surveillance-package	surveillance-package
.hcl.colors	hcl.colors
abattoir	abattoir
add1.twinstim	twinstim_step
addFormattedXAxis	addFormattedXAxis
addSeason2formula	addSeason2formula
aggregate,sts-method	stsAggregate
aggregate.disProg	aggregate.disProg
aggregate.hhh4sims	hhh4_simulate_plot
aggregate.hhh4simslist	hhh4_simulate_plot
aggregate.sts	stsAggregate
AIC.twinSIR	twinSIR_methods
alarms	stsSlots
alarms,sts-method	sts-class
alarms<-	stsSlots
alarms<-,sts-method	sts-class
algo.bayes	algo.bayes
algo.bayes1	algo.bayes
algo.bayes2	algo.bayes
algo.bayes3	algo.bayes
algo.bayesLatestTimepoint	algo.bayes
algo.call	algo.call
algo.cdc	algo.cdc
algo.cdcLatestTimepoint	algo.cdc
algo.compare	algo.compare
algo.cusum	algo.cusum
algo.farrington	algo.farrington
algo.farrington.assign.weights	algo.farrington.assign.weights
algo.farrington.fitGLM	algo.farrington.fitGLM
algo.farrington.fitGLM.fast	algo.farrington.fitGLM
algo.farrington.fitGLM.populationOffset	algo.farrington.fitGLM
algo.farrington.threshold	algo.farrington.threshold
algo.glrnb	algo.glrnb
algo.glrpois	algo.glrnb
algo.hhh	surveillance-defunct
algo.hhh.grid	surveillance-defunct
algo.hmm	algo.hmm
algo.outbreakP	algo.outbreakP
algo.quality	algo.quality
algo.rki	algo.rki
algo.rki1	algo.rki
algo.rki2	algo.rki
algo.rki3	algo.rki
algo.rkiLatestTimepoint	algo.rki
algo.rogerson	algo.rogerson
algo.summary	algo.summary
algo.twins	surveillance-defunct
all.equal.hhh4	all.equal
all.equal.twinstim	all.equal
animate	animate
animate.epidata	epidata_animate
animate.epidataCS	epidataCS_animate
animate.sts	sts_animate
animate.summary.epidata	epidata_animate
animate_nowcasts	stsNClist_animate
anscombe.residuals	anscombe.residuals
arlCusum	arlCusum
as.data.frame,sts-method	sts-class
as.data.frame.sts	sts-class
as.epidata	epidata
as.epidata.data.frame	epidata
as.epidata.default	epidata
as.epidata.epidataCS	epidataCS_aggregate
as.epidataCS	epidataCS
as.hhh4simslist	hhh4_simulate_plot
as.stepfun.epidataCS	epidataCS
as.ts.sts	sts_coerce
as.xts.sts	sts_coerce
at2ndChange	addFormattedXAxis
atChange	addFormattedXAxis
atMedian	addFormattedXAxis
autoplot.sts	sts_ggplot
backprojNP	backprojNP
bayes	wrap.algo
bestCombination	bestCombination
boda	boda
bodaDelay	bodaDelay
calc.outbreakP.statistic	algo.outbreakP
calibrationTest	calibration
calibrationTest.default	calibration
calibrationTest.hhh4	hhh4_validation
calibrationTest.oneStepAhead	hhh4_validation
campyDE	campyDE
catcusum.LLRcompute	categoricalCUSUM
categoricalCUSUM	categoricalCUSUM
checkResidualProcess	checkResidualProcess
clapply	clapply
coef.epitest	twinstim_epitest
coef.hhh4	hhh4_methods
coeflist	coeflist
coeflist.default	coeflist
coeflist.hhh4	hhh4_methods
coeflist.twinstim	twinstim_methods
coefW	hhh4_W_utils
coerce,epidataCS,SpatialPointsDataFrame-method	epidataCS
coerce,sts,stsBP-method	stsBP-class
coerce,sts,stsNC-method	stsNC-class
