Modeling, Analysis, Validation and Visualization of Observer Performance Studies in Diagnostic Radiology

Tools for quantitative assessment of medical imaging systems, radiologists or computer aided ('CAD') algorithms. Implements methods described in a book: 'Chakraborty' 'DP' (2017), "Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples", Taylor-Francis < https://www.crcpress.com/9781482214840> and its Online Appendices < https://github.com/dpc10ster/onlinebookk21778>. Data collection paradigms include receiver operating characteristic ('ROC') and a location specific extension, namely free-response 'ROC' ('FROC'). 'ROC' data consists of a single rating per image, where the rating is the perceived confidence level the image is of a diseased patient. 'FROC' data consists of a variable number (including zero) of mark-rating pairs per image, where a mark is the location of a clinically reportable suspicious region and the rating is the corresponding confidence level that it is a true lesion. The software supersedes the current Windows version of 'JAFROC' software < http://www.devchakraborty.com> which is no longer supported. 'RJafroc' is derived from it being an enhanced R version of original Windows 'JAFROC'. Implemented are a number of figures of merit quantifying performance, functions for visualizing operating characteristics; three ROC ratings data curve-fitting algorithms: the 'binormal' model ('BM'), the contaminated binormal model ('CBM') and the radiological search model ('RSM'). Also implemented is maximum likelihood fitting of paired ROC data utilizing the correlated 'CBM' model ('CORCBM'). Unlike the 'BM', 'CBM', 'CORCBM' and the 'RSM' predict proper ROC curves that do not cross the chance diagonal or display inappropriate hooks, usually near the upper right corner of the plots. 'RSM' fitting yields measures of search and lesion-classification performances, in addition to the usual case-classification performance measured by the area under the 'ROC' curve. Search performance is the ability to find lesions while avoiding finding non-lesions. Lesion-classification performance is the ability to discriminate between found lesions and non-lesions. For fully crossed study designs, termed multiple-reader multiple-case, significance testing of reader-averaged figure-of-merit differences between modalities is implemented via both 'Dorfman', 'Berbaum' and 'Metz' ('DBM') and the 'Obuchowski' and 'Rockette' ('OR') methods, both substantially improved by 'Hillis'. Single treatment analysis allows comparison of performance of a group of radiologists to a specified value, or comparison of 'CAD' performance to a group of radiologists interpreting the same cases. Sample size estimation tools are provided for 'ROC' studies that allow estimation of relevant variances from a pilot study to predict required numbers of readers and cases in a pivotal study. 'FROC' sample size estimation is implemented in Online Appendix Chapter 19 available at < https://github.com/dpc10ster/onlinebookk21778>. Utility and data file manipulation functions allow data to be read in any of the currently used input formats, including Excel, and the results of the analysis can be viewed in text or Excel output files.


News

Update History

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RJafroc 1.0.2

Minor bug

StSignificanceTestingCadVsRadiologists was not working for different numbers of readers. As noted by Alejandro, the number of readers was hard coded. Fixed this and extended DfExtractDataset to include LROC datasets. Removed function SsFROCPowerGivenJK: FROC power is implemented in Online Appendix Chapter 19 (see email exchange with Kota Aoyagi)

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RJafroc 1.0.1

Minor bug

Package was not installing on Solaris - overloading errors. Changed sqrt(2) in RsmFuncs.cpp to sqrt(2.0). However, Solaris is incompatible with ggplot2; so will recommend that Solaris version not be distributed on CRAN.

Sorry, but I'm not sure what's different between the CRAN Solaris machine and R-hub's Solaris machine. You could prepare a new package submission for CRAN with the caveat that, since you do not have access to a Solaris machine, your fix is speculative and may yet fail to compile on the CRAN Solaris machine. The CRAN Repository Policy (https://cran.r-project.org/web/packages/policies.html) also states: Package authors should make all reasonable efforts to provide cross-platform portable code. Packages will not normally be accepted that do not run on at least two of the major R platforms. Cases for Windows-only packages will be considered, but CRAN may not be the most appropriate place to host them. So you could in theory argue your case that your package does not support Solaris, and request that CRAN not distribute your package on that platform. But given that the issue you're bumping to is (not) documented explicitly in the R manuals, I'm not sure how much success you would have.

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RJafroc 1.0.0

Major changes

Renamed functions for better organization; Removed shiny GUI interface Support for LROC datasets and cross-modality datasets CAD vs. radiologist analysis, both single modality and dual modality

RJafroc 0.1.1

Bug fixes

  • A critcal error in the p value calculation that gave incorrect p value (possibly exceeding one) when the first modality performed better than 2nd has been fixed. Thanks to Lucy D'Agostino McGowan for pointing out the error and the fix. This error, which does not occur in Windows version of JAFROC V 4.2.1, was not noticed as in all example files the 2nd modality performed better.

RJafroc 0.1.0

Major change

  • A "shiny" based GUI has been added, accessed by the function RJafrocGui(). This allows a user only interested in analyzing a data file to access the underlying code in a "user friendly way. The GUI is similar in functionality to that of Windows JAFROC 4.2.1 software.

Minor bug and aesthetic fixes

  • For the curve plotting functions, legend position and direction are automatically decided if they are not explicityly specified.
  • The the output number of significant digits for statistical power in power table has been set to 3.
  • Variance and covariance calculation error for ROI data has been fixed.
  • A bug in the JAFROC data reading function that caused an error when encountering non-numeric values has been fixed.
  • Floating point ratings are rounded to 6 significant digits when saving a dataset in JAFROC format.
  • A bug in the plotting routine that affected plots for a single rating FROC dataset has been fixed.
  • A bug in the plotting of AFROC curves for a dataset containing only non-diseased cases has been fixed.

RJafroc 0.0.1

Original version posted to CRAN website

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("RJafroc")

1.1.0 by Dev Chakraborty, 2 months ago


http://www.devchakraborty.com


Browse source code at https://github.com/cran/RJafroc


Authors: Dev Chakraborty [cre, aut, cph] , Xuetong Zhai [aut] , Lucy D'Agostino McGowan [ctb] , Alejandro RodriguezRuiz [ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports openxlsx, ggplot2, stringr, tools, utils, stats, bbmle, binom, mvtnorm, numDeriv, Rcpp

Suggests testthat, knitr, rmarkdown

Linking to Rcpp


See at CRAN