| abattoir | Abattoir Data |
| addFormattedXAxis | Formatted Time Axis for '"sts"' Objects |
| addSeason2formula | Function that adds a sine-/cosine formula to an existing... |
| aggregate.disProg | Aggregate the observed counts |
| algo.bayes | The Bayes System |
| algo.call | Query Transmission to Specified Surveillance Algorithm |
| algo.cdc | The CDC Algorithm |
| algo.compare | Comparison of Specified Surveillance Systems using Quality... |
| algo.cusum | CUSUM method |
| algo.farrington | Surveillance for a count data time series using the... |
| algo.farrington.assign.weights | Assign weights to base counts |
| algo.farrington.fitGLM | Fit the Poisson GLM of the Farrington procedure for a single... |
| algo.farrington.threshold | Compute prediction interval for a new observation |
| algo.glrnb | Count 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.outbreakP | Semiparametric surveillance of outbreaks |
| algo.quality | Computation of Quality Values for a Surveillance System... |
| algo.rki | The system used at the RKI |
| algo.rogerson | Modified CUSUM method as proposed by Rogerson and Yamada... |
| algo.summary | Summary Table Generation for Several Disease Chains |
| algo.twins | Model fit based on a two-component epidemic model |
| animate | Generic animation of spatio-temporal objects |
| anscombe.residuals | Compute Anscombe residuals |
| arlCusum | Calculation of Average Run Length for discrete CUSUM schemes |
| backprojNP | Non-parametric back-projection of incidence cases to exposure... |
| bestCombination | Partition of a number into two factors |
| boda | Surveillance for an univariate count data time series using... |
| bodaDelay | Bayesian aberration detection in presence of reporting... |
| calibration | Calibration Test for Poisson or Negative Binomial Predictions |
| campyDE | Cases of Campylobacteriosis and Absolute Humidity in Germany... |
| categoricalCUSUM | CUSUM detector for time-varying categorical time series |
| checkResidualProcess | Check the residual process of a fitted 'twinSIR' or... |
| coeflist | List Coefficients by Model Component |
| 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 |
| deleval | Surgical failures data |
| discpoly | Polygonal Approximation of a Disc/Circle |
| disProg2sts | Convert disProg object to sts and vice versa |
| earsC | Surveillance for a count data time series using the EARS C1,... |
| enlargeData | Data Enlargement |
| epidata | Continuous-Time SIR Event History of a Fixed Population |
| epidata_animate | Spatio-Temporal Animation of an Epidemic |
| epidataCS | Continuous Space-Time Marked Point Patterns with Grid-Based... |
| epidataCS_aggregate | Conversion (aggregation) of '"epidataCS"' to '"epidata"' or... |
| epidataCS_animate | Spatio-Temporal Animation of a Continuous-Time... |
| epidataCS_permute | Randomly Permute Time Points or Locations of '"epidataCS"' |
| epidataCS_plot | Plotting the Events of an Epidemic over Time and Space |
| epidataCS_update | Update method for '"epidataCS"' |
| epidata_intersperse | Impute Blocks for Extra Stops in '"epidata"' Objects |
| epidata_plot | Plotting the Evolution of an Epidemic |
| epidata_summary | Summarizing an Epidemic |
| estimateGLRNbHook | Hook function for in-control mean estimation |
| estimateGLRPoisHook | Hook function for in-control mean estimation |
| farringtonFlexible | Surveillance for an univariate count data time series using... |
| findH | Find decision interval for given in-control ARL and reference... |
| findK | Find reference value |
| find.kh | Determine the k and h values in a standard normal setting |
| fluBYBW | Influenza in Southern Germany |
| formatPval | Pretty p-Value Formatting |
| glm_epidataCS | Fit an Endemic-Only 'twinstim' as a Poisson-'glm' |
| ha | Hepatitis A in Berlin |