coerce,sts,ts-method	sts_coerce
coerce,ts,sts-method	sts_coerce
compMatrix.writeTable	surveillance-defunct
confint.hhh4	hhh4_methods
confint.oneStepAhead	hhh4_validation
control	stsSlots
control,sts-method	sts-class
control<-	stsSlots
control<-,sts-method	sts-class
correct53to52	surveillance-defunct
cox	twinSIR_cox
create.disProg	create.disProg
create.grid	surveillance-defunct
cusum	wrap.algo
decompose.hhh4	hhh4_internals
delayCDF	stsNC-class
delayCDF,stsNC-method	stsNC-class
deleval	deleval
dim,sts-method	sts-class
dimnames,sts-method	sts-class
discpoly	discpoly
disProg2sts	disProg2sts
drop1.twinstim	twinstim_step
dss	scores
earsC	earsC
enlargeData	surveillance-defunct
epidata	epidata
epidataCS	epidataCS
epidataCS2sts	epidataCS_aggregate
epidataCSplot_space	epidataCS_plot
epidataCSplot_time	epidataCS_plot
epitest	twinstim_epitest
epoch	stsSlots
epoch,sts-method	sts-class
epoch<-	stsSlots
epoch<-,sts-method	sts-class
epochInYear	sts-class
epochInYear,sts-method	sts-class
estimateGLRNbHook	estimateGLRNbHook
extractAIC.twinSIR	twinSIR_methods
fanplot	fanplot
farrington	algo.farrington
farringtonFlexible	farringtonFlexible
fe	hhh4_formula
find.kh	find.kh
findH	findH
findK	findK
fixef	ranef
fixef.hhh4	hhh4_methods
fluBYBW	fluBYBW
fooepidata	twinSIR_exData
formatDate	formatDate
formatPval	formatPval
formula.hhh4	hhh4_methods
frequency,sts-method	sts-class
getMaxEV	hhh4_plot
getMaxEV_season	hhh4_plot
getNEweights	hhh4_W_utils
getSourceDists	epidataCS
glm_epidataCS	glm_epidataCS
glrnb	wrap.algo
glrpois	wrap.algo
h1_nrwrp	m1
ha	ha
ha.sts	ha
hagelloch	hagelloch
hagelloch.df	hagelloch
head.epidataCS	epidataCS
hepatitisA	hepatitisA
hhh4	hhh4
husO104Hosp	husO104Hosp
hValues	findH
iafplot	twinstim_iafplot
imdepi	imdepi
imdepifit	imdepifit
influMen	influMen
inside.gpc.poly	surveillance-defunct
intensity.twinstim	twinstim_intensity
intensityplot	intensityplot
intensityplot.simEpidata	twinSIR_intensityplot
intensityplot.simEpidataCS	twinstim_intensity
intensityplot.twinSIR	twinSIR_intensityplot
intensityplot.twinstim	twinstim_intensity
intersectPolyCircle	intersectPolyCircle
intersectPolyCircle.gpc.poly	surveillance-defunct
intersectPolyCircle.owin	intersectPolyCircle
intersperse	epidata_intersperse
isoWeekYear	isoWeekYear
k1	m1
knox	knox
ks.plot.unif	ks.plot.unif
layout.labels	layout.labels
layout.scalebar	layout.labels
linelist2sts	linelist2sts
logLik.hhh4	hhh4_methods
logLik.twinSIR	twinSIR_methods
logLik.twinstim	twinstim_methods
logs	scores
LRCUSUM.runlength	LRCUSUM.runlength
m1	m1
m2	m1
m3	m1
m4	m1
m5	m1
magic.dim	magic.dim
makeControl	makeControl
makePlot	surveillance-defunct
marks	marks
marks.epidataCS	epidataCS
meanHHH	hhh4_internals
measles.weser	measles.weser
measlesDE	measlesDE
measlesWeserEms	measles.weser
meningo.age	meningo.age
MMRcoverageDE	MMRcoverageDE
momo	momo
multinomialTS	stsSlots
