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>.

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 publication2016-12-20 18:31:08
MaintainerSebastian Meyer <seb.meyer@fau.de>
LicenseGPL-2
Version1.13.0
http://surveillance.r-forge.r-project.org/

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 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

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-earsc.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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.