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MMRcoverageDE MMR coverage levels in the 16 states of Germany
R0 Computes reproduction numbers from fitted
models
W_powerlaw Power-Law and Nonparametric Neighbourhood
Weights for 'hhh4'-Models
[,sts-method Extraction and Subsetting of '"sts"' Objects
abattoir Abattoir Data
addFormattedXAxis Formatted Time Axis for '"sts"' Objects
addSeason2formula Function that adds a sine-/cosine formula to an
existing formula.
aggregate,sts,ANY,ANY-method
Aggregate an '"sts"' Object Over Time or Across
Units
aggregate.disProg Aggregate the observed counts
alarms Generic functions to access '"sts"' slots
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 Values
algo.cusum CUSUM method
algo.farrington Surveillance for a count data time series using
the Farrington method.
algo.farrington.assign.weights
Assign weights to base counts
algo.farrington.fitGLM
Fit the Poisson GLM of the Farrington procedure
for a single time point
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 Values
algo.hmm Hidden Markov Model (HMM) method
algo.outbreakP Semiparametric surveillance of outbreaks
algo.quality Computation of Quality Values for a
Surveillance System Result
algo.rki The system used at the RKI
algo.rogerson Modified CUSUM method as proposed by Rogerson
and Yamada (2004)
algo.summary Summary Table Generation for Several Disease
Chains
algo.twins Model fit based on a two-component epidemic
model
all.equal.twinstim Test if Two Model Fits are (Nearly) Equal
animate Generic animation of spatio-temporal objects
animate.epidata Spatio-Temporal Animation of an Epidemic
animate.epidataCS Spatio-Temporal Animation of a Continuous-Time
Continuous-Space Epidemic
animate.sts Animated Maps and Time Series of Disease Counts
or Incidence
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 cases using a known
incubation time as in Becker et al (1991).
bestCombination Partition of a number into two factors
boda Surveillance for an univariate count data time
series using the Bayesian Outbreak Detection
Algorithm (BODA) described in Manitz and Hoehle
(2013)
bodaDelay Bayesian Outbreak Detection in the Presence of
Reporting Delays
calibrationTest Calibration Test for Poisson or Negative
Binomial Predictions
calibrationTest.hhh4 Test Calibration of a 'hhh4' Model
campyDE Cases of Campylobacteriosis and Absolute
Humidity in Germany 2002-2011
categoricalCUSUM CUSUM detector for time-varying categorical
time series
checkResidualProcess Check the residual process of a fitted
'twinSIR' or 'twinstim'
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
disProg2sts Convert disProg object to sts and vice versa
discpoly Polygonal Approximation of a Disc/Circle
earsC Surveillance for a count data time series using
the EARS C1, C2 or C3 method and its extensions
enlargeData Data Enlargement
epidata Continuous-Time SIR Event History of a Fixed
Population
epidataCS Continuous Space-Time Marked Point Patterns
with Grid-Based Covariates
epidataCS2sts Conversion (aggregation) of '"epidataCS"' to
'"epidata"' or '"sts"'
epitest Permutation Test for Space-Time Interaction in
'"twinstim"'
farringtonFlexible Surveillance for an univariate count data time
series using the improved Farrington method
described in Noufaily et al. (2012).
