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A set of R functions to assist researchers working on tuberculosis diagnostics.
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README.md

tbdiag

This package provides functions for working with TB diagnostics data. At the moment, it includes two families of functions: one for the interpretation of Cellestis Quantiferon Gold In-Tube results, and one for interpreting Oxford Immunotec T.SPOT results. These function-families can interpret by the manufacturers' criteria for North America and at least one non-American country (e.g., one QFT criteria set excludes the nil/mitogen indeterminate and one T.SPOT criteria set excludes the borderline category). More criteria will be added shortly; users can also extend the functions by creating new S3 methods for the qft.criteria and tspot.criteria functions.

Package Info

The most reliable version of the package is available on CRAN; just type install.packages("tbdiag") in R to get it. The master branch in this repository is the most recent functioning version; it's the one I'm probably using in my day-to-day work, but probably isn't ready for CRAN just yet. New features and other works-in-progress live on their own branches until they're ready to pulled into master; there's no guarantee they work.

You can install any of the GitHub branches by installing the devtools package and typing install_github("mmparker/tbdiag/branch").

Results Validation

I've compared the results of these functions to several thousand lab-reported Quantiferon and T.SPOT results, and hand-calculated the correct results when faced with discrepancies. While I believe that the current versions of these functions are very robust, they are provided with no warranty and I strongly encourage users to investigate any unusual results (and report back!)

Acknowledgements

Special thanks to Randall Reves, MD and Bob Belknap, MD of the Denver Metropolitan Tuberculosis Clinic and the CDC's Tuberculosis Epidemiologic Studies Consortium (TBESC) for supporting the development of this package.

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