Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

abattoir | Abattoir Data |

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 Systems |

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 | Cound 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 |

categoricalCUSUM | CUSUM detector for time-varying categorical time series |

checkResidualProcess | Check the residual process of a fitted 'twinSIR' or... |

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 |

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 |

ha | Hepatitis A in Berlin |

hagelloch | 1861 measles epidemic in the city of Hagelloch, Germany |

hepatitisA | Hepatitis A in Germany |

hhh4 | Random effects HHH model fit as described in Paul and Held... |

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 | Simulates data based on the model proposed by Paul and Held... |

hhh4_validation | Predictive Model Assessment for 'hhh4' models |

hhh4_W_powerlaw | Power-Law Neighbourhood Weights for 'hhh4' Models |

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 |

isScalar | Checks if the Argument is Scalar |

ks.plot.unif | Plot the ECDF of a uniform sample with Kolmogorov-Smirnov... |

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 |

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 | Count Number of Instances of Points |

nbOrder | Determine Neighbourhood Order Matrix from Binary Adjacency... |

nowcast | Adjust observed epidemic curve for reporting delay of cases |

pairedbinCUSUM | Paired binary CUSUM and its run-length computation |

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 basic 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 |

runifdisc | Sample Points Uniformly on a Disc |

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 |

stsAggregate | Aggregate the the series of an sts object |

stsBP-class | Class "stsBP" - a class inheriting from class 'sts' which... |

sts-class | Class '"sts"' - surveillance time series |

stsDisp | Display Methods for Surveillance Time-Series 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 |

surveillance-package | Temporal and Spatio-Temporal Modeling and Monitoring of... |

test | Print xtable for several diseases and the summary |

testSim | Print xtable for a Simulated Disease and the Summary |

toFileDisProg | Writing of Disease Data |

twinSIR | Fit an Additive-Multiplicative Intensity Model for SIR Data |

twinSIR_cox | Identify Endemic Components in an Intensity Model |

twinSIR_epidata | Class for Epidemic Data Discrete in Space and Continuous in... |

twinSIR_epidata_animate | Spatio-Temporal Animation of an Epidemic |

twinSIR_epidata_intersperse | Impute Blocks for Extra Stops in '"epidata"' Objects |

twinSIR_epidata_plot | Plotting the Evolution of an Epidemic |

twinSIR_epidata_summary | Summarizing an Epidemic |

twinSIR_exData | Artificial data and data from the German Federal State... |

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_epidataCS | Class for Representing Continuous Space-Time Point Process... |

twinstim_epidataCS_aggregate | Conversion (aggregation) of '"epidataCS"' to '"epidata"' or... |

twinstim_epidataCS_animate | Spatio-Temporal Animation of a Continuous-Time... |

twinstim_epidataCS_plot | Plotting the Events of an Epidemic over Time and Space |

twinstim_epidataCS_update | Update method for '"epidataCS"' |

twinstim_iaf | Temporal and Spatial Interaction Functions for 'twinstim' |

twinstim_iafplot | Plot the spatial or temporal interaction function of a... |

twinstim_intensityplot | 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_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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