API for surveillance
Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Global functions
AIC.twinSIR Man page Source code
Egd Source code
LLR.fun Man page Source code
LRCUSUM.runlength Man page Source code
Lambda Source code
MMRcoverageDE Man page
OSAICpenalty Source code
R0 Man page Source code
R0.simEpidataCS Man page Source code
R0.twinstim Man page Source code
RPS Man page Source code
W_np Man page Source code
W_powerlaw Man page Source code
Ztilde.chibarsq Source code
[,sts,ANY,ANY,ANY-method Man page
[,sts-method Man page
[.epidata Man page
[.epidataCS Man page
abattoir Man page
add.legend Source code
add.on.exit Source code
add1.twinstim Man page
addFormattedXAxis Man page Source code
addSeason2formula Man page Source code
aggregate,sts,ANY,ANY-method Man page
aggregate,sts-method Man page
aggregate.disProg Man page Source code
aggregate.hhh4sims Man page Source code
aggregate.hhh4simslist Man page Source code
alarms Man page
alarms,sts-method Man page
alarms<- Man page
alarms<-,sts-method Man page
algo.bayes Man page Source code
algo.bayes1 Man page Source code
algo.bayes2 Man page Source code
algo.bayes3 Man page Source code
algo.bayesLatestTimepoint Man page Source code
algo.call Man page Source code
algo.cdc Man page Source code
algo.cdcLatestTimepoint Man page Source code
algo.compare Man page Source code
algo.cusum Man page Source code
algo.farrington Man page Source code
algo.farrington.assign.weights Man page Source code
algo.farrington.data.glm Source code
algo.farrington.fitGLM Man page Source code
algo.farrington.fitGLM.fast Man page Source code
algo.farrington.fitGLM.flexible Source code
algo.farrington.fitGLM.populationOffset Man page Source code
algo.farrington.glm Source code
algo.farrington.referencetimepoints Source code
algo.farrington.threshold Man page Source code
algo.farrington.threshold.farrington Source code
algo.farrington.threshold.noufaily Source code
algo.glrnb Man page Source code
algo.glrpois Man page Source code
algo.hhh Man page Source code
algo.hhh.grid Man page Source code
algo.hmm Man page Source code
algo.outbreakP Man page Source code
algo.quality Man page Source code
algo.rki Man page Source code
algo.rki1 Man page Source code
algo.rki2 Man page Source code
algo.rki3 Man page Source code
algo.rkiLatestTimepoint Man page Source code
algo.rogerson Man page Source code
algo.summary Man page Source code
algo.twins Man page Source code
all.equal.hhh4 Man page Source code
all.equal.twinstim Man page Source code
amplitudeShift2sinCos Source code
animate Man page Source code
animate.epidata Man page Source code
animate.epidataCS Man page Source code
animate.sts Man page Source code
animate.summary.epidata Man page Source code
animate_nowcasts Man page Source code
anscombe.residuals Man page Source code
anscombeNB Source code
areaSpatialPolygons Source code
arlCusum Man page Source code
as.SpatialPointsDataFrame.epidataCS Source code
as.data.frame,sts-method Man page
as.epidata Man page Source code
as.epidata.data.frame Man page Source code
as.epidata.default Man page Source code
as.epidata.epidataCS Man page Source code
as.epidataCS Man page Source code
as.hhh4simslist Man page Source code
as.hhh4simslist.hhh4sims Source code
as.hhh4simslist.hhh4simslist Source code
as.hhh4simslist.list Source code
as.stepfun.epidataCS Man page Source code
as.ts.sts Source code
as.twinstim.simEpidataCS Source code
as.xts.sts Man page Source code
at2ndChange Man page Source code
atChange Man page Source code
atMedian Man page Source code
autoplot.sts Man page Source code
backprojNP Man page Source code
backprojNP.fit Man page Source code
bayes Man page Source code
bdist Source code
bestCombination Man page Source code
bisection Source code
blocks Source code
boda Man page Source code
bodaDelay Man page Source code
bodaDelay.data.glm Source code
bodaDelay.fitGLM Source code
bodaDelay.threshold Source code
bodaFit Source code
calc.outbreakP.statistic Man page Source code
calibrationTest Man page Source code
calibrationTest.default Man page Source code
calibrationTest.hhh4 Man page Source code
calibrationTest.oneStepAhead Man page Source code
calibrationZ Source code
call.polyCub.iso Source code
campyDE Man page
catcusum.LLRcompute Man page Source code
categoricalCUSUM Man page Source code
