API for surveillance
Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
| Global functions | |
|---|---|
| .eh | Source code |
| .fisherinfo | Source code |
| .hcl.colors | Man page |
| .lmarg.lambda | Source code |
| .loglik | Source code |
| .pfisherinfo | Source code |
| .ploglik | Source code |
| .pscore | Source code |
| .score | Source code |
| .updateMoveExpr | Source code |
| AIC.twinSIR | Man page |
| Egd | Source code |
| LLR.fun | Man page Source code |
| LRCUSUM.runlength | Man page Source code |
| MMRcoverageDE | Man page |
| R0 | Man page |
| R0.simEpidataCS | Man page |
| R0.twinstim | Man page |
| RPS | Man page Source code |
| W_np | Man page |
| W_powerlaw | Man page |
| 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 |
| add1.twinstim | Man page |
| addFormattedXAxis | Man page Source code |
| addSeason2formula | Man page |
| aggregate,sts-method | Man page |
| aggregate.disProg | Man page Source code |
| aggregate.hhh4sims | Man page |
| aggregate.hhh4simslist | Man page |
| aggregate.sts | 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 |
| algo.hhh.grid | Man page |
| algo.hmm | Man page Source code |
| algo.outbreakP | Man page Source code |
| algo.quality | Man page |
| 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 |
| all.equal.hhh4 | Man page |
| all.equal.twinstim | Man page |
| amplitudeShift2sinCos | Source code |
| animate | Man page |
| animate.epidata | Man page |
| animate.epidataCS | Man page |
| animate.sts | Man page |
| animate.summary.epidata | Man page |
| animate_nowcasts | Man page Source code |
| anscombe.residuals | Man page Source code |
| anscombeNB | Source code |
| arlCusum | Man page Source code |
| as.data.frame,sts-method | Man page |
| as.data.frame.sts | Man page Source code |
| as.epidata | Man page |
| as.epidata.data.frame | Man page |
| as.epidata.default | Man page Source code |
| as.epidata.epidataCS | Man page |
| as.epidataCS | Man page |
| as.hhh4simslist | Man page |
| as.stepfun.epidataCS | Man page |
| as.ts.sts | Man page |
| as.xts.sts | Man page |
| at2ndChange | Man page Source code |
| atChange | Man page Source code |
| atMedian | Man page Source code |
| autoplot.sts | Man page |
| backprojNP | Man page Source code |
| backprojNP.fit | Man page Source code |
| bayes | Man page 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 |
| calibrationTest.default | Man page |
| calibrationTest.hhh4 | Man page |
| calibrationTest.oneStepAhead | Man page |
| campyDE | Man page |
| catcusum.LLRcompute | Man page Source code |
| categoricalCUSUM | Man page Source code |
| checkDerivatives.maxLik | Source code |
| checkDerivatives.numDeriv | Source code |
| checkFormula | Source code |
| checkResidualProcess | Man page |
| clapply | Man page |
| coef.epitest | Man page |
| coef.hhh4 | Man page Source code |
| coefW | Man page |
| coeflist | Man page |
| coeflist.default | Man page |
| coeflist.hhh4 | Man page |
| 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 |
| commonDenom | Source code |
| compMatrix.writeTable | Man page |
| confint.hhh4 | Man page |
| confint.oneStepAhead | Man page |
| control | Man page |
| control,sts-method | Man page |
| control<- | Man page |
| control<-,sts-method | Man page |
| correct53to52 | Man page |
| cox | Man page |
| create.disProg | Man page Source code |
| create.grid | Man page |
| 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 |
| delayCDF | Man page |
| delayCDF,stsNC-method | Man page |
| deleval | Man page |
| dim,sts-method | Man page |
| dimnames,sts-method | Man page |
| disProg2sts | Man page Source code |
| discpoly | Man page |
| dist.median | Man page Source code |
| dpost.bnb | Source code |
| dpost.bnb.unorm | Source code |
| drop1.twinstim | Man page |
| dss | Man page |
| earsC | Man page Source code |
| em.step.becker | Man page Source code |
| enlargeData | Man page |
| epidata | Man page |
| epidataCS | Man page |
| epidataCS2sts | Man page |
| epidataCSplot_space | Man page |
| epidataCSplot_time | Man page |
| epitest | Man page |
| 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 |
| extractAIC.twinSIR | Man page |
| fanplot | Man page |
| 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 |
| fitHHH | Source code |
| fix.dimnames | Source code |
| fixef | Man page |
| fixef.hhh4 | Man page |
| fluBYBW | Man page |
| fooepidata | Man page |
