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hhh4contacts (version 0.13.1)

Age-Structured Spatio-Temporal Models for Infectious Disease Counts

Description

Meyer and Held (2017) present an age-structured spatio-temporal model for infectious disease counts. The approach is illustrated in a case study on norovirus gastroenteritis in Berlin, 2011-2015, by age group, city district and week, using additional contact data from the POLYMOD survey. This package contains the data and code to reproduce the results from the paper, see 'demo("hhh4contacts")'.

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Version

Install

install.packages('hhh4contacts')

Monthly Downloads

311

Version

0.13.1

License

GPL-2

Maintainer

Sebastian Meyer

Last Published

March 20th, 2020

Functions in hhh4contacts (0.13.1)

contactmatrix

POLYMOD Contact Matrices for Germany
plotHHH4_maps_groups

Plot Mean Components of a hhh4 Fit by District Averaged Over Time
stratum

Extract Strata
plotHHH4_season_groups

Plot Seasonality of a hhh4 Fit by Group
stationary

Stationary Distribution of a Transition Matrix
pop2011

Berlin and German Population by Age Group, 2011
powerC

Exponentiate a Matrix via Eigendecomposition
plotHHH4_fitted_groups

Plot Mean Components of a hhh4 Fit by Group
plotC

Generate an Image of a Contact Matrix
stsplothook

Hook functions for stsplot_time1
subset.array

Subset an Array in one Dimension
dssAggregate

Compute the DSS on Aggregated Predictions and Observations
aggregateC

Aggregate a Contact Matrix
addGroups2WFUN

Group-Dependent Parametric Weights
fitC

Estimate the Power of the Contact Matrix in a "hhh4" Model
expandC

Expand the Contact Matrix over Regions
adaptP

Adapt a Transition Matrix to a Specific Stationary Distribution
C2pop

Adapt a Contact Matrix to Population Fractions
noroBE

Create "sts" Objects from the Berlin Norovirus Data
aggregateCountsArray

Aggregate an Array of Counts wrt One Dimension (Stratum)