| abattoir | Abattoir Data |
| addFormattedXAxis | Formatted Time Axis for '"sts"' Objects |
| addSeason2formula | Add Harmonics to an Existing Formula |
| aggregate.disProg | Aggregate a 'disProg' Object |
| 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 Count Time Series Using the Classic... |
| algo.farrington.assign.weights | Assign weights to base counts |
| algo.farrington.fitGLM | Fit Poisson GLM of the Farrington procedure for a single time... |
| algo.farrington.threshold | Compute prediction interval for a new observation |
| algo.glrnb | Count Data Regression Charts |
| 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 |
| all.equal | Test if Two Model Fits are (Nearly) Equal |
| 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 | Bayesian Outbreak Detection Algorithm (BODA) |
| bodaDelay | Bayesian Outbreak Detection in the Presence of Reporting... |
| calibration | Calibration Tests for Poisson or Negative Binomial... |
| campyDE | Campylobacteriosis and Absolute Humidity in Germany 2002-2011 |
| categoricalCUSUM | CUSUM detector for time-varying categorical time series |
| checkResidualProcess | Check the residual process of a fitted 'twinSIR' or... |
| clapply | Conditional 'lapply' |
| coeflist | List Coefficients by Model Component |
| create.disProg | Creating an object of class 'disProg' (DEPRECATED) |
| 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,... |
| 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 |
| fanplot | Fan Plot of Forecast Distributions |
| farringtonFlexible | Surveillance for Univariate Count Time Series Using an... |
| 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 |
| formatDate | Convert Dates to Character (Including Quarter Strings) |
| 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 |
| hcl.colors | HCL-based Heat Colors from the 'colorspace' Package |
| hepatitisA | Hepatitis A in Germany |
| hhh4 | Fitting HHH Models with Random Effects and Neighbourhood... |
| hhh4_formula | Specify Formulae in a Random Effects HHH Model |
| hhh4_internals | Internal Functions Dealing with 'hhh4' Models |
| 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 | Plot Simulations from '"hhh4"' Models |
| hhh4_simulate_scores | Proper Scoring Rules for 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... |
| hhh4_W_utils | Extract Neighbourhood Weights from a Fitted 'hhh4' Model |
| 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 |
| intensityplot | Plot Paths of Point Process Intensities |
| intersectPolyCircle | Intersection of a Polygonal and a Circular Domain |
| isoWeekYear | Find ISO Week and Year of Date Objects |
| 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 Dates of Individual Case Reports into a Time Series... |
| LRCUSUM.runlength | Run length computation of a CUSUM detector |
| m1 | RKI SurvStat Data |
| magic.dim | Compute Suitable k1 x k2 Layout for Plotting |
| makeControl | Generate 'control' Settings for an 'hhh4' Model |
| marks | Import from package 'spatstat.geom' |
| 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 1985-1997 |
| MMRcoverageDE | MMR coverage levels in the 16 states of Germany |
| momo | Danish 1994-2008 all-cause mortality data for eight age... |
| multiplicity | Import from package 'spatstat.geom' |
| 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.disProg | Plot Observed Counts and Defined Outbreak States of a... |
| plot.survRes | Plot a 'survRes' object |
| poly2adjmat | Derive Adjacency Structure of '"SpatialPolygons"' |
| polyAtBorder | Indicate Polygons at the Border |
| primeFactors | Prime Number Factorization |
| print.algoQV | Print Quality Value Object |
| R0 | Computes reproduction numbers from fitted models |
| ranef | Import from package 'nlme' |
| refvalIdxByDate | Compute indices of reference value using Date class |
| 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 |
| salmonella.agona | Salmonella Agona cases in the UK 1990-1995 |
| scores | Proper Scoring Rules for Poisson or Negative Binomial... |
| shadar | Salmonella Hadar cases in Germany 2001-2006 |
| sim.pointSource | Simulate Point-Source Epidemics |
| 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 an '"sts"' Object Over Time or Across Units |
| sts_animate | Animated Maps and Time Series of Disease Counts or Incidence |
| stsBP-class | Class "stsBP" - a class inheriting from class 'sts' which... |
| sts-class | Class '"sts"' - surveillance time series |
| sts_creation | Simulate Count Time Series with Outbreaks |
| sts_ggplot | Time-Series Plots for '"sts"' Objects Using 'ggplot2' |
| stsNC-class | Class "stsNC" - a class inheriting from class 'sts' which... |
| stsNClist_animate | Animate a Sequence of Nowcasts |
| stsNewport | Salmonella Newport cases in Germany 2001-2015 |
| sts_observation | Create an 'sts' object with a given observation date |
| stsplot | Plot Methods for Surveillance Time-Series Objects |
| stsplot_space | Map of Disease Counts/Incidence accumulated over a Given... |
| stsplot_time | Time-Series Plots for '"sts"' Objects |
| stsSlots | Generic Functions to Access '"sts"' Slots |
| sts_tidy | Convert an '"sts"' Object to a Data Frame in Long (Tidy)... |
| stsXtrct | Subsetting '"sts"' Objects |
| surveillance-defunct | Defunct Functions in Package 'surveillance' |
| surveillance.options | Options of the 'surveillance' Package |
| toLatex.sts | 'toLatex'-Method for '"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_simEndemicEvents | Quick Simulation from an Endemic-Only 'twinstim' |
| 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... |
| zetaweights | Power-Law Weights According to Neighbourhood Order |
