Files in jimhester/surveillance

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

R/AllClass.R R/AllGeneric.R R/LRCUSUM.runlength.R R/addSeason2formula.R R/algo_bayes.R R/algo_call.R R/algo_cdc.R R/algo_cusum.R R/algo_farrington.R R/algo_glrnb.R R/algo_glrpois.R R/algo_hhh.R R/algo_hmm.R R/algo_outbreakP.R R/algo_rki.R R/algo_rogerson.R R/algo_twins.R R/backprojNP.R R/boda.R R/bodaDelay.R R/calibration.R R/calibration_null.R R/catCUSUM.R R/checkDerivatives.R R/earsC.R R/epidata.R R/epidataCS.R R/epidataCS_aggregate.R R/epidataCS_animate.R R/epidataCS_methods.R R/epidataCS_plot.R R/epidata_animate.R R/epidata_plot.R R/farringtonFlexible.r R/gd.R R/glm_epidataCS.R R/gpc.poly-methods.R R/graphs.R R/hhh4.R R/hhh4_W.R R/hhh4_W_np.R R/hhh4_W_powerlaw.R R/hhh4_calibration.R R/hhh4_methods.R R/hhh4_oneStepAhead.R R/hhh4_plot.R R/hhh4_simulate.R R/hhh4_simulate_plot.R R/hhh4_simulate_scores.R R/intersectPolyCircle.R R/isoWeekYear.R R/knox.R R/ks.plot.unif.R R/linelist2sts.R R/misc_dataProcessing.R R/modifyListcall.R R/newtonRaphson.R R/nowcast.R R/options.R R/pairedbinCUSUM.R R/permutationTest.R R/pit.R R/plapply.R R/plot_graphics.R R/plot_multi.R R/plot_xtable.R R/qlomax.R R/scores.R R/sim_HHH.R R/sim_background.R R/sim_pointSource.R R/spatial_tools.R R/stK.R R/stcd.R R/sts.R R/stsBP.R R/stsNC.R R/sts_animate.R R/sts_coerce.R R/sts_creation.R R/sts_observation.R R/stsplot_space.R R/stsplot_spacetime.R R/stsplot_time.R R/testcalls.R R/twinSIR.R R/twinSIR_helper.R R/twinSIR_intensity.R R/twinSIR_methods.R R/twinSIR_profile.R R/twinSIR_simulation.R R/twinstim.R R/twinstim_epitest.R R/twinstim_helper.R R/twinstim_iafplot.R R/twinstim_intensity.R R/twinstim_methods.R R/twinstim_siaf.R R/twinstim_siaf_gaussian.R R/twinstim_siaf_powerlaw.R R/twinstim_siaf_powerlawL.R R/twinstim_siaf_step.R R/twinstim_siaf_student.R R/twinstim_simulation.R R/twinstim_step.R R/twinstim_tiaf.R R/twinstim_tiaf_exponential.R R/twinstim_tiaf_step.R R/untie.R R/wrap_univariate.R R/zzz.R demo/biosurvbook.R demo/cost.R inst/doc/glrnb.R inst/doc/glrnb.pdf inst/doc/hhh4.R inst/doc/hhh4.pdf inst/doc/surveillance.R inst/doc/surveillance.pdf man/LRCUSUM.runlength.Rd man/MMRcoverageDE.Rd man/R0.Rd man/abattoir.Rd man/addFormattedXAxis.Rd man/addSeason2formula.Rd man/aggregate.disProg.Rd man/algo.bayes.Rd man/algo.call.Rd man/algo.cdc.Rd man/algo.compare.Rd man/algo.cusum.Rd man/algo.farrington.Rd man/algo.farrington.assign.weights.Rd man/algo.farrington.fitGLM.Rd man/algo.farrington.threshold.Rd man/algo.glrnb.Rd man/algo.glrpois.Rd man/algo.hhh.Rd man/algo.hhh.grid.Rd man/algo.hmm.Rd man/algo.outbreakP.Rd man/algo.quality.Rd man/algo.rki.Rd man/algo.rogerson.Rd man/algo.summary.Rd man/algo.twins.Rd man/animate.Rd man/anscombe.residuals.Rd man/arlCusum.Rd man/backprojNP.Rd man/bestCombination.Rd man/boda.Rd man/bodaDelay.Rd man/calibration.Rd man/campyDE.Rd man/categoricalCUSUM.Rd man/checkResidualProcess.Rd man/coeflist.Rd man/compMatrix.writeTable.Rd man/correct53to52.Rd man/create.disProg.Rd man/create.grid.Rd man/deleval.Rd man/disProg2sts.Rd man/discpoly.Rd man/earsC.Rd man/enlargeData.Rd man/epidata.Rd man/epidataCS.Rd man/epidataCS_aggregate.Rd