Debian Med Project
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Summary
Epidemiology
Debian Med epidemiology related packages

This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for statistical investigation. It might be a good idea to read the paper "A short introduction to R for Epidemiology" at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf

The list to the right includes various software projects which are of some interest to the Debian Med Project. Currently, only a few of them are available as Debian packages. It is our goal, however, to include all software in Debian Med which can sensibly add to a high quality Debian Pure Blend.

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks

Debian Med Epidemiology packages

Official Debian packages with high relevance

Epigrass
scientific tool for simulations and scenario analysis in network epidemiology
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Epigrass is a software for visualizing, analyzing and simulating of epidemic processes on geo-referenced networks.

EpiGrass can interact with the GRASS GIS from which it can obtain maps and other geo-referenced information. However, EpiGrass does not require an installation of the GRASS GIS for most of its features.

The package is enhanced by the following packages: epigrass-doc
Please cite: Flavio Coelho, Oswaldo Cruz and Claudia Codeco: Epigrass: a tool to study disease spread in complex networks. (PubMed) Source Code for Biology and Medicine 3(1):3 (2008)
R-cran-diagnosismed
medical diagnostic test accuracy analysis toolkit
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DiagnosisMed is a GNU R package to analyze the accuracy of data from diagnostic tests evaluating health conditions. It was designed to be used by health professionals. This package helps estimating sensitivity and specificity from categorical and continuous test results including some evaluations of indeterminate results, or compare different categorical tests, and estimate reasonable cut-offs of tests and display it in a way commonly used by health professionals. No graphical interface is available yet.

R-cran-epi
GNU R epidemiological analysis
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Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, including interval censored data and representation of multistate data. Also some useful functions for tabulation and plotting. Contains some epidemiological datasets.

The Epi package is mainly focused on "classical" chronic disease epidemiology. The package has grown out of the course Statistical Practice in Epidemiology using R (see http://www.pubhealth.ku.dk/~bxc/SPE).

There is A short introduction to R for Epidemiology available at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf Beware that the pages 38-120 of this is merely the manual pages for the Epi package.

Epi is not the only R-package for epidemiological analysis, a package with more affinity to infectious disease epidemiology is the epitools package which is also evailable in Debian.

Epi is used in the Department of Biostatistics of the University of Copenhagen.

Please cite: Martyn Plummer and Bendix Carstensen: Lexis: An R Class for Epidemiological Studies with Long-Term Follow-Up. Journal of Statistical Software 38(5):1-12 (2011)
R-cran-epibasix
GNU R Elementary Epidemiological Functions
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Elementary Epidemiological Functions for a Graduate Epidemiology / Biostatistics Course.

This package contains elementary tools for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement (kappa, sensitivity/specificity). Appropriate print and summary statements are also written to facilitate interpretation wherever possible. This package is a work in progress, so any comments or suggestions would be appreciated. Source code is commented throughout to facilitate modification. The target audience includes graduate students in various epi/biostatistics courses.

Epibasix was developed in Canada.

R-cran-epicalc
GNU R Epidemiological calculator
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Functions making R easy for epidemiological calculation.

Datasets from Dbase (.dbf), Stata (.dta), SPSS(.sav), EpiInfo(.rec) and Comma separated value (.csv) formats as well as R data frames can be processed to do make several epidemiological calculations.

R-cran-epir
GNU R Functions for analysing epidemiological data
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A package for analysing epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.

R-cran-epitools
GNU R Epidemiology Tools for Data and Graphics
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GNU R Tools for public health epidemiologists and data analysts. Epitools provides numerical tools and programming solutions that have been used and tested in real-world epidemiologic applications.

Many practical problems in the analysis of public health data require programming or special software, and investigators in different locations may duplicate programming efforts. Often, simple analyses, such as the construction of confidence intervals, are not calculated and thereby complicate appropriate statistical inferences for small geographic areas. There are many examples of simple and useful numerical tools that would enhance the work of epidemiologists at local health departments and yet are not readily available for the problem in front of them. The availability of these tools will encourage wider use of appropriate methods and promote evidence-based public health practices.

R-cran-surveillance
development and the evaluation of epidemiological outbreak detection algorithms
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The R-package 'surveillance' is a framework for the development and the evaluation of outbreak detection algorithms in univariate and multivariate routine collected public health surveillance data. It is hosted on CRAN..

The intention of the R-package surveillance is to provide open source software for the visualization and monitoring of count data time series in public health surveillance. Potential users are epidemiologists and others working in applied infectious disease epidemiology. Furthermore, surveillance also provides a data structure and framework for methodological developments of surveillance algorithms.

Please cite: Michael Höhle: Surveillance: An R package for the surveillance of infectious diseases. (eprint) Computational Statistics 22(4):571-582 (2007)

Official Debian packages with lower relevance

R-cran-msm
GNU R Multi-state Markov and hidden Markov models in continuous time
Maintainer: Debian Science Team
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Functions for fitting general continuous-time Markov and hidden Markov multi-state models to longitudinal data. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates. A variety of observation schemes are supported, including processes observed at arbitrary times, completely-observed processes, and censored states.

