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Task: Epidemiology
Description: 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
Depends: epigrass
Suggests: r-cran-msm
Depends: r-cran-epibasix
Depends: r-cran-epitools
X-Comment: See also: http://sites.google.com/site/medepi/epitools
Depends: r-cran-surveillance
Depends: r-cran-epi
Depends: r-cran-diagnosismed, r-cran-epicalc, r-cran-epir
Depends: netepi-analysis
Homepage: http://sourceforge.net/projects/netepi
Responsible: Andreas Tille <tille@debian.org>
License: MPL 1.1
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/netepi-analysis/trunk
Pkg-Description: network-enabled tools for epidemiology and public health practice
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.
.
There is also a Google code project page at http://code.google.com/p/netepi/
.
See also: http://www.stockholmchallenge.se/data/2123 and
http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf
Depends: netepi-collection
Homepage: http://sourceforge.net/projects/netepi
Responsible: Andreas Tille <tille@debian.org>
License: MPL 1.1
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/netepi-collection/trunk
Pkg-Description: network-enabled tools for epidemiology and public health practice
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.
.
See also: http://www.stockholmchallenge.se/data/2123 and
http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf
Suggests: repast
Homepage: http://repast.sourceforge.net/
License: BSD
WNPP: 179183
Pkg-Description: framework for creating agent based simulations
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: Please read also
http://www.tbiomed.com/content/5/1/11
http://lists.debian.org/debian-med/2009/08/msg00013.html (and following mails)
Suggests: swarm
Homepage: http://www.swarm.org/
License: GPL
WNPP: 179182
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/swarm/trunk/
Pkg-Description: multi-agent simulation of complex systems
Swarm is a software package for multi-agent simulation of complex
systems, originally developed at the Santa Fe Institute. Swarm is
intended to be a useful tool for researchers in a variety of
disciplines. The basic architecture of Swarm is the simulation of
collections of concurrently interacting agents: with this architecture,
we can implement a large variety of agent based models.
X-Remark: Jakson Alves de Aquino has a guide to installing Swarm 2.2 on Ubuntu and Debian
This guide vanished from the web but the WayBackMachine conserved
a copy at
http://web.archive.org/web/20071225020842/http://jalvesaq.googlepages.com/swarm.html
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