multinomialTS,sts-method	sts-class
multinomialTS<-	stsSlots
multinomialTS<-,sts-method	sts-class
multiplicity	multiplicity
multiplicity.Spatial	multiplicity.Spatial
n1	m1
n2	m1
nbOrder	nbOrder
neighbourhood	stsSlots
neighbourhood,sts-method	sts-class
neighbourhood<-	stsSlots
neighbourhood<-,sts-method	sts-class
nobs.epidataCS	epidataCS
nobs.hhh4	hhh4_methods
nobs.twinstim	twinstim_methods
nowcast	nowcast
observed	stsSlots
observed,sts-method	sts-class
observed<-	stsSlots
observed<-,sts-method	sts-class
oneStepAhead	hhh4_validation
outbreakP	wrap.algo
pairedbinCUSUM	pairedbinCUSUM
pairedbinCUSUM.LLRcompute	pairedbinCUSUM
pairedbinCUSUM.runlength	pairedbinCUSUM
permutationTest	permutationTest
permute.epidataCS	epidataCS_permute
pit	pit
pit.default	pit
pit.hhh4	hhh4_validation
pit.oneStepAhead	hhh4_validation
plapply	plapply
plot,sts,missing-method	stsplot
plot,stsNC,missing-method	stsplot
plot.atwins	surveillance-defunct
plot.disProg	plot.disProg
plot.epidata	epidata_plot
plot.epidataCS	epidataCS_plot
plot.epitest	twinstim_epitest
plot.hhh4	hhh4_plot
plot.hhh4sims	hhh4_simulate_plot
plot.hhh4simslist	hhh4_simulate_plot
plot.knox	knox
plot.oneStepAhead	hhh4_validation
plot.profile.twinSIR	twinSIR_profile
plot.stKtest	stK
plot.sts	stsplot
plot.summary.epidata	epidata_plot
plot.survRes	plot.survRes
plot.twinSIR	twinSIR_intensityplot
plot.twinstim	twinstim_plot
plotHHH4sims_fan	hhh4_simulate_plot
plotHHH4sims_size	hhh4_simulate_plot
plotHHH4sims_time	hhh4_simulate_plot
plotHHH4_fitted	hhh4_plot
plotHHH4_fitted1	hhh4_plot
plotHHH4_maps	hhh4_plot
plotHHH4_maxEV	hhh4_plot
plotHHH4_neweights	hhh4_plot
plotHHH4_ri	hhh4_plot
plotHHH4_season	hhh4_plot
poly2adjmat	poly2adjmat
polyAtBorder	polyAtBorder
population	stsSlots
population,sts-method	sts-class
population<-	stsSlots
population<-,sts-method	sts-class
predict.hhh4	hhh4_predict
predint	stsNC-class
predint,stsNC-method	stsNC-class
primeFactors	primeFactors
print.algoQV	print.algoQV
print.epidata	epidata
print.epidataCS	epidataCS
print.hhh4	hhh4_methods
print.summary.epidata	epidata_summary
print.summary.epidataCS	epidataCS
print.summary.twinSIR	twinSIR_methods
print.summary.twinstim	twinstim_methods
print.twinSIR	twinSIR_methods
print.twinstim	twinstim_methods
profile.twinSIR	twinSIR_profile
profile.twinstim	twinstim_profile
q1_nrwh	m1
q2	m1
qlomax	surveillance-defunct
quantile.oneStepAhead	hhh4_validation
R0	R0
R0.simEpidataCS	R0
R0.twinstim	R0
ranef	ranef
ranef.hhh4	hhh4_methods
readData	surveillance-defunct
refvalIdxByDate	refvalIdxByDate
reportingTriangle	stsNC-class
reportingTriangle,stsNC-method	stsNC-class
reset.surveillance.options	surveillance.options
residuals.hhh4	hhh4_methods
residuals.simEpidataCS	residualsCT
residuals.twinSIR	residualsCT
residuals.twinstim	residualsCT
ri	hhh4_formula
rki	wrap.algo
rotaBB	rotaBB
rps	scores
runifdisc	runifdisc
s1	m1
s2	m1