Please cite: Christopher H. Jackson: Multi-State Models for Panel Data: The msm Package for R. Journal of Statistical Software 38(8):1-29 (2011)

Packaging has started and developers might try the packaging code in VCS

Netepi-analysis
network-enabled tools for epidemiology and public health practice
License: HACOS
Debian package not available
Svn
Version: 0.9.0-1

NetEpi, which is short for "Network-enabled Epidemiology", is a collaborative project to create a suite of free, open source software tools for epidemiology and public health practice. Anyone with an interest in population health epidemiology or public health informatics is encouraged to examine the prototype tools and to consider contributing to their further development. Contributions which involve formal and/or informal testing of the tools in a wide range of circumstances and environments are particularly welcome, as is assistance with design, programming and documentation tasks.

This is a tool for conducting epidemiological analysis of data sets, both large and small, either through a Web browser interface, or via a programmatic interface. In many respects it is similar to the analysis facilities included in the Epi Info suite, except that NetEpi Analysis is designed to be installed on servers and accessed remotely via Web browsers, although it can also be installed on individual desktop or laptop computers.

The software was developed by New South Wales Department of Health.

Remark of Debian Med team: See also: http://www.stockholmchallenge.se/data/2123 and
Netepi-collection
network-enabled tools for epidemiology and public health practice
License: HACOS
Debian package not available
Svn
Version: 1.8.4.-1

NetEpi, which is short for "Network-enabled Epidemiology", is a collaborative project to create a suite of free, open source software tools for epidemiology and public health practice. Anyone with an interest in population health epidemiology or public health informatics is encouraged to examine the prototype tools and to consider contributing to their further development. Contributions which involve formal and/or informal testing of the tools in a wide range of circumstances and environments are particularly welcome, as is assistance with design, programming and documentation tasks.

NetEpi Case Manager is a tool for securely collecting structured information about cases and contacts of communicable (and other) diseases through Web browsers and the Internet. New data collection forms can be designed and deployed quickly by epidemiologists, using a "point-and-click" interface, without the need for knowledge of or training in any programming language. Data can then be collected from users of the system, who can be located anywhere in the world, into a centralised database. All that is needed by users of the system is a relatively recent Web browser and an Internet connection ("NetEpi" is short for "Network-enabled Epidemiology"). In many respects, NetEpi Case Manager is like a Web-enabled version of the data entry facilities in the very popular Epi Info suite of programmes published by the US Centers for Disease Control and Prevention, and in the Danish EpiData project, which is available for several languages. The software was developed by the Centre for Epidemiology and Research of the New South Wales Department of Health, with contributions from Population Health Division of the Australian Government Department of Health and Ageing.

The software was developed by New South Wales Department of Health.

Remark of Debian Med team: See also: http://www.stockholmchallenge.se/data/2123 and

No known packages available but some record of interest (WNPP bug)

Repast - wnpp
framework for creating agent based simulations
License: BSD
Debian package not available

Repast Simphony is a free and open source agent-based modeling toolkit that simplifies model creation and use. Repast Simphony offers users a rich variety of features including the following:

  • Fluid model component development using any mixture of Java, Groovy, and flowcharts in each project;
  • A pure Java point-and-click model execution environment that includes built-in results logging and graphing tools as well as automated connections to a variety of optional external tools including the R statistics environment, *ORA and Pajek network analysis plugins, A live agent SQL query tool plugin, the VisAD scientific visualization package, the Weka data mining platform, many popular spreadsheets, the MATLAB computational mathematics environment, and the iReport visual report designer;
  • An extremely flexible hierarchically nested definition of space including the ability to do point-and-click and modeling and visualization of 2D environments; 3D environments; networks including full integration with the JUNG network modeling library as well as Microsoft Excel spreadsheets and UCINET DL file importing; and geographical spaces including 2D and 3D Geographical Information Systems (GIS) support;
  • A range of data storage "freeze dryers" for model check pointing and restoration including XML file storage, text file storage, and database storage;
  • A fully concurrent multithreaded discrete event scheduler;
  • Libraries for genetic algorithms, neural networks, regression, random number generation, and specialized mathematics;
  • An automated Monte Carlo simulation framework which supports multiple modes of model results optimization;
  • Built-in tools for integrating external models;
  • Distributed computing with Terracotta;
  • Full object-orientation;
  • Optional end-to-end XML simulation
  • A point-and-click model deployment system
Remark of Debian Med team: Please read also
 [http://www.tbiomed.com/content/5/1/11](http://www.tbiomed.com/content/5/1/11)
 [http://lists.debian.org/debian-med/2009/08/msg00013.html](http://lists.debian.org/debian-med/2009/08/msg00013.html) (and following mails)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 167387