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: r-cran-seroincidence
X-Comment: Needs to wait for processing of r-cran-knitr

Suggests: r-cran-cmprsk

Depends: ushahidi

Suggests: shiny-server

Depends: r-cran-lexrankr

Depends: netepi-analysis
Remark: See also: http://www.stockholmchallenge.se/data/2123 and
 http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf

Depends: netepi-collection
Remark: 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)

X-Suggests: swarm
X-Homepage: http://www.swarm.org/
X-License: GPL
X-WNPP: 179182
X-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/swarm/trunk/
X-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