checkAnalyticals Source code
checkCoefs Source code
checkDerivatives.maxLik Source code
checkDerivatives.numDeriv Source code
checkFormula Source code
checkNeighbourhood Source code
checkParBounds Source code
checkQ Source code
checkResidualProcess Man page Source code
checkWeights Source code
checkWeightsArray Source code
checkWeightsFUN Source code
check_W Source code
check_W_area Source code
check_events Source code
check_groups Source code
check_stgrid Source code
check_tiles Source code
check_tiles_areas Source code
check_tiles_events Source code
check_twinstim_start Source code
checkat Source code
checknargs3 Source code
checksiaf Source code
checksiaf.Deriv Source code
checksiaf.F Source code
checksiaf.Fcircle Source code
checksiaf.deriv Source code
checksiaf.simulate Source code
clapply Man page Source code
coef.ah Man page Source code
coef.ahg Man page Source code
coef.epitest Man page Source code
coef.hhh4 Man page Source code
coef.summary.twinstim Source code
coefW Man page Source code
coeflist Man page Source code
coeflist.default Man page Source code
coeflist.hhh4 Man page Source code
coeflist.twinstim Man page
coerce,epidataCS,SpatialPointsDataFrame-method 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
colSumsGrouped Source code
commonDenom Source code
compMatrix.writeTable Man page Source code
componentsHHH4 Source code
compute_wijlist Source code
confint.hhh4 Man page Source code
confint.oneStepAhead Man page Source code
control Man page
control,sts-method Man page
control2nlminb Source code
control<- Man page
control<-,sts-method Man page
correct53to52 Man page Source code
countunique Source code
cox Man page Source code
create.disProg Man page Source code
create.grid Man page Source code
createLambda Source code
crudebeta0 Source code
cusum Man page Source code
d2Sigma1 Source code
d2Sigma2 Source code
d2Sigma3 Source code
dSigma1 Source code
dSigma2 Source code
dSigma3 Source code
dbnb Source code
decompose.hhh4 Man page Source code
defaultOptimControl Source code
delayCDF Man page
delayCDF,stsNC-method Man page
deleval Man page
determineSources Source code
determineSources.epidataCS Source code
determineSources1 Source code
determineSourcesC Source code
diameter.gpc.poly Source code
dim,sts-method Man page
dimnames,sts-method Man page
disProg2sts Man page Source code
discpoly Man page Source code
dist.median Man page Source code
dpost.bnb Source code
dpost.bnb.unorm Source code
drop1.twinstim Man page
dss Man page Source code Source code
dss_EV Source code
dss_sims Source code
earsC Man page Source code
eh Source code
em.step.becker Man page Source code
enlargeData Man page Source code
epidata Man page
epidataCS Man page
epidataCS2sts Man page Source code
epidataCSplot_space Man page Source code
epidataCSplot_time Man page Source code
epilink Source code
epitest Man page Source code
epoch Man page
epoch,sts-method Man page
epoch<- Man page
epoch<-,sts-method Man page
epochInYear Man page
epochInYear,sts-method Man page
estimateGLRNbHook Man page Source code
expAlpha.mm Source code
extractAIC.twinSIR Man page Source code
extractAIC.twinstim Source code
fanplot Man page Source code
farrington Man page Source code
farringtonFlexible Man page Source code
fe Man page Source code
find.kh Man page Source code
findH Man page Source code
findK Man page Source code
fisherinfo Source code
fitHHH Source code
fix.dimnames Source code
fix.dimnamesBP Source code
fixef Man page
fixef.hhh4 Man page Source code
fluBYBW Man page
foodata Man page
fooepidata Man page
foofit Man page
formatDate Man page Source code
formatPval Man page Source code
formula.hhh4 Man page Source code
formulaGLM Source code
formulaGLMDelay Source code
functionTable Source code
get.surveillance.options Source code
getCoefIdxRenamed Source code
getCumCounts Source code
getFcircle Source code
getHHH4list Source code
getHK Source code
getLambda Source code
getMaxEV Man page Source code
getMaxEV_season Man page Source code
getModel Source code
getModel.simEpidata Source code
getModel.twinSIR Source code
getNEweights Man page Source code
getPrettyIntervals Source code
getREmat Source code
getRelDiff Source code
getSeason Source code
getSeasonStart Source code
getSigma Source code
getSigmaInv Source code