| hagelloch | 1861 Measles Epidemic in the City of Hagelloch, Germany |
| hepatitisA | Hepatitis A in Germany |
| hhh4 | Fitting HHH Models with Random Effects and Neighbourhood... |
| hhh4_calibration | Test Calibration of a 'hhh4' Model |
| hhh4_formula | Specify Formulae in a Random Effects HHH Model |
| hhh4_methods | Print, Summary and other Standard Methods for '"hhh4"'... |
| hhh4_plot | Plots for Fitted 'hhh4'-models |
| hhh4_predict | Predictions from a 'hhh4' Model |
| hhh4_simulate | Simulate '"hhh4"' Count Time Series |
| hhh4_simulate_plot | Summarize Simulations from '"hhh4"' Models |
| hhh4_update | 'update' a fitted '"hhh4"' model |
| hhh4_validation | Predictive Model Assessment for 'hhh4' Models |
| hhh4_W | Power-Law and Nonparametric Neighbourhood Weights for... |
| husO104Hosp | Hospitalization date for HUS cases of the STEC outbreak in... |
| imdepi | Occurrence of Invasive Meningococcal Disease in Germany |
| influMen | Influenza and meningococcal infections in Germany, 2001-2006 |
| inside.gpc.poly | Test Whether Points are Inside a '"gpc.poly"' Polygon |
| intensityplot | Plot Paths of Point Process Intensities |
| intersectPolyCircle | Intersection of a Polygonal and a Circular Domain |
| isoWeekYear | Find ISO week and ISO year of a vector of Date objects on... |
| isScalar | Checks if the Argument is Scalar |
| knox | Knox Test for Space-Time Interaction |
| ks.plot.unif | Plot the ECDF of a uniform sample with Kolmogorov-Smirnov... |
| layout.labels | Layout Items for 'spplot' |
| linelist2sts | Convert individual case information based on dates into an... |
| loglikelihood | Calculation of the loglikelihood needed in algo.hhh |
| LRCUSUM.runlength | Run length computation of a CUSUM detector |
| m1 | RKI SurvStat Data |
| magic.dim | Returns a suitable k1 x k2 for plotting the disProgObj |
| make.design | Create the design matrices |
| makePlot | Plot Generation |
| marks | Import from package 'spatstat' |
| meanResponse | Calculate mean response needed in algo.hhh |
| measlesDE | Measles in the 16 states of Germany |
| measles.weser | Measles in the Weser-Ems region of Lower Saxony, Germany,... |
| meningo.age | Meningococcal infections in France 1985-1995 |
| MMRcoverageDE | MMR coverage levels in the 16 states of Germany |
| momo | Danish 1994-2008 all cause mortality data for six age groups |
| multiplicity | Import from package 'spatstat' |
| multiplicity.Spatial | Count Number of Instances of Points |
| nbOrder | Determine Neighbourhood Order Matrix from Binary Adjacency... |
| nowcast | Adjust a univariate time series of counts for observed... |
| pairedbinCUSUM | Paired binary CUSUM and its run-length computation |
| permutationTest | Monte Carlo Permutation Test for Paired Individual Scores |
| pit | Non-Randomized Version of the PIT Histogram (for Count Data) |
| plapply | Verbose and Parallel 'lapply' |
| plot.atwins | Plot results of a twins model fit |
| plot.disProg | Plot Generation of the Observed and the defined Outbreak... |
| plot.survRes | Plot a survRes object |
| poly2adjmat | Derive Adjacency Structure of '"SpatialPolygons"' |
| polyAtBorder | Indicate Polygons at the Border |
| predict.ah | Predictions from a HHH model |
| primeFactors | Prime number factorization |
| print.algoQV | Print quality value object |
| qlomax | Quantile Function of the Lomax Distribution |
| R0 | Computes reproduction numbers from fitted models |
| readData | Reading of Disease Data |
| refvalIdxByDate | Compute indices of reference value using Date class |
| residuals.ah | Residuals from a HHH model |
| residualsCT | Extract Cox-Snell-like Residuals of a Fitted Point Process |
| rotaBB | Rotavirus cases in Brandenburg, Germany, during 2002-2013... |
| runifdisc | Sample Points Uniformly on a Disc |