man/epidataCS_animate.Rd man/epidataCS_permute.Rd man/epidataCS_plot.Rd man/epidataCS_update.Rd man/epidata_animate.Rd man/epidata_intersperse.Rd man/epidata_plot.Rd man/epidata_summary.Rd man/estimateGLRNbHook.Rd man/estimateGLRPoisHook.Rd man/farringtonFlexible.Rd man/find.kh.Rd man/findH.Rd man/findK.Rd man/fluBYBW.Rd man/formatPval.Rd man/glm_epidataCS.Rd man/ha.Rd man/hagelloch.Rd man/hepatitisA.Rd man/hhh4.Rd man/hhh4_W.Rd man/hhh4_calibration.Rd man/hhh4_formula.Rd man/hhh4_methods.Rd man/hhh4_plot.Rd man/hhh4_predict.Rd man/hhh4_simulate.Rd man/hhh4_simulate_plot.Rd man/hhh4_update.Rd man/hhh4_validation.Rd man/husO104Hosp.Rd man/imdepi.Rd man/influMen.Rd man/inside.gpc.poly.Rd man/intensityplot.Rd man/intersectPolyCircle.Rd man/isScalar.Rd man/isoWeekYear.Rd man/knox.Rd man/ks.plot.unif.Rd man/layout.labels.Rd man/linelist2sts.Rd man/loglikelihood.Rd man/m1.Rd man/magic.dim.Rd man/make.design.Rd man/makePlot.Rd man/marks.Rd man/meanResponse.Rd man/measles.weser.Rd man/measlesDE.Rd man/meningo.age.rd man/momo.Rd man/multiplicity.Rd man/multiplicity.Spatial.Rd man/nbOrder.Rd man/nowcast.Rd man/pairedbinCUSUM.Rd man/permutationTest.Rd man/pit.Rd man/plapply.Rd man/plot.atwins.Rd man/plot.disProg.Rd man/plot.survRes.Rd man/poly2adjmat.Rd man/polyAtBorder.Rd man/predict.ah.Rd man/primeFactors.Rd man/print.algoQV.Rd man/qlomax.Rd man/readData.Rd man/refvalIdxByDate.Rd man/residuals.ah.Rd man/residualsCT.Rd man/rotaBB.Rd man/runifdisc.Rd man/salmAllOnset.Rd man/salmHospitalized.Rd man/salmNewport.Rd man/salmNewportTruncated.Rd man/salmonella.agona.Rd man/scale.gpc.poly.Rd man/shadar.Rd man/sim.pointSource.Rd man/sim.seasonalNoise.Rd man/simHHH.Rd man/stK.Rd man/stcd.Rd man/sts-class.Rd man/stsAggregate.Rd man/stsBP-class.Rd man/stsNC-class.Rd man/stsSlots.Rd man/stsXtrct.Rd man/sts_animate.Rd man/sts_creation.Rd man/sts_observation.Rd man/stsplot.Rd man/stsplot_space.Rd man/stsplot_spacetime.Rd man/stsplot_time.Rd man/sumNeighbours.Rd man/surveillance.options.Rd man/test.Rd man/testSim.Rd man/toFileDisProg.Rd man/toLatex.sts.Rd man/twinSIR.Rd man/twinSIR_cox.Rd man/twinSIR_exData.Rd man/twinSIR_intensityplot.Rd man/twinSIR_methods.Rd man/twinSIR_profile.Rd man/twinSIR_simulation.Rd man/twinstim.Rd man/twinstim_epitest.Rd man/twinstim_iaf.Rd man/twinstim_iafplot.Rd man/twinstim_intensity.Rd man/twinstim_methods.Rd man/twinstim_plot.Rd man/twinstim_profile.Rd man/twinstim_siaf.Rd man/twinstim_siaf_simulatePC.Rd man/twinstim_simulation.Rd man/twinstim_step.Rd man/twinstim_tiaf.Rd man/twinstim_update.Rd man/unionSpatialPolygons.Rd man/untie.Rd man/wrap.algo.Rd man/xtable.algoQV.Rd man/zetaweights.Rd tests/testthat.R tests/testthat/test-algo.glrnb.R tests/testthat/test-bodaDelay.R tests/testthat/test-calibration.R tests/testthat/test-farringtonFlexible.R tests/testthat/test-formatDate.R tests/testthat/test-hhh4+algo.hhh.R tests/testthat/test-hhh4+derivatives.R tests/testthat/test-hhh4_ARasNE.R tests/testthat/test-hhh4_NegBinGrouped.R tests/testthat/test-nbOrder.R tests/testthat/test-plapply.R tests/testthat/test-siafs.R tests/testthat/test-tiafs.R tests/testthat/test-toLatex.sts.R tests/testthat/test-twinstim_score.R