getSigmai Source code
getSigmaiInv Source code
getSourceDists Man page Source code
getSummary Source code
getTheta1 Source code
glm_epidataCS Man page Source code
glrnb Man page Source code
glrpois Man page Source code
gpclibCheck Source code
gradient Source code
gridcellOfEvent Source code
gsub2 Source code
h1_nrwrp Man page
hGrid Source code
hValues Man page Source code
ha Man page
ha.sts Man page
hagelloch Man page
hagelloch.df Man page
haz2pmf Source code Source code
hcl.colors Man page Source code
head.epidataCS Man page Source code
hepatitisA Man page
hhh4 Man page Source code
hhh4coef2start Source code
hhh4simslist Source code
hmm Man page Source code
husO104Hosp Man page
hypgeom2F1special Source code
iafplot Man page Source code
idxNonMarks Source code
imdepi Man page
imdepifit Man page
influMen Man page
init.sts Source code
init.stsBP Source code
init.stsNC Source code
initialize,sts-method Man page
inside.gpc.poly Man page Source code
intensity.twinstim Man page Source code
intensityplot Man page Source code
intensityplot.simEpidata Man page Source code
intensityplot.simEpidataCS Man page Source code
intensityplot.twinSIR Man page Source code
intensityplot.twinstim Man page Source code
intensityplot_twinSIR Source code
interpretControl Source code
intersectPolyCircle Man page Source code
intersectPolyCircle.SpatialPolygons Man page Source code
intersectPolyCircle.gpc.poly Man page Source code
intersectPolyCircle.owin Man page Source code
intersperse Man page Source code
intrfr.powerlaw Source code
intrfr.powerlaw.dlogd Source code
intrfr.powerlaw.dlogsigma Source code
intrfr.powerlawL Source code
intrfr.powerlawL.dlogd Source code
intrfr.powerlawL.dlogsigma Source code
intrfr.student Source code
intrfr.student.dlogd Source code
intrfr.student.dlogsigma Source code
isInModel Source code
isScalar Man page Source code
isoWeekYear Man page Source code
jacobian Source code
jacobianAmplitudeShift Source code
k1 Man page
knox Man page Source code
ks.plot.unif Man page Source code
layout.labels Man page Source code
layout.scalebar Man page Source code
likelihood.ci Source code
linelist2sts Man page Source code
lmarg.lambda Source code
logInterpolation Source code
logLik.ah Source code
logLik.ahg Source code
logLik.hhh4 Man page Source code
logLik.twinSIR Man page Source code
logLik.twinstim Man page Source code
logS Man page Source code
loglik Source code
loglikelihood Man page Source code
lognormDiscrete Source code
logs Man page Source code Source code
logs_EV_1NB Source code
logs_EV_1P Source code
logs_sims Source code
m1 Man page
m2 Man page
m3 Man page
m4 Man page
m5 Man page
magic.dim Man page Source code
make.design Man page Source code
make.nu Source code
make.pois Source code
makeControl Man page Source code
makePlot Man page Source code
mapplyCall Source code
mapplyFUN Source code
marFisher Source code
marLogLik Source code
marScore Source code
marks Man page
marks.epidataCS Man page Source code
maxEV Source code
meanHHH Man page Source code
meanResponse Man page Source code
measles.weser Man page
measlesDE Man page
measlesWeserEms Man page
meningo.age Man page
momo Man page
multinomialTS Man page
multinomialTS,sts-method Man page
multinomialTS<- Man page
multinomialTS<-,sts-method Man page
multiplicity Man page
multiplicity.Spatial Man page Source code
n1 Man page
n2 Man page
na2FALSE Source code
naninf2zero Man page Source code
nbOrder Man page Source code
neOffsetArray Source code
neOffsetFUN Source code
neighbourhood Man page
neighbourhood,sts-method Man page
neighbourhood<- Man page
neighbourhood<-,sts-method Man page
newtonRaphson Source code
nfluenceRegions Source code
nobs.epidataCS Man page Source code
nobs.hhh4 Man page Source code
nobs.twinstim Man page Source code
normalizeW Source code
nowcast Man page Source code
nses Source code
observed Man page
observed,sts-method Man page
observed<- Man page
observed<-,sts-method Man page
onAttach Source code
onLoad Source code
oneStepAhead Man page Source code
outbreakP Man page Source code
outcomeFunStandard Man page Source code
outside.ci Man page Source code
pairedbinCUSUM Man page Source code
pairedbinCUSUM.LLRcompute Man page Source code
pairedbinCUSUM.runlength Man page Source code
parse_population_argument Source code
