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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/

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/

Gwyddion

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Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM), however it can be generally used for any other height field and image analysis, for instance for analysis of profilometry data.

It aims to provide multiplatform modular program for 2D data analysis that could be easily extended by modules and plug-ins.

Homepage: 
http://gwyddion.net/

The 'medAdherence' R Package

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Adherence is defined as "the extent to which a person’s behavior coincides with medical or health
advice", which is very important, for both clinical researchers and physicians, to identify the treatment
effect of a specific medication(s).

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

CASE

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The main goal of the Computer Assisted Search for Epidemics (CASE) project is to develop a reliable system that generates warnings when the number of reported cases of a particular infectious disease reaches a level that indicates an unusual or unexpected rate. The system is currently in use at the Swedish Institute for Infectious Disease Control (SMI). It performs daily surveillance using data obtained from the database to which all notifiable diseases are reported in Sweden.

Homepage: 
https://smisvn.smi.se/case/

EGADSS

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EGADSS (Evidence-based Guideline and Decision Support System) is an open source tool that is designed to work in conjunction with primary care Electronic Medical Record (EMR) systems to provide patient specific point of care reminders in order to aid physicians provide high quality care. EGADSS is designed as a stand alone system that would respond to requests from existing Electronic Medical Records such as Wolf, Med Access, and MedOffIS to provide patient specific clinical guidance based on its internal collection of guidelines.

Homepage: 
http://egadss.sourceforge.net/

The 'epitools' R Package

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"epitools (epidemiology tools) is an R package for epidemiologic computing and graphics."

Homepage: 
http://www.medepi.com/?q=epitools

OBsched

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Occupancy in certain hospital patient care units is impacted by procedure scheduling policies and practices. For example, intensive care unit occupancy is strongly related to open heart surgery schedules. Similarly, occupancy in obstetrical postpartum units is impacted by the daily number of scheduled labor inductions and cesarean sections. That was the motivation for this project.

OBsched is a set of optimization models and supporting software for exploring the relationship between patient scheduling and nursing unit occupancy in hospitals.

Homepage: 
http://www.hselab.org/projects/obsched/

The 'surveillance' R Package

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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. Hence, potential users are biostatisticians, epidemiologists and others working in applied infectious disease epidemiology. However, applications could just as well originate from environmetrics, reliability engineering, econometrics or social sciences.

Homepage: 
http://surveillance.r-forge.r-project.org/

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