Outbreak detection algorithms for surveillance data


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Documentation for package ‘surveillance’ version 1.0-3

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A B C D E F G H I K L M N O P Q R S T W X Y misc

-- --

surveillance-package Outbreak detection algorithms for surveillance data

-- A --

aggregate,sts,ANY,ANY-method Aggregate the the series of an sts object
aggregate,sts-method Aggregate the the series of an sts object
aggregate.disProg Aggregate the observed counts
algo.bayes The Bayes System
algo.bayes1 The Bayes System
algo.bayes2 The Bayes System
algo.bayes3 The Bayes System
algo.bayesLatestTimepoint The Bayes System
algo.call Query Transmission to Specified Surveillance Systems
algo.cdc The CDC Algorithm
algo.cdcLatestTimepoint The CDC Algorithm
algo.compare Comparison of Specified Surveillance Systems using Quality Values
algo.cusum CUSUM method
algo.farrington Surveillance for a time series using the Farrington procedure.
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 Threshold computations using a two sided confidence interval
algo.glrnb Cound data regression charts
algo.glrpois Poisson regression charts
algo.hhh Model fit based on the Held, Hoehle, Hofman paper
algo.hhh.grid Function to try multiple starting values
algo.hmm Hidden Markov Model (HMM) method
algo.quality Computation of Quality Values for a Surveillance System Result
algo.rki The system used at the RKI
algo.rki1 The system used at the RKI
algo.rki2 The system used at the RKI
algo.rki3 The system used at the RKI
algo.rkiLatestTimepoint 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
anscombe.residuals Compute Anscombe residuals
arlCusum Calculation of Average Run Length for discrete CUSUM schemes
as.data.frame,sts-method Class "sts" - surveillance time series

-- B --

bayes Multivariate Surveillance through independent univariate algorithms
bestCombination Partition of a number into two factors

-- C --

cdc Multivariate Surveillance through independent univariate algorithms
CIdata Confidence-Interval for the Mean of the Poisson Distribution
coef.ah Model fit based on the Held, Hoehle, Hofman paper
coef.ahg Function to try multiple starting values
colnames,sts,missing,missing-method Class "sts" - surveillance time series
compMatrix.writeTable Latex Table Generation
correct53to52 Data Correction from 53 to 52 weeks
create.disProg Creating an object of class disProg
create.grid Computes a matrix of initial values
cusum Multivariate Surveillance through independent univariate algorithms

-- D --

dim,sts-method Class "sts" - surveillance time series
disProg2sts Convert disProg object to sts and vice versa

-- E --

enlargeData Data Enlargement
estimateGLRNbHook Hook function for in-control mean estimation
estimateGLRPoisHook Hook function for in-control mean estimation

-- F --

farrington Multivariate Surveillance through independent univariate algorithms
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

-- G --

glrnb Multivariate Surveillance through independent univariate algorithms
glrpois Multivariate Surveillance through independent univariate algorithms

-- H --

h1_nrwrp RKI SurvStat Data
ha Hepatitis A in Berlin
hepatitisA Hepatitis A in Germany
hmm Multivariate Surveillance through independent univariate algorithms
hValues Find decision interval for given in-control ARL and reference value

-- I --

influMen Influenza and meningococcal infections in Germany, 2001-2006
initialize,sts-method Class "sts" - surveillance time series

-- K --

k1 RKI SurvStat Data

-- L --

loglikelihood Calculation of the loglikelihood needed in algo.hhh

-- M --

m1 RKI SurvStat Data
m2 RKI SurvStat Data
m3 RKI SurvStat Data
m4 RKI SurvStat Data
m5 RKI SurvStat Data
magic.dim Returns a suitable k1 x k2 for plotting the disProgObj
make.design Create the design matrices
makePlot Plot Generation
meanResponse Calculate mean response needed in algo.hhh
measles.weser Measles epidemics in Lower Saxony in 2001-2002
meningo.age Meningococcal infections in France 1985-1995

-- N --

n1 RKI SurvStat Data
n2 RKI SurvStat Data
ncol,sts-method Class "sts" - surveillance time series
nrow,sts-method Class "sts" - surveillance time series

-- O --

obsinyear ~~ Methods for Function obsinyear ~~
obsinyear,sts-method ~~ Methods for Function obsinyear ~~
obsinyear-methods ~~ Methods for Function obsinyear ~~

-- P --

plot Display Methods for Surveillance Time-Series Objects
plot,sts,missing-method Display Methods for Surveillance Time-Series Objects
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.disProg.one Plot Generation of the Observed and the defined Outbreak States of a (multivariate) time series
plot.sts.alarm Display Methods for Surveillance Time-Series Objects
plot.sts.spacetime Display Methods for Surveillance Time-Series Objects
plot.sts.time Display Methods for Surveillance Time-Series Objects
plot.sts.time.one Display Methods for Surveillance Time-Series Objects
plot.survRes Plot a survRes object
plot.survRes.one Plot a survRes object
predict.ah Predictions from a HHH model
predict.ahg Predictions from a HHH model
primeFactors Prime number factorization
print.ah Model fit based on the Held, Hoehle, Hofman paper
print.ahg Function to try multiple starting values
print.algoQV Print quality value object

-- Q --

q1_nrwh RKI SurvStat Data
q2 RKI SurvStat Data

-- R --

readData Reading of Disease Data
residuals.ah Residuals from a HHH model
residuals.ahg Residuals from a HHH model
rki Multivariate Surveillance through independent univariate algorithms
rogerson Multivariate Surveillance through independent univariate algorithms

-- S --

s1 RKI SurvStat Data
s2 RKI SurvStat Data
s3 RKI SurvStat Data
salmonella.agona Salmonella Agona cases in the UK 1990-1995
shadar Salmonella Hadar cases in Germany 2001-2006
show,sts-method Display Methods for Surveillance Time-Series Objects
sim.pointSource Generation of Simulated Point Source Epidemy
sim.seasonalNoise Generation of Background Noise for Simulated Timeseries
simHHH Simulates data based on the model proposed by Held et. al (2005)
simHHH.ah Simulates data based on the model proposed by Held et. al (2005)
simHHH.default Simulates data based on the model proposed by Held et. al (2005)
sts-class Class "sts" - surveillance time series
sts2disProg Convert disProg object to sts and vice versa
sumNeighbours Calculates the sum of counts of adjacent areas
surveillance Outbreak detection algorithms for surveillance data

-- T --

test Print xtable for several diseases and the summary
testSim Print xtable for a Simulated Disease and the Summary
toFileDisProg Writing of Disease Data

-- W --

wrap.algo Multivariate Surveillance through independent univariate algorithms

-- X --

xtable.algoQV Xtable quality value object

-- Y --

year Methods for Function year
year,sts-method Methods for Function year
year-methods Methods for Function year

-- misc --

[,sts-method Methods for "[": Extraction or Subsetting in Package 'surveillance'
[-methods Methods for "[": Extraction or Subsetting in Package 'surveillance'