parseiaf Source code
penFisher Source code
penLogLik Source code
penScore Source code
permtestplot Source code
permutationTest Man page Source code
permute.epidataCS Man page Source code
pfisherinfo Source code
pit Man page Source code Source code
pit.default Man page Source code
pit.hhh4 Man page Source code
pit.oneStepAhead Man page Source code
pit1 Source code
pitPxPxm1 Source code
plapply Man page Source code
ploglik Source code
plot,sts,missing-method Man page
plot,stsNC,missing-method Man page
plot.atwins Man page Source code
plot.disProg Man page Source code
plot.disProg.one Man page Source code
plot.epidata Man page Source code
plot.epidataCS Man page Source code
plot.epitest Man page Source code
plot.hhh4 Man page Source code
plot.hhh4sims Man page Source code
plot.hhh4simslist Man page Source code
plot.knox Man page Source code
plot.oneStepAhead Man page Source code
plot.pit Source code
plot.profile.twinSIR Man page Source code
plot.simEpidataCSlist Source code
plot.stKtest Man page Source code
plot.summary.epidata Man page Source code
plot.survRes Man page Source code
plot.survRes.one Man page Source code
plot.twinSIR Man page Source code
plot.twinstim Man page Source code
plotComponentPolygons Source code
plotHHH4_fitted Man page Source code
plotHHH4_fitted1 Man page Source code
plotHHH4_fitted_check_col_decompose Source code
plotHHH4_maps Man page Source code
plotHHH4_maxEV Man page Source code
plotHHH4_neweights Man page Source code
plotHHH4_ri Man page Source code
plotHHH4_season Man page Source code
plotHHH4sims_fan Man page Source code
plotHHH4sims_size Man page Source code
plotHHH4sims_time Man page Source code
pmfQuantile Source code
pmix Source code
pois.plot Source code
poly2adjmat Man page Source code
polyAtBorder Man page Source code
population Man page
population,sts-method Man page
population<- Man page
population<-,sts-method Man page
predict.ah Man page Source code
predict.ahg Man page Source code
predict.hhh4 Man page Source code
predint Man page
predint,stsNC-method Man page
primeFactors Man page Source code
print.ah Man page Source code
print.ahg Man page Source code
print.algoQV Man page Source code
print.disProg Man page Source code
print.epidata Man page Source code
print.epidataCS Man page Source code
print.epidataCS_header Source code
print.hhh4 Man page Source code
print.knox Source code
print.simEpidataCSlist Source code
print.summary.epidata Man page Source code
print.summary.epidataCS Man page Source code
print.summary.hhh4 Man page Source code
print.summary.twinSIR Man page Source code
print.summary.twinstim Man page Source code
print.twinSIR Man page Source code
print.twinstim Man page Source code
printREmat Source code
profile.twinSIR Man page Source code
profile.twinstim Man page Source code
pscore Source code
psi2size.hhh4 Source code
psi2size.oneStepAhead Source code
q1_nrwh Man page
q2 Man page
qlomax Man page Source code
qmix Source code
quantile.oneStepAhead Man page Source code
ranef Man page
ranef.hhh4 Man page Source code
rangeOfDataToPlot Source code
read.design Source code
readData Man page Source code
refvalIdxByDate Man page Source code
removeSeasonFromFormula Source code
removeTimeFromFormula Source code
reportingTriangle Man page
reportingTriangle,stsNC-method Man page
reset.surveillance.options Man page Source code
residuals.ah Man page Source code
residuals.ahg Man page Source code
residuals.hhh4 Man page Source code
residuals.simEpidataCS Man page Source code
residuals.twinSIR Man page Source code
residuals.twinstim Man page Source code
rgd Source code
ri Man page Source code
rki Man page Source code
rmarks Source code
rogerson Man page Source code
rotaBB Man page
rowSumsBy.matrix Source code
rowSumsBy.sts Source code
rpost.bnb Source code
rps Man page Source code Source code
rps_1NB Source code
rps_1P Source code
rps_EV_1NB Source code
rps_EV_1P Source code
rps_sims Source code
runifdisc Man page Source code
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 Source code
scale2longlat Source code
scaleNEweights.default Source code
scaleNEweights.list Source code
score Man page Source code
score,stsNC-method Man page
score_EV Source code
scores Man page Source code
scores.default Man page Source code
scores.hhh4 Man page Source code