s3	m1
salmAllOnset	salmAllOnset
salmHospitalized	salmHospitalized
salmNewport	salmNewport
salmonella.agona	salmonella.agona
scale.gpc.poly	surveillance-defunct
score	stsNC-class
score,stsNC-method	stsNC-class
scores	scores
scores.default	scores
scores.hhh4	hhh4_validation
scores.hhh4sims	hhh4_simulate_scores
scores.hhh4simslist	hhh4_simulate_scores
scores.oneStepAhead	hhh4_validation
ses	scores
shadar	shadar
siaf	twinstim_siaf
siaf.constant	twinstim_iaf
siaf.exponential	twinstim_iaf
siaf.gaussian	twinstim_iaf
siaf.powerlaw	twinstim_iaf
siaf.powerlaw1	twinstim_iaf
siaf.powerlawL	twinstim_iaf
siaf.simulatePC	twinstim_siaf_simulatePC
siaf.step	twinstim_iaf
siaf.student	twinstim_iaf
sim.pointSource	sim.pointSource
sim.seasonalNoise	sim.seasonalNoise
simEndemicEvents	twinstim_simEndemicEvents
simEpidata	twinSIR_simulation
simEpidataCS	twinstim_simulation
simpleR0	R0
simulate.hhh4	hhh4_simulate
simulate.twinSIR	twinSIR_simulation
simulate.twinstim	twinstim_simulation
sizeHHH	hhh4_internals
start,sts-method	sts-class
stateplot	epidata_plot
stcd	stcd
stepComponent	twinstim_step
stKtest	stK
sts	sts-class
sts-class	sts-class
sts2disProg	disProg2sts
stsBP-class	stsBP-class
stsNC-class	stsNC-class
stsNClist_animate	stsNClist_animate
stsNewport	stsNewport
stsplot	stsplot
stsplot_alarm	stsplot_time
stsplot_space	stsplot_space
stsplot_time	stsplot_time
stsplot_time1	stsplot_time
sts_creation	sts_creation
sts_observation	sts_observation
subset.epidataCS	epidataCS
summary.epidata	epidata_summary
summary.epidataCS	epidataCS
summary.hhh4	hhh4_methods
summary.twinSIR	twinSIR_methods
summary.twinstim	twinstim_methods
surveillance	surveillance-package
surveillance-defunct	surveillance-defunct
surveillance.options	surveillance.options
tail.epidataCS	epidataCS
test	surveillance-defunct
testSim	surveillance-defunct
tiaf	twinstim_tiaf
tiaf.constant	twinstim_iaf
tiaf.exponential	twinstim_iaf
tiaf.step	twinstim_iaf
tidy.sts	sts_tidy
toFileDisProg	surveillance-defunct
toLatex,sts-method	toLatex.sts
toLatex.knox	knox
toLatex.sts	toLatex.sts
toLatex.summary.twinstim	twinstim_methods
twinSIR	twinSIR
twinstim	twinstim
unionSpatialPolygons	unionSpatialPolygons
untie	untie
untie.default	untie
untie.epidataCS	untie
untie.matrix	untie
update.epidata	epidata
update.epidataCS	epidataCS_update
update.hhh4	hhh4_update
update.twinstim	twinstim_update
upperbound	stsSlots
upperbound,sts-method	sts-class
upperbound<-	stsSlots
upperbound<-,sts-method	sts-class
vcov.hhh4	hhh4_methods
vcov.twinSIR	twinSIR_methods
vcov.twinstim	twinstim_methods
wrap.algo	wrap.algo
W_np	hhh4_W
W_powerlaw	hhh4_W
xtable.algoQV	algo.quality
xtable.summary.twinstim	twinstim_methods
xtable.twinstim	twinstim_methods
year	sts-class
year,sts-method	sts-class
zetaweights	zetaweights
[,sts,ANY,ANY,ANY-method	stsXtrct
[,sts-method	stsXtrct
[.epidata	epidata
[.epidataCS	epidataCS
