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

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

## Man pages

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