scores.hhh4sims Man page Source code
scores.hhh4simslist Man page Source code
scores.oneStepAhead Man page Source code
ses Man page Source code
setControl Source code
setOptimControl Source code
shadar Man page
siaf Man page Source code
siaf.constant Man page Source code
siaf.fallback.Deriv Source code
siaf.fallback.F Source code
siaf.gaussian Man page Source code
siaf.powerlaw Man page Source code
siaf.powerlawL Man page Source code
siaf.simulatePC Man page Source code
siaf.step Man page Source code
siaf.student Man page Source code
siafIntFUN Source code
siaf_Deriv_polyCub_iso Source code
siaf_F_polyCub_iso Source code
siaf_polyCub1_iso Source code
siaf_polyCub_iso Source code
sim.pointSource Man page Source code
sim.seasonalNoise Man page Source code
simEndemicEvents Man page Source code
simEpidata Man page Source code
simEpidataCS Man page Source code
simHHH Man page Source code
simHHH.ah Man page Source code
simHHH.default Man page Source code
simHHH4 Source code
simpleR0 Man page Source code
simulate.hhh4 Man page Source code
simulate.twinSIR Man page Source code
simulate.twinstim Man page Source code
sinCos2amplitudeShift Source code
sizeHHH Man page Source code
splitParams Source code
sqrtOf1pr2 Source code
stKcall Source code
stKtest Man page Source code
stateplot Man page Source code
stcd Man page Source code
step2twinstim Source code
stepComponent Man page Source code
sts Man page Source code
sts-class Man page
sts2disProg Man page Source code
stsBP-class Man page
stsNC-class Man page
stsNC_plotDelay Source code
stsNClist_animate Man page
stsNewport Man page
stsTime2text Source code
stsTimeRange2text Source code
sts_creation Man page Source code
sts_observation Man page Source code
stsplot Man page
stsplot_alarm Man page Source code
stsplot_space Man page Source code
stsplot_spacetime Man page Source code
stsplot_time Man page Source code
stsplot_time1 Man page Source code
stsplot_timeSimple Source code
stsplot_time_as1 Source code
subset.epidataCS Man page Source code
subset_hhh4sims_attributes Source code
summary.epidata Man page Source code
summary.epidataCS Man page Source code
summary.hhh4 Man page Source code
summary.twinSIR Man page Source code
summary.twinstim Man page Source code
surveillance-deprecated Man page
surveillance.options Man page Source code
tail.epidataCS Man page Source code
terms.hhh4 Man page Source code
terms.twinstim Source code
test Man page Source code
testSim Man page Source code
tiaf Man page Source code
tiaf.constant Man page Source code
tiaf.exponential Man page Source code
tiaf.step Man page Source code
tiafIntFUN Source code
tidy.sts Man page Source code
tiles2stgrid Source code
tms.plot Source code
toFileDisProg Man page Source code
toLatex,sts-method Man page
toLatex.knox Man page Source code
toLatex.sts Man page Source code
toLatex.summary.twinstim Man page Source code
tooClose Source code
twinSIR Man page Source code
twinstim Man page Source code
unionSpatialPolygons Man page Source code
unpackParams Source code
untie Man page Source code Source code
untie.default Man page Source code
untie.epidataCS Man page Source code
untie.matrix Man page Source code
update.epidata Man page Source code
update.epidataCS Man page Source code
update.hhh4 Man page Source code
update.twinstim Man page Source code
update.twinstim.model Source code
update.twinstim_stependemic Source code
update.twinstim_stepepidemic Source code
updateMoveExpr Source code
updateParams_nlm Source code
updateParams_nlminb Source code
updateParams_nr Source code
updateParams_optim Source code
upperbound Man page
upperbound,sts-method Man page
upperbound<- Man page
upperbound<-,sts-method Man page
vcov.hhh4 Man page Source code
vcov.summary.twinstim Source code
vcov.twinSIR Man page Source code
vcov.twinstim Man page Source code
w.chibarsq.sim Source code
wait Source code
weightedSumNE Source code
weightedSumNeighbours Source code
wrap.algo Man page Source code
xtable.algoQV Man page Source code
xtable.knox Source code
xtable.summary.twinstim Man page Source code
xtable.twinstim Man page Source code
year Man page
year,sts-method Man page
yearepoch2point Source code
zScore1 Source code
zScore2 Source code
zetaweights Man page Source code
surveillance documentation built on May 29, 2018, 1:07 a.m.