RJafroc: Analysis of Data Acquired Using the Receiver Operating Characteristic Paradigm and Its Extensions

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A common task in medical imaging is assessing whether a new imaging system or device is an improvement over an existing one. Observer performance methodology, such as receiver operating characteristic analysis, is widely used for this purpose. Receiver operating characteristic studies are often required for regulatory approval of new devices. The purpose of this work is to software for the analysis of data acquired using the receiver operating characteristic paradigm and its location specific extensions. It is an enhanced implementation of existing Windows software (http://www.devchakraborty.com). In this paradigm the radiologist rates each image for confidence in presence of disease. The images are typically split equally between actually non-diseased and diseased. A common figure of merit is the area under the receiver operating characteristic curve, which has the physical interpretation as the probability that a diseased image is rated higher than a non-diseased one. In receiver operating characteristic studies a number of radiologists (readers) rate images in two or more treatments, and the object of the analysis is to determine the significance of the inter-treatment difference between reader-averaged figures of merit. In the free-response paradigm the reader marks the locations of suspicious regions and rates each region for confidence in presence of disease, and credit for detection is only given if a true lesion is correctly localized. In the region of interest paradigm each image is divided into a number of regions and the reader rates each region. Each paradigm requires definition of a valid figure of merit that rewards correct decisions and penalizes incorrect ones and specialized significance testing procedures are applied. The package reads data in all currently used data formats including Excel. Significance testing uses two models in widespread use, a jackknife pseudo-value based model and an analysis of variance model with correlated errors. Included are tools for (1) calculating a variety of free-response figures of merit; (2) sample size estimation for planning a future study based on pilot data; (3) viewing empirical operating characteristics in receiver operating characteristic and free-response paradigms; (4) producing formatted report files; and (5) saving a data file in appropriate format for analysis with alternate software. In addition to open-source access to the functions, the package includes a graphical interface for users already familiar with the Windows software, who simply wish to run the program.

Author
Xuetong Zhai [aut, cre], Dev Chakraborty [aut, ths]
Date of publication
2015-08-14 20:13:33
Maintainer
Xuetong Zhai <xuetong.zhai@gmail.com>
License
GPL-3
Version
0.1.1
URLs

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Man pages

DBMHAnalysis
DBM analysis with Hillis improvements
EmpiricalOpCharac
Plot empirical operating characteristic
FigureOfMerit
Calculate figure of merit
FROC2HrROC
Convert FROC dataset
frocData
An example FROC dataset provided by Dr. Federica Zanca.
ORHAnalysis
Obuchowski-Rockette analysis with Hillis improvements
OutputReport
Generate a formatted report of the analysis
PowerGivenJK
Calculate statistical power given numbers of readers J and...
PowerTable
Calculate power table, different combinations, of J and K for...
ReadDataFile
Reads the data file and creates a dataset object
RJafrocGui
Graphical user interface to 'RJafroc' functions
RJafroc-package
JAFROC analysis for MRMC data
rocData
An ROC dataset originally provided by Dr. Kevin Berbaum, U of...
roiData
An ROI dataset produced by a data simulator
SampleSizeGivenJ
Calculate number of cases for specified number of readers J...
SaveDataFile
Save ROC data file in a different format

Files in this package

RJafroc
RJafroc/inst
RJafroc/inst/tests
RJafroc/inst/tests/rocData.lrc
RJafroc/inst/tests/rocData.csv
RJafroc/inst/tests/roiData.xlsx
RJafroc/inst/tests/rocData.xlsx
RJafroc/inst/tests/rocData.imrmc
RJafroc/inst/tests/frocData.xlsx
RJafroc/inst/GUI
RJafroc/inst/GUI/ui.R
RJafroc/inst/GUI/server.R
RJafroc/inst/doc
RJafroc/inst/doc/RJafroc.Rnw
RJafroc/inst/doc/RJafroc.R
RJafroc/inst/doc/RJafroc.pdf
RJafroc/NAMESPACE
RJafroc/data
RJafroc/data/roiData.rda
RJafroc/data/rocData.rda
RJafroc/data/frocData.rda
RJafroc/R
RJafroc/R/roiData.R
RJafroc/R/ORHAnalysis.R
RJafroc/R/SaveOrDbmMrmc.R
RJafroc/R/PowerTable.R
RJafroc/R/PlotROC.R
RJafroc/R/CalculateAvgROCPoints.R
RJafroc/R/CalculateAvgAFROCPoints.R
RJafroc/R/ReadOrDbmMrmc.R
RJafroc/R/SampleSizeGivenJ.R
RJafroc/R/ReadDataFile.R
RJafroc/R/CalculateAvgFROCPoints.R
RJafroc/R/CalculateFROCPoints.R
RJafroc/R/ResamplingEstimateVarCovs.R
RJafroc/R/ReadImrmc.R
RJafroc/R/FigureOfMerit.R
RJafroc/R/FindOptimalCutoffs.R
RJafroc/R/CalculateTrapezoidalArea.R
RJafroc/R/ReadLrc.R
RJafroc/R/ReadJAFROC.R
RJafroc/R/FROC2HrROC.R
RJafroc/R/VarCovs.R
RJafroc/R/CalculateTrapezoidalAreaWeighted.R
RJafroc/R/DBMHAnalysis.R
RJafroc/R/RJafrocGui.R
RJafroc/R/SaveDataFile.R
RJafroc/R/SaveLrc.R
RJafroc/R/EstimateVarCov.R
RJafroc/R/CalculateROCPoints.R
RJafroc/R/EmpiricalOpCharac.R
RJafroc/R/PlotFROC.R
RJafroc/R/CalculateAFROCPoints.R
RJafroc/R/GlobalVariables.R
RJafroc/R/SaveJAFROC.R
RJafroc/R/PlotAFROC.R
RJafroc/R/rocData.R
RJafroc/R/PowerGivenJK.R
RJafroc/R/frocData.R
RJafroc/R/MyFOM.R
RJafroc/R/OutputReport.R
RJafroc/R/SaveImrmc.R
RJafroc/vignettes
RJafroc/vignettes/Report.png
RJafroc/vignettes/RJafroc.Rnw
RJafroc/vignettes/SelectFile.png
RJafroc/vignettes/RJafroc.bib
RJafroc/vignettes/Opening.png
RJafroc/vignettes/DataViewer.png
RJafroc/vignettes/jsslogo.jpg
RJafroc/vignettes/Analysis.png
RJafroc/MD5
RJafroc/build
RJafroc/build/vignette.rds
RJafroc/DESCRIPTION
RJafroc/man
RJafroc/man/DBMHAnalysis.Rd
RJafroc/man/EmpiricalOpCharac.Rd
RJafroc/man/ORHAnalysis.Rd
RJafroc/man/ReadDataFile.Rd
RJafroc/man/RJafrocGui.Rd
RJafroc/man/SampleSizeGivenJ.Rd
RJafroc/man/FROC2HrROC.Rd
RJafroc/man/FigureOfMerit.Rd
RJafroc/man/RJafroc-package.Rd
RJafroc/man/frocData.Rd
RJafroc/man/SaveDataFile.Rd
RJafroc/man/OutputReport.Rd
RJafroc/man/roiData.Rd
RJafroc/man/PowerGivenJK.Rd
RJafroc/man/PowerTable.Rd
RJafroc/man/rocData.Rd