Analyzing Diagnostic Observer Performance Studies

Implements software for assessing medical imaging systems, radiologists or computer aided detection algorithms. Models of observer performance are implemented, including the binormal model (BM), the contaminated binormal model (CBM), the correlated contaminated binormal model (CORCBM), and the radiological search model (RSM). The software and applications are described in a book - Chakraborty DP: Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples. Taylor-Francis LLC; 2017 - and its vignettes < https://dpc10ster.github.io/RJafroc/>. Observer performance data collection paradigms are the receiver operating characteristic (ROC) and its location specific extensions, primarily free-response ROC (FROC) and the location ROC (LROC). ROC data consists of single ratings per images. A rating is the perceived confidence level that the image is that 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 real lesion. LROC data consists of a rating and a forced localization of the most suspicious region on every image. RJafroc supersedes the Windows version of JAFROC software V4.2.1, < http://www.devchakraborty.com>:. Package functions are organized as follows. Data file related function names are preceded by Df, curve fitting functions by Fit, included data sets by dataset, plotting functions by Plot, significance testing functions by St, sample size related functions by Ss, data simulation functions by Simulate and utility functions by Util. Implemented are figures of merit (FOMs) for quantifying performance, functions for visualizing empirical operating characteristics: e.g., ROC, FROC, alternative FROC (AFROC) and weighted AFROC (wAFROC) curves. Four maximum likelihood curve-fitting algorithms are implemented: the binormal model (BM), the contaminated binormal model (CBM), the correlated contaminated binormal model (CORCBM) and the radiological search model (RSM). Unlike the binormal model, CBM, CORCBM and RSM predict "proper" ROC curves that do not cross the chance diagonal. RSM fitting additionally yields measures of search and lesion-classification performances. Search performance is the ability to find lesions while avoiding finding non-lesions. Lesion-classification performance is the ability to correctly classify found lesions from found non-lesions. For fully crossed study designs significance testing of reader-averaged FOM differences between modalities is implemented via both Dorfman-Berbaum-Metz and the Obuchowski-Rockette methods, including Hillis' extensions. Also implemented are single treatment analyses, which allow comparison of performance of a group of radiologists to a specified value, or comparison to CAD to a group of radiologists interpreting the same cases. Crossed-modality analysis is implemented wherein there are two crossed treatment factors and the desire is to determined performance in each treatment factor averaged over all levels of the other factor. Sample size estimation tools are provided for ROC and FROC studies; these use estimates of the relevant variances from a pilot study to predict required numbers of readers and cases in a pivotal study to achieve a desired power. 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. The methods are illustrated with several included datasets from the author's international collaborations. This version corrects a few bugs noticed by users and extends the Excel file input format for greater flexibility in handling non-crossed datasets and the sample size routines have been rewritten for ease of use.


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

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install.packages("RJafroc")

1.3.2 by Dev Chakraborty, 4 months ago


https://dpc10ster.github.io/RJafroc/


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


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


Documentation:   PDF Manual  


GPL-3 license


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

Suggests rmarkdown

Linking to Rcpp


See at CRAN