| salmAllOnset | Salmonella cases in Germany 2001-2014 by data of symptoms... |
| salmHospitalized | Hospitalized Salmonella cases in Germany 2004-2014 |
| salmNewport | Salmonella Newport cases in Germany 2004-2013 |
| salmNewportTruncated | Salmonella Newport cases in Germany 2001-2011 by data of... |
| salmonella.agona | Salmonella Agona cases in the UK 1990-1995 |
| scale.gpc.poly | Centering and Scaling a '"gpc.poly"' Polygon |
| shadar | Salmonella Hadar cases in Germany 2001-2006 |
| simHHH | Simulates data based on the model proposed by Held et. al... |
| sim.pointSource | Generation of Simulated Point Source Epidemy |
| sim.seasonalNoise | Generation of Background Noise for Simulated Timeseries |
| stcd | Spatio-temporal cluster detection |
| stK | Diggle et al (1995) K-function test for space-time clustering |
| stsAggregate | Aggregate the the series of an sts object |
| sts_animate | Animated Maps and Time Series of Disease Incidence |
| stsBP-class | Class "stsBP" - a class inheriting from class 'sts' which... |
| sts-class | Class '"sts"' - surveillance time series |
| sts_creation | Function for simulating a time series |
| stsNC-class | Class "stsNC" - a class inheriting from class 'sts' which... |
| sts_observation | Function for creating a sts-object with a given observation... |
| stsplot | Plot-Methods for Surveillance Time-Series Objects |
| stsplot_space | Map of Disease Incidence During a Given Period |
| stsplot_spacetime | Map of Disease Incidence |
| stsplot_time | Time-Series Plots for '"sts"' Objects |
| stsSlots | Generic functions to access '"sts"' slots |
| stsXtrct | Extraction and Subsetting of 'sts' objects |
| sumNeighbours | Calculates the sum of counts of adjacent areas |
| surveillance.options | Options of the 'surveillance' Package |
| test | Print xtable for several diseases and the summary |
| testSim | Print xtable for a Simulated Disease and the Summary |
| toFileDisProg | Writing of Disease Data |
| toLatex.sts | 'toLatex'-Method for (lists of) '"sts"' Objects |
| twinSIR | Fit an Additive-Multiplicative Intensity Model for SIR Data |
| twinSIR_cox | Identify Endemic Components in an Intensity Model |
| twinSIR_exData | Toy Data for 'twinSIR' |
| twinSIR_intensityplot | Plotting Paths of Infection Intensities for 'twinSIR' Models |
| twinSIR_methods | Print, Summary and Extraction Methods for '"twinSIR"' Objects |
| twinSIR_profile | Profile Likelihood Computation and Confidence Intervals |
| twinSIR_simulation | Simulation of Epidemic Data |
| twinstim | Fit a Two-Component Spatio-Temporal Point Process Model |
| twinstim_epitest | Permutation Test for Space-Time Interaction in '"twinstim"' |
| twinstim_iaf | Temporal and Spatial Interaction Functions for 'twinstim' |
| twinstim_iafplot | Plot the spatial or temporal interaction function of a... |
| twinstim_intensity | Plotting Intensities of Infection over Time or Space |
| twinstim_methods | Print, Summary and Extraction Methods for '"twinstim"'... |
| twinstim_plot | Plot methods for fitted 'twinstim"s |
| twinstim_profile | Profile Likelihood Computation and Confidence Intervals for... |
| twinstim_siaf | Spatial Interaction Function Objects |
| twinstim_siaf_simulatePC | Simulation from an Isotropic Spatial Kernel via Polar... |
| twinstim_simulation | Simulation of a Self-Exciting Spatio-Temporal Point Process |
| twinstim_step | Stepwise Model Selection by AIC |
| twinstim_tiaf | Temporal Interaction Function Objects |
| twinstim_update | 'update'-method for '"twinstim"' |
| unionSpatialPolygons | Compute the Unary Union of '"SpatialPolygons"' |
| untie | Randomly Break Ties in Data |
| wrap.algo | Multivariate Surveillance through independent univariate... |
| xtable.algoQV | Xtable quality value object |
| zetaweights | Power-Law Weights According to Neighbourhood Order |
