Surveillance for Count Time Series Using the Classic Farrington Method
Count Data Regression Charts
algo.farrington.assign.weights
Assign weights to base counts
Comparison of Specified Surveillance Systems using Quality Values
CUSUM method
Hidden Markov Model (HMM) method
Summary Table Generation for Several Disease Chains
Non-parametric back-projection of incidence cases to exposure cases
using a known incubation time as in Becker et al (1991)
Calculation of Average Run Length for discrete CUSUM schemes
Compute Anscombe Residuals
Modified CUSUM method as proposed by Rogerson and Yamada (2004)
Partition of a number into two factors
The system used at the RKI
Test if Two Model Fits are (Nearly) Equal
algo.farrington.threshold
Compute prediction interval for a new observation
CUSUM detector for time-varying categorical time series
Fit Poisson GLM of the Farrington procedure for a single time point
Conditional lapply
List Coefficients by Model Component
Generic animation of spatio-temporal objects
Computation of Quality Values for a Surveillance System Result
Semiparametric surveillance of outbreaks
Bayesian Outbreak Detection Algorithm (BODA)
Fit a Two-Component Epidemic Model using MCMC
Check the residual process of a fitted twinSIR
or twinstim
Creating an object of class disProg
(DEPRECATED)
Calibration Tests for Poisson or Negative Binomial Predictions
Campylobacteriosis and Absolute Humidity in Germany 2002-2011
Surgical Failures Data
Surveillance for a count data time series using the EARS C1, C2
or C3 method and its extensions
Update method for "epidataCS"
Plotting the Events of an Epidemic over Time and Space
Continuous-Time SIR Event History of a Fixed Population
Spatio-Temporal Animation of a Continuous-Time Continuous-Space Epidemic
Determine the k and h values in a standard normal setting
Randomly Permute Time Points or Locations of "epidataCS"
Surveillance for Univariate Count Time Series Using an Improved Farrington Method
Bayesian Outbreak Detection in the Presence of Reporting Delays
Continuous Space-Time Marked Point Patterns with Grid-Based Covariates
Spatio-Temporal Animation of an Epidemic
Conversion (aggregation) of "epidataCS"
to "epidata"
or "sts"
Find Reference Value
Find decision interval for given in-control ARL and reference value
Convert disProg object to sts and vice versa
Impute Blocks for Extra Stops in "epidata"
Objects
Polygonal Approximation of a Disc/Circle
Summarizing an Epidemic
Plotting the Evolution of an Epidemic
Hook function for in-control mean estimation
Fitting HHH Models with Random Effects and Neighbourhood Structure
Fan Plot of Forecast Distributions
Hepatitis A in Berlin
Influenza in Southern Germany
Power-Law and Nonparametric Neighbourhood Weights for hhh4
-Models
Pretty p-Value Formatting
Convert Dates to Character (Including Quarter Strings)
Simulate "hhh4"
Count Time Series
Extract Neighbourhood Weights from a Fitted hhh4
Model
1861 Measles Epidemic in the City of Hagelloch, Germany
Specify Formulae in a Random Effects HHH Model
Fit an Endemic-Only twinstim
as a Poisson-glm
Plots for Fitted hhh4
-models
Influenza and meningococcal infections in Germany, 2001-2006
Plot Paths of Point Process Intensities
Predictions from a hhh4
Model
Import from package spatstat.geom
Proper Scoring Rules for Simulations from hhh4
Models
Measles in the Weser-Ems region of Lower Saxony, Germany, 2001-2002
Intersection of a Polygonal and a Circular Domain
HCL-based Heat Colors from the colorspace Package
Compute Suitable k1 x k2 Layout for Plotting
Checks if the Argument is Scalar
Danish 1994-2008 all-cause mortality data for eight age groups
Hepatitis A in Germany
Import from package spatstat.geom
Generate control
Settings for an hhh4
Model
Plot Simulations from "hhh4"
Models
Plot Observed Counts and Defined Outbreak States of a
(Multivariate) Time Series
Find ISO Week and Year of Date Objects
Internal Functions Dealing with hhh4
Models
Print, Summary and other Standard Methods for "hhh4"
Objects
Count Number of Instances of Points
Knox Test for Space-Time Interaction
Plot a survRes
object
Occurrence of Invasive Meningococcal Disease in Germany
update
a fitted "hhh4"
model
Salmonella Hadar cases in Germany 2001-2006
Plot the ECDF of a uniform sample with Kolmogorov-Smirnov bounds
Simulate Point-Source Epidemics