fe Specify Formulae in a Random Effects HHH Model
find.kh Determine the k and h values in a standard
normal setting
findH Find decision interval for given in-control ARL
and reference value
findK Find reference value
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 Structure
husO104Hosp Hospitalization date for HUS cases of the STEC
outbreak in Germany, 2011
iafplot Plot the Spatial or Temporal Interaction
Function of a 'twimstim'
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
intensityplot.twinstim
Plotting Intensities of Infection over Time or
Space
intersectPolyCircle Intersection of a Polygonal and a Circular
Domain
intersperse Impute Blocks for Extra Stops in '"epidata"'
Objects
isoWeekYear Find ISO week and ISO year of a vector of Date
objects on Windows
knox Knox Test for Space-Time Interaction
ks.plot.unif Plot the ECDF of a uniform sample with
Kolmogorov-Smirnov bounds
layout.labels Layout Items for 'spplot'
linelist2sts Convert individual case information based on
dates into an aggregated time series of counts
m1 RKI SurvStat Data
magic.dim Returns a suitable k1 x k2 for plotting the
disProgObj
makePlot Plot Generation
marks Import from package 'spatstat'
measles.weser Measles in the Weser-Ems region of Lower
Saxony, Germany, 2001-2002
measlesDE Measles in the 16 states of Germany
meningo.age Meningococcal infections in France 1985-1995
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 Matrix
nowcast Adjust a univariate time series of counts for
observed but-not-yet-reported events
oneStepAhead Predictive Model Assessment for 'hhh4' Models
pairedbinCUSUM Paired binary CUSUM and its run-length
computation
permutationTest Monte Carlo Permutation Test for Paired
Individual Scores
permute.epidataCS Randomly Permute Time Points or Locations of
'"epidataCS"'
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 States of a (multivariate) time series
plot.epidata Plotting the Evolution of an Epidemic
plot.epidataCS Plotting the Events of an Epidemic over Time
and Space
plot.hhh4 Plots for Fitted 'hhh4'-models
plot.hhh4sims Summarize Simulations from '"hhh4"' Models
plot.survRes Plot a survRes object
plot.twinSIR Plotting Paths of Infection Intensities for
'twinSIR' Models
plot.twinstim Plot methods for fitted 'twinstim"s
poly2adjmat Derive Adjacency Structure of
'"SpatialPolygons"'
polyAtBorder Indicate Polygons at the Border
predict.ah Predictions from a HHH model
predict.hhh4 Predictions from a 'hhh4' Model
primeFactors Prime number factorization
print.algoQV Print quality value object
print.hhh4 Print, Summary and other Standard Methods for
'"hhh4"' Objects
print.twinSIR Print, Summary and Extraction Methods for
'"twinSIR"' Objects
print.twinstim Print, Summary and Extraction Methods for
'"twinstim"' Objects
profile.twinSIR Profile Likelihood Computation and Confidence
Intervals
profile.twinstim Profile Likelihood Computation and Confidence
Intervals for 'twinstim' objects
qlomax Quantile Function of the Lomax Distribution
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
residuals.twinSIR Extract Cox-Snell-like Residuals of a Fitted
Point Process
rotaBB Rotavirus cases in Brandenburg, Germany, during
2002-2013 stratified by 5 age categories
runifdisc Sample Points Uniformly on a Disc
salmAllOnset Salmonella cases in Germany 2001-2014 by data
of symptoms onset
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
siaf Spatial Interaction Function Objects
siaf.constant Temporal and Spatial Interaction Functions for
'twinstim'
sim.pointSource Simulate Point-Source Epidemics
sim.seasonalNoise Generation of Background Noise for Simulated
Timeseries
simEpidata Simulation of Epidemic Data
simEpidataCS Simulation of a Self-Exciting Spatio-Temporal
Point Process
simHHH Simulates data based on the model proposed by
Held et. al (2005)
simulate.hhh4 Simulate '"hhh4"' Count Time Series
stKtest Diggle et al (1995) K-function test for
space-time clustering
stcd Spatio-temporal cluster detection
stepComponent Stepwise Model Selection by AIC
sts-class Class '"sts"' - surveillance time series
stsBP-class Class "stsBP" - a class inheriting from class
'sts' which allows the user to store the
results of back-projecting or nowcasting
surveillance time series
stsNC-class Class "stsNC" - a class inheriting from class
'sts' which allows the user to store the
results of back-projecting surveillance time
series
stsNClist_animate Animate a sequence of nowcasts
stsNewport Salmonella Newport cases in Germany 2004-2013
sts_creation Function for simulating a time series
sts_observation Function for creating a sts-object with a given
observation date
stsplot Plot-Methods for Surveillance Time-Series
Objects
stsplot_space Map of Disease Counts/Incidence accumulated
over a Given Period
stsplot_spacetime Map of Disease Incidence
stsplot_time Time-Series Plots for '"sts"' Objects
summary.epidata Summarizing an Epidemic
surveillance-package Temporal and Spatio-Temporal Modeling and
Monitoring of Epidemic Phenomena
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
tiaf Temporal Interaction Function Objects
toFileDisProg Writing of Disease Data
toLatex.sts 'toLatex'-Method for '"sts"' Objects
twinSIR Fit an Additive-Multiplicative Intensity Model
for SIR Data
twinstim Fit a Two-Component Spatio-Temporal Point
Process Model
unionSpatialPolygons Compute the Unary Union of '"SpatialPolygons"'
untie Randomly Break Ties in Data
update.epidataCS Update method for '"epidataCS"'
update.hhh4 'update' a fitted '"hhh4"' model
update.twinstim 'update'-method for '"twinstim"'
wrap.algo Multivariate Surveillance through independent
univariate algorithms
xtable.algoQV Xtable quality value object
zetaweights Power-Law Weights According to Neighbourhood
Order
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