Age-Structured Spatio-Temporal Models for Infectious Disease Counts

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")'.


hhh4contacts 0.13.0 (2017-06-29)

This is the first version published on CRAN. It requires surveillance >= 1.14.0. The main change is in the documentation, which became more comprehensive, especially for the included datasets.

Other changes include:

  • Changed the default agegroups parameter in noroBE() (and grouping parameter in contactmatrix()) such that it corresponds to the six age groups used by Meyer and Held (2017).

  • The aggregateC() function is now exported.

hhh4contacts 0.12.6 (2017-01-23)

This version has been used for the publication

Held L, Meyer S and Bracher J (2017). "Probabilistic forecasting in infectious disease epidemiology: The 13th Armitage lecture." Statistics in Medicine, doi: 10.1002/sim.7363.

New features

  • An additional year of norovirus surveillance counts has been added, such that noroBE() can now extract data from the time range 2011-w01 to 2016-w30.

  • noroBE(by = "none") extracts the overall univariate time series.

  • update() method for "fitC" objects, which enables modification of the "hhh4" model with automatic refitting of the power parameter of the contact matrix.

  • plotHHH4_season_groups() gained an option to disable confidence intervals.

Bug fixes

  • A typical drop=FALSE bug prevented aggregateC() from aggregating a contact matrix to only two groups.

hhh4contacts 0.12.1 (2016-07-28)

This is the original version published as supplementary data of

Meyer S and Held L (2017). "Incorporating social contact data in spatio-temporal models for infectious disease spread." Biostatistics, 18(2), pp. 338-351, doi: 10.1093/biostatistics/kxw051.

Reference manual

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0.13.1 by Sebastian Meyer, a year ago

Browse source code at

Authors: Sebastian Meyer [aut, cre] , Leonhard Held [ctb, ths]

Documentation:   PDF Manual  

GPL-2 license

Depends on grDevices, graphics, methods, stats, utils, surveillance

Suggests MASS, lattice, gridExtra, scales, numDeriv

Suggested by surveillance.

See at CRAN