surveillance1.24.0 package

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

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 Values

algo.cusum

CUSUM method

algo.farrington.assign.weights

Assign weights to base counts

algo.farrington.fitGLM

Fit Poisson GLM of the Farrington procedure for a single time point

algo.farrington

Surveillance for Count Time Series Using the Classic Farrington Method

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 Result

algo.rki

The system used at the RKI

algo.rogerson

Modified CUSUM method as proposed by Rogerson and Yamada (2004)

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 cases us...

bestCombination

Partition of a number into two factors

boda

Bayesian Outbreak Detection Algorithm (BODA)

bodaDelay

Bayesian Outbreak Detection in the Presence of Reporting Delays

calibration

Calibration Tests for Poisson or Negative Binomial Predictions

categoricalCUSUM

CUSUM detector for time-varying categorical time series

checkResidualProcess

Check the residual process of a fitted twinSIR or twinstim

clapply

Conditional lapply

coeflist

List Coefficients by Model Component

create.disProg

Creating an object of class disProg (DEPRECATED)

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, C2 or C3 ...

epidata_animate

Spatio-Temporal Animation of an Epidemic

epidata_intersperse

Impute Blocks for Extra Stops in "epidata" Objects

epidata_plot

Plotting the Evolution of an Epidemic

epidata_summary

Summarizing an Epidemic

epidata

Continuous-Time SIR Event History of a Fixed Population

epidataCS_aggregate

Conversion (aggregation) of "epidataCS" to "epidata" or "sts"

epidataCS_animate

Spatio-Temporal Animation of a Continuous-Time Continuous-Space Epidem...

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"

epidataCS

Continuous Space-Time Marked Point Patterns with Grid-Based Covariates

estimateGLRNbHook

Hook function for in-control mean estimation

fanplot

Fan Plot of Forecast Distributions

farringtonFlexible

Surveillance for Univariate Count Time Series Using an Improved Farrin...

find.kh

Determine the k and h values in a standard normal setting

findH

Find decision interval for given in-control ARL and reference value

findK

Find Reference Value

formatDate

Convert Dates to Character (Including Quarter Strings)

formatPval

Pretty p-Value Formatting

glm_epidataCS

Fit an Endemic-Only twinstim as a Poisson-glm

hcl.colors

HCL-based Heat Colors from the colorspace Package

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" Objects

hhh4_plot

Plots for Fitted hhh4-models

hhh4_predict

Predictions from a hhh4 Model

hhh4_simulate_plot

Plot Simulations from "hhh4" Models

hhh4_simulate_scores

Proper Scoring Rules for Simulations from hhh4 Models

hhh4_simulate

Simulate "hhh4" Count Time Series

hhh4_update

update a fitted "hhh4" model

hhh4_validation

Predictive Model Assessment for hhh4 Models

hhh4_W_utils

Extract Neighbourhood Weights from a Fitted hhh4 Model

hhh4_W

Power-Law and Nonparametric Neighbourhood Weights for hhh4-Models

hhh4

Fitting HHH Models with Random Effects and Neighbourhood Structure

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 bounds

layout.labels

Layout Items for spplot

linelist2sts

Convert Dates of Individual Case Reports into a Time Series of Counts

LRCUSUM.runlength

Run length computation of a CUSUM detector

magic.dim

Compute Suitable k1 x k2 Layout for Plotting

makeControl

Generate control Settings for an hhh4 Model

marks

Import from package spatstat.geom

multiplicity

Import from package spatstat.geom

multiplicity.Spatial

Count Number of Instances of Points

nbOrder

Determine Neighbourhood Order Matrix from Binary Adjacency Matrix

nowcast

Adjust a univariate time series of counts for observed but-not-yet-rep...

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 (Multivariate) T...

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

runifdisc

Sample Points Uniformly on a Disc

scores

Proper Scoring Rules for Poisson or Negative Binomial Predictions

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

sts_animate

Animated Maps and Time Series of Disease Counts or Incidence

sts_creation

Simulate Count Time Series with Outbreaks

sts_ggplot

Time-Series Plots for "sts" Objects Using ggplot2

sts_observation

Create an sts object with a given observation date

sts_tidy

Convert an "sts" Object to a Data Frame in Long (Tidy) Format

sts-class

Class "sts" -- surveillance time series

stsAggregate

Aggregate an "sts" Object Over Time or Across Units

stsBP-class

Class "stsBP" -- a class inheriting from class sts which allows the ...

stsNC-class

Class "stsNC" -- a class inheriting from class sts which allows the ...

stsNClist_animate

Animate a Sequence of Nowcasts

stsplot_space

Map of Disease Counts/Incidence accumulated over a Given Period

stsplot_spacetime

Animated Map of Disease Incidence (DEPRECATED)

stsplot_time

Time-Series Plots for "sts" Objects

stsplot

Plot Methods for Surveillance Time-Series Objects

stsSlots

Generic Functions to Access "sts" Slots

stsXtrct

Subsetting "sts" Objects

surveillance-defunct

Defunct Functions in Package surveillance

surveillance-package

surveillance: tools:::Rd_package_title("surveillance")

surveillance.options

Options of the surveillance Package

toLatex.sts

toLatex-Method for "sts" Objects

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

twinSIR

Fit an Additive-Multiplicative Intensity Model for SIR Data

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 twimstim

twinstim_intensity

Plotting Intensities of Infection over Time or Space

twinstim_methods

Print, Summary and Extraction Methods for "twinstim" Objects

twinstim_plot

Plot methods for fitted twinstim's

twinstim_profile

Profile Likelihood Computation and Confidence Intervals for twinstim...

twinstim_siaf_simulatePC

Simulation from an Isotropic Spatial Kernel via Polar Coordinates

twinstim_siaf

Spatial Interaction Function Objects

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"

twinstim

Fit a Two-Component Spatio-Temporal Point Process Model

unionSpatialPolygons

Compute the Unary Union of "SpatialPolygons"

untie

Randomly Break Ties in Data

wrap.algo

Multivariate Surveillance through independent univariate algorithms

zetaweights

Power-Law Weights According to Neighbourhood Order

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.