Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

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 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.hhh | Fit a Classical HHH Model (DEPRECATED) |

algo.hhh.grid | Fit a Classical HHH Model (DEPRECATED) with Varying Start... |

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 |

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 |

compMatrix.writeTable | LaTeX Table Generation |

correct53to52 | Data Correction from 53 to 52 weeks |

create.disProg | Creating an object of class disProg |

create.grid | Create a Matrix of Initial Values for 'algo.hhh.grid' |

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 |

fanplot | Fan Plot of Forecast Distributions |

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 |

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 |

imdepifit | Example 'twinstim' Fit for the 'imdepi' Data |

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 |

makeControl | Generate 'control' Settings for an 'hhh4' Model |

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 |

ranef | Import from package 'nlme' |

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 |

salmonella.agona | Salmonella Agona cases in the UK 1990-1995 |

scale.gpc.poly | Centering and Scaling a '"gpc.poly"' Polygon |

scores | Proper Scoring Rules for Poisson or Negative Binomial... |

shadar | Salmonella Hadar cases in Germany 2001-2006 |

simHHH | Simulates data based on the model proposed by Held et. al... |

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 | Function for simulating a time series |

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 2004-2013 |

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 Counts/Incidence accumulated over a Given... |

stsplot_spacetime | Map of Disease Incidence |

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 | 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 '"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... |

xtable.algoQV | Xtable quality value object |

zetaweights | Power-Law Weights According to Neighbourhood Order |

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