findK.Rd
surveillance/man/stsplot_spacetime.Rd
surveillance/man/epidataCS_update.Rd
surveillance/man/stsplot_space.Rd
surveillance/man/nbOrder.Rd
surveillance/man/sim.pointSource.Rd
surveillance/man/hhh4_W.Rd
surveillance/man/stsBP-class.Rd
surveillance/man/ha.Rd
surveillance/man/hhh4_formula.Rd
surveillance/man/algo.summary.Rd
surveillance/man/algo.rki.Rd
surveillance/man/sts_creation.Rd
surveillance/man/deleval.Rd
surveillance/man/MMRcoverageDE.Rd
surveillance/man/plot.disProg.Rd
surveillance/man/bodaDelay.Rd
surveillance/man/algo.cusum.Rd
surveillance/man/enlargeData.Rd
surveillance/man/sim.seasonalNoise.Rd
surveillance/man/twinstim_iafplot.Rd
surveillance/man/hhh4_update.Rd
surveillance/man/make.design.Rd
surveillance/man/twinstim_simulation.Rd
surveillance/man/algo.glrnb.Rd
surveillance/man/isScalar.Rd
surveillance/man/salmonella.agona.Rd
surveillance/man/bestCombination.Rd
surveillance/man/plot.atwins.Rd
surveillance/man/qlomax.Rd
surveillance/man/hhh4_plot.Rd
surveillance/man/twinstim.Rd
surveillance/man/meanResponse.Rd
surveillance/man/boda.Rd
surveillance/man/algo.quality.Rd
surveillance/man/sts_animate.Rd
surveillance/man/multiplicity.Spatial.Rd
surveillance/man/farringtonFlexible.Rd
surveillance/man/poly2adjmat.Rd
surveillance/man/zetaweights.Rd
surveillance/man/abattoir.Rd
surveillance/man/salmNewport.Rd
surveillance/man/stK.Rd
surveillance/man/aggregate.disProg.Rd