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The 'DiagnosisMed' R Package

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DiagnosisMed is a package to analyze data from diagnostic test accuracy evaluating health conditions. It is being built to be used by health professionals. This package is able to estimate sensitivity and specificity from categorical and continuous test results including some evaluations of indeterminate results, or compare different categorical tests, and estimate reasonble cut-offs of tests and display it in a way commonly used by health professionals. No graphical interface is avalible yet. Partners are most welcome.

Homepage: 
http://r-forge.r-project.org/projects/diagnosismed/

The 'epi' R Package

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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.

Homepage: 
http://staff.pubhealth.ku.dk/~bxc/Epi/

The 'epibasix' R Package

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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.

Homepage: 
http://cran.r-project.org/web/packages/epibasix/

Caisis

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Caisis is an open source, web-based cancer data management system that integrates research with patient care. The system is freely distributed to promote scientific collaboration, and over the course of the last five years many other institutions have adopted the system. Collaboration with multiple centers has allowed Caisis to develop and evolve in an environment of constant feedback and scrutiny. This environment has shaped the features, usability, and accessibility of Caisis.

Homepage: 
http://www.caisis.org/

The 'epicalc' R Package

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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.

Homepage: 
http://cran.r-project.org/web/packages/epicalc/

The 'epiR' R Package

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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.

Homepage: 
http://cran.r-project.org/web/packages/epiR/

Bioconductor

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Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.

The Bioconductor release version is updated twice each year, and is appropriate for most users. There is also a development version, to which new features and packages are added prior to incorporation in the release. A large number of meta-data packages provide pathway, organism, microarray and other annotations.

Homepage: 
http://www.bioconductor.org/

ACHILLES

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ACHILLES is a platform which enables the characterization, quality assessment and visualization of observational health databases. ACHILLES provides users with an interactive, exploratory framework to assess patient demographics, the prevalence of conditions, drugs and procedures, and to evaluate the distribution of values for clinical observations.

ACHILLES is intended to be implemented by organizations that have patient-level observational health databases available in their local environment.

Homepage: 
http://www.ohdsi.org/analytic-tools/achilles-for-data-characterization/

Tolven Health Record

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The Tolven platform and ePHR and eCHR applications enable interoperability across electronic health records for consumers and clinicians. Using Java, EJB3, Faces, Facelets, AJAX, relational database, and LDAP for security.

Homepage: 
http://www.tolven.org/

popHealth

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popHealth is a prototype open source tool that automates population health reporting. popHealth integrates with a provider’s electronic health record (EHR) system to produce summary quality measures on the provider’s patient population and streamlines the reporting of these measures.

Homepage: 
http://projectpophealth.org/

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