salmNewport

Reported number of cases of the Salmonella Newport serovar in the 16 German
  federal states 2004-2013.

datasets

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 H�hle 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 H�hle (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. (2015)
        <http://arxiv.org/abs/1411.0416>.

Sebastian Meyer

surveillance

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
        Phenomena

salmNewport function

format

The data are queried from the Survstat@RKI database of the German
  Robert Koch Institute (http://www3.rki.de/SurvStat/). A detailed
  description of the 2011 outbreak can be found in the publication

  Bayer, C., Bernard, H., Prager, R., Rabsch, W., Hiller, P., Malorny,
  B., Pfefferkorn, B., Frank, C., de Jong, A., Friesema, I., Start, K.,
  Rosner, B.M. (2014), An outbreak of Salmonella Newport associated with
  mung bean sprouts in Germany and the Netherlands, October to November
  2011, Eurosurveillance 19(1):pii=20665.

salmNewport: Salmonella Newport cases in Germany 2004-2013

Description

Usage

Arguments

format

source

Examples