| formatDate | Man page Source code |
| formatPval | Man page |
| formula.hhh4 | Man page |
| formulaGLM | Source code |
| formulaGLMDelay | Source code |
| frequency,sts-method | Man page |
| getHK | Source code |
| getMaxEV | Man page |
| getMaxEV_season | Man page |
| getNEweights | Man page |
| getSeason | Source code |
| getSigma | Source code |
| getSigmaInv | Source code |
| getSigmai | Source code |
| getSigmaiInv | Source code |
| getSourceDists | Man page |
| getTheta1 | Source code |
| glm_epidataCS | Man page |
| glrnb | Man page Source code |
| glrpois | Man page Source code |
| gsub2 | Source code |
| h1_nrwrp | Man page |
| hValues | Man page Source code |
| ha | Man page |
| ha.sts | Man page |
| hagelloch | Man page |
| hagelloch.df | Man page |
| haz2pmf | Source code |
| head.epidataCS | Man page |
| hepatitisA | Man page |
| hhh4 | Man page |
| hmm | Man page Source code |
| husO104Hosp | Man page |
| hypgeom2F1special | Source code |
| iafplot | Man page |
| imdepi | Man page |
| influMen | Man page |
| init.sts | Source code |
| init.stsBP | Source code |
| init.stsNC | Source code |
| inside.gpc.poly | Man page |
| intensity.twinstim | Man page |
| intensityplot | Man page |
| intensityplot.simEpidata | Man page |
| intensityplot.simEpidataCS | Man page |
| intensityplot.twinSIR | Man page |
| intensityplot.twinstim | Man page |
| intensityplot_twinSIR | Source code |
| intersectPolyCircle | Man page |
| intersectPolyCircle.SpatialPolygons | Man page |
| intersectPolyCircle.gpc.poly | Man page |
| intersectPolyCircle.owin | Man page |
| intersperse | Man page |
| isInModel | Source code |
| isoWeekYear | Man page Source code |
| jacobianAmplitudeShift | Source code |
| k1 | Man page |
| knox | Man page |
| ks.plot.unif | Man page |
| layout.labels | Man page |
| layout.scalebar | Man page |
| linelist2sts | Man page Source code |
| logInterpolation | Source code |
| logLik.hhh4 | Man page Source code |
| logLik.twinSIR | Man page |
| logLik.twinstim | Man page |
| logS | Man page Source code |
| lognormDiscrete | Source code |
| logs | Man page |
| m1 | Man page |
| m2 | Man page |
| m3 | Man page |
| m4 | Man page |
| m5 | Man page |
| magic.dim | Man page Source code |
| makeControl | Man page |
| makePlot | Man page |
| marFisher | Source code |
| marLogLik | Source code |
| marScore | Source code |
| marks | Man page |
| marks.epidataCS | Man page |
| meanHHH | 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 |
| n1 | Man page |
| n2 | Man page |
| na2FALSE | Source code |
| naninf2zero | Man page Source code |
| nbOrder | Man page |
| neighbourhood | Man page |
| neighbourhood,sts-method | Man page |
| neighbourhood<- | Man page |
| neighbourhood<-,sts-method | Man page |
| nobs.epidataCS | Man page |
| nobs.hhh4 | Man page |
| nobs.twinstim | Man page |
| nowcast | Man page Source code |
| observed | Man page |
| observed,sts-method | Man page |
| observed<- | Man page |
| observed<-,sts-method | Man page |
| 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 |
| penFisher | Source code |
| penLogLik | Source code |
| penScore | Source code |
| permutationTest | Man page Source code |
| permute.epidataCS | Man page |
| pit | Man page |
| pit.default | Man page |
| pit.hhh4 | Man page |
| pit.oneStepAhead | Man page |
| plapply | Man page |
| plot,sts,missing-method | Man page |
| plot,stsNC,missing-method | Man page |
| plot.atwins | Man page |
| plot.disProg | Man page Source code |
| plot.epidata | Man page Source code |
| plot.epidataCS | Man page |
| plot.epitest | Man page |
| plot.hhh4 | Man page |
| plot.hhh4sims | Man page |
| plot.hhh4simslist | Man page |
| plot.knox | Man page |
| plot.oneStepAhead | Man page |
| plot.profile.twinSIR | Man page Source code |
| plot.stKtest | Man page |
| plot.sts | Man page |
| plot.summary.epidata | Man page |
| plot.survRes | Man page Source code |
| plot.twinSIR | Man page |
| plot.twinstim | Man page |
| plotHHH4_fitted | Man page |
| plotHHH4_fitted1 | Man page Source code |
| plotHHH4_maps | Man page |
| plotHHH4_maxEV | Man page |
| plotHHH4_neweights | Man page |
| plotHHH4_ri | Man page |
| plotHHH4_season | Man page |
| plotHHH4sims_fan | Man page |
| plotHHH4sims_size | Man page |
| plotHHH4sims_time | Man page |
| pmfQuantile | Source code |
| pmix | Source code |
| poly2adjmat | Man page |
| polyAtBorder | Man page |
