Debian Med Epidemiology packages

Epigrass er et program for visualisering, analyse og simulering af epidemiske processer på geo-refererede netværk.

EpiGrass kan interagere med GRASS GIS hvorfra den kan hente kort og andre georefererede informationer. EpiGrass kræver dog ikke en installation af GRASS GIS for de fleste af sine funktioner.

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.

Funktioner til demografisk og epidemiologisk analyse i Lexis-programmet, dvs. register- og kohort-opfølgningsdata, inklusive intervalcensorerede data og repræsentation af data i flere tilstande. Indeholder også nyttige funktioner til tabulering og plotning. Indeholder også nogle epidemiologisk datasæt.

Epi-pakken er primært fokuseret på "klassisk" kronisk sydomsepidemiologi. Pakken er vokset ud af kurset "Statistical Practice in Epidemiology using R" (se http://www.pubhealth.ku.dk/~bxc/SPE).

Der er en kort introduktion til epidemiologi med R tilgængelig på http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf Vær opmærksom på at siderne 38-120 fra denne blot er manualsiderne til Epi- pakken.

Epi er ikke den eneste R-pakke til epidemiologisk analyse. En pakke med tættere tilhørsforhold til smitsom sygdomsepidemiologi er pakken epitools, der også er tilgængelig gennem Debian.

Epi anvendes af Biostatistisk Afdeling ved Københavns Universitet.

Elementary Epidemiological-funktioner for et Epidemiology/Biostatistics-forskningskursus.

Denne pakke indeholder elementære værktøjer for analyse af gængse epidemiologiske problemer, fra estimering af prøvestørrelse, via 2x2 kontingens tabelanalyse og grundlæggende målinger for aftale (kappa, sensitivitet). Passende udskrivnings- og summeringsudtryk skrives også for at facilitere fortolkning når det er muligt. Denne pakke er under udvikling, så der tages godt imod alle kommentarer eller forslag. Kildekoden er kommenteret udførligt for at facilitere ændring. Målgruppen inkluderer forskningsstuderende i forskellige epi/biostatistiske kurser.

Epibasix blev udviklet i Canada.

Funktioner der gør det let at foretage epidemiologiske beregninger med R.

Flere datasæt fra formaterne Dbase (.dbf), Stata (.dta), SPSS (.sav), EpiInfo (.rec) og kommaseparerede værdier (.csv) såvel som R-datarammer, kan behandles til foretagelse af adskillige epidemiologiske beregninger.

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.

GNU R-værktøjer til epidemiologer og dataanalytikere i den offentlige sundhedssektor. Epitools tilbyder talmæssige værktøjer og programmeringsløsninger som er blevet anvendt og testet i epidemiologiske anvendelsesområder fra den virkelige verden.

Mange praktiske problemer i analysen af offentlige sundhedsdata kræver programmering eller specialprogrammel, og undersøgelsespersonale på forskellige steder kan duplikere programmeringsindsatsen. Ofte vil simple analyser, såsom konstruktionen af fortrolighedsintervaller, ikke blive beregnet og dermed komplicere passende statistiske slutninger for mindre geografiske områder. Der er mange eksempler på simple og talmæssige værktøjer som ville forbedre epidemiologers arbejde på lokale sundhedsafdelinger, og og endnu ikke er parate og tilgængelige til problemet foran dem. Tilgængeligheden af disse værktøjer vil fremme bredere anvendelse af passende metoder og fremme evidensbaseret praksis i den offentlige sundhedssektor.

Funktioner for tilpasning af generel Markov i sammenhængende tid og skjulte Markov flertilstandsmodeller til data i længderetningen. Både overgangsrater for Markov og den skjulte Markov-resultatproces kan modelleres i form af kovariater. Et udvalg af observationsskemaer er understøttet, inklusive processer observeret på arbitrære tidspunkter, fuldstændig-observerede processer, og censorerede tilstande.

R-pakken »surveillance« er en ramme til udviklingen og evalueringen af algoritmer for registrering af udbrud gennem univariate og multivariate overvågningsdata som rutinemæssigt indsamles af den offentlige sundhedssektor. Det holdes i drift på CRAN.

Formålet med R-pakken surveillance er at tilbyde open source software til visualisering og overvågning af optalte datatidsserier over overvågning fra den offentlige sundhedssektor. Potentielle brugere er epidemiologer og andre som med praksis i smitsom sygdomsepidemiologi. I tillæg tilbyder surveillance også en datastruktur og en ramme til metodisk udvikling af algoritmer for »surveillance«.

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.

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.

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