Determine Neighbourhood Order Matrix from Binary Adjacency Matrix
Example twinstim
Fit for the imdepi
Data
Predictive Model Assessment for hhh4
Models
Layout Items for spplot
Hospitalized Salmonella cases in Germany 2004-2014
Salmonella Newport cases in Germany 2004-2013
Class "stsNC" -- a class inheriting from class sts
which
allows the user to store the results of back-projecting
surveillance time series
Subsetting "sts"
Objects
Hospitalization date for HUS cases of the STEC outbreak in Germany, 2011
Derive Adjacency Structure of "SpatialPolygons"
Convert Dates of Individual Case Reports into a
Time Series of Counts
Indicate Polygons at the Border
Measles in the 16 states of Germany
Meningococcal infections in France 1985-1997
Verbose and Parallel lapply
RKI SurvStat Data
Animated Maps and Time Series of Disease Counts or Incidence
Monte Carlo Permutation Test for Paired Individual Scores
Plot Methods for Surveillance Time-Series Objects
Generation of Background Noise for Simulated Timeseries
Map of Disease Counts/Incidence accumulated over a Given Period
Print, Summary and Extraction Methods for "twinstim"
Objects
Plots for Fitted algo.twins
Models
Import from package nlme
Diggle et al (1995) K-function test for space-time clustering
Aggregate an "sts"
Object Over Time or Across Units
Defunct Functions in Package surveillance
Compute indices of reference value using Date class
Adjust a univariate time series of counts for observed
but-not-yet-reported events
Animate a Sequence of Nowcasts
surveillance : tools:::Rd_package_title("surveillance")
Options of the surveillance Package
toLatex
-Method for "sts"
Objects
Profile Likelihood Computation and Confidence Intervals for
twinstim
objects
Animated Map of Disease Incidence (DEPRECATED)
Time-Series Plots for "sts"
Objects
Plot methods for fitted twinstim
's
Paired binary CUSUM and its run-length computation
Spatial Interaction Function Objects
Simulation of a Self-Exciting Spatio-Temporal Point Process
Non-Randomized Version of the PIT Histogram (for Count Data)
Stepwise Model Selection by AIC
Print, Summary and Extraction Methods for "twinSIR"
Objects
Profile Likelihood Computation and Confidence Intervals
Class "stsBP" -- a class inheriting from class sts
which
allows the user to store the results of back-projecting or nowcasting
surveillance time series
Simulate Count Time Series with Outbreaks
Time-Series Plots for "sts"
Objects Using ggplot2
Toy Data for twinSIR
Simulation from an Isotropic Spatial Kernel via Polar Coordinates
Prime Number Factorization
twinstim_simEndemicEvents
Quick Simulation from an Endemic-Only twinstim
Multivariate Surveillance through independent univariate algorithms
Extract Cox-Snell-like Residuals of a Fitted Point Process
Rotavirus cases in Brandenburg, Germany, during 2002-2013 stratified by 5 age categories
Plotting Paths of Infection Intensities for twinSIR
Models
Salmonella Agona cases in the UK 1990-1995
Proper Scoring Rules for Poisson or Negative Binomial Predictions
Plot the Spatial or Temporal Interaction Function of a twimstim
Power-Law Weights According to Neighbourhood Order
Plotting Intensities of Infection over Time or Space
Salmonella Newport cases in Germany 2001-2015
Print Quality Value Object
Generic Functions to Access "sts"
Slots
Create an sts
object with a given observation date
Sample Points Uniformly on a Disc
Salmonella cases in Germany 2001-2014 by data of symptoms onset
Spatio-temporal cluster detection
Convert an "sts"
Object to a Data Frame in Long (Tidy) Format
Simulation of Epidemic Data
Class "sts"
-- surveillance time series
Fit an Additive-Multiplicative Intensity Model for SIR Data
Identify Endemic Components in an Intensity Model
Fit a Two-Component Spatio-Temporal Point Process Model
Permutation Test for Space-Time Interaction in "twinstim"
Temporal and Spatial Interaction Functions for twinstim
Compute the Unary Union of "SpatialPolygons"
Temporal Interaction Function Objects
update
-method for "twinstim"
Randomly Break Ties in Data
Aggregate a disProg
Object
Add Harmonics to an Existing Formula
Run length computation of a CUSUM detector
Formatted Time Axis for "sts"
Objects
The CDC Algorithm
Query Transmission to Specified Surveillance Algorithm
Abattoir Data
The Bayes System
MMR coverage levels in the 16 states of Germany
Computes reproduction numbers from fitted models