| population | Man page |
| population,sts-method | Man page |
| population<- | Man page |
| population<-,sts-method | Man page |
| predict.hhh4 | Man page Source code |
| predint | Man page |
| predint,stsNC-method | Man page |
| primeFactors | Man page Source code |
| print.algoQV | Man page Source code |
| print.disProg | Source code |
| print.epidata | Man page |
| print.epidataCS | Man page |
| print.hhh4 | Man page |
| print.summary.epidata | Man page Source code |
| print.summary.epidataCS | Man page |
| print.summary.hhh4 | Man page |
| print.summary.twinSIR | Man page |
| print.summary.twinstim | Man page |
| print.twinSIR | Man page |
| print.twinstim | Man page |
| profile.twinSIR | Man page |
| profile.twinstim | Man page |
| q1_nrwh | Man page |
| q2 | Man page |
| qlomax | Man page |
| qmix | Source code |
| quantile.oneStepAhead | Man page |
| ranef | Man page |
| ranef.hhh4 | Man page |
| readData | Man page |
| refvalIdxByDate | Man page Source code |
| reportingTriangle | Man page |
| reportingTriangle,stsNC-method | Man page |
| reset.surveillance.options | Man page |
| residuals.hhh4 | Man page |
| residuals.simEpidataCS | Man page |
| residuals.twinSIR | Man page Source code |
| residuals.twinstim | Man page |
| rgd | Source code |
| ri | Man page Source code |
| rki | Man page Source code |
| rogerson | Man page Source code |
| rotaBB | Man page |
| rpost.bnb | Source code |
| rps | Man page |
| runifdisc | Man page |
| 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 |
| score | Man page |
| score,stsNC-method | Man page |
| scores | Man page |
| scores.default | Man page Source code |
| scores.hhh4 | Man page |
| scores.hhh4sims | Man page |
| scores.hhh4simslist | Man page |
| scores.oneStepAhead | Man page |
| ses | Man page |
| shadar | Man page |
| siaf | Man page |
| siaf.constant | Man page |
| siaf.exponential | Man page |
| siaf.gaussian | Man page |
| siaf.powerlaw | Man page |
| siaf.powerlaw1 | Man page |
| siaf.powerlawL | Man page |
| siaf.simulatePC | Man page |
| siaf.step | Man page |
| siaf.student | Man page |
| sim.pointSource | Man page Source code |
| sim.seasonalNoise | Man page Source code |
| simEndemicEvents | Man page |
| simEpidata | Man page |
| simEpidataCS | Man page |
| simHHH4 | Source code |
| simpleR0 | Man page |
| simulate.hhh4 | Man page |
| simulate.twinSIR | Man page |
| simulate.twinstim | Man page |
| sinCos2amplitudeShift | Source code |
| sizeHHH | Man page |
| splitParams | Source code |
| sqrtOf1pr2 | Source code |
| stKtest | Man page |
| start,sts-method | Man page |
| stateplot | Man page Source code |
| stcd | Man page Source code |
| stepComponent | Man page |
| sts | Man page |
| 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 |
| 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 |
| stsplot_spacetime | Man page Source code |
| stsplot_time | Man page Source code |
| stsplot_time1 | Man page Source code |
| subset.epidataCS | Man page |
| summary.epidata | Man page |
| summary.epidataCS | Man page |
| summary.hhh4 | Man page |
| summary.twinSIR | Man page |
| summary.twinstim | Man page |
| surveillance-defunct | Man page |
| surveillance.options | Man page |
| tail.epidataCS | Man page |
| terms.hhh4 | Man page |
| test | Man page |
| testSim | Man page |
| tiaf | Man page |
| tiaf.constant | Man page |
| tiaf.exponential | Man page |
| tiaf.step | Man page |
| tidy.sts | Man page |
| toFileDisProg | Man page |
| toLatex,sts-method | Man page |
| toLatex.knox | Man page |
| toLatex.sts | Man page Source code |
| toLatex.summary.twinstim | Man page |
| twinSIR | Man page |
| twinstim | Man page |
| unionSpatialPolygons | Man page |
| untie | Man page |
| untie.default | Man page |
| untie.epidataCS | Man page |
| untie.matrix | Man page |
| update.epidata | Man page |
| update.epidataCS | Man page |
| update.hhh4 | Man page |
| update.twinstim | Man page |
| upperbound | Man page |
| upperbound,sts-method | Man page |
| upperbound<- | Man page |
| upperbound<-,sts-method | Man page |
| vcov.hhh4 | Man page |
| vcov.twinSIR | Man page |
| vcov.twinstim | Man page |
| w.chibarsq.sim | Source code |
| wrap.algo | Man page Source code |
| xtable.algoQV | Man page Source code |
| xtable.summary.twinstim | Man page |
| xtable.twinstim | Man page |
| year | Man page |
| year,sts-method | Man page |
| zetaweights | Man page |
