Calculate figure of merit

Description

Caclulate the figure of merit (an objective measure of observer performance) for each treatment-reader combination.

Usage

FigureOfMerit(dataset, fom = "wJAFROC")

Arguments

Details

Allowed figures of merit are: (1) "Wilcoxon" for ROC data; (2) "JAFROC1", "JAFROC", "wJAFROC1", "wJAFROC" (the default), "HrAuc", "SongA1", "SongA2"** , "HrSe", "HrSp", "MaxLLF", "MaxNLF", "MaxNLFAllCases", "ExpTrnsfmSp", for free-response data and (3) "ROI" for ROI data. The JAFROC FOMs are described in the paper by Chakraborty and Berbaum. The Song FOMs are described in the paper by Song et al. The "MaxLLF", "MaxNLF" and "MaxNLFAllCases" FOMs correspond to ordinate, abscissa and abscissa, respectively, of the highest point on the FROC operating characteristic obtained by counting all the LL marks on diseased, all NL marks on non-diseased cases, and all NL marks on all cases, respectively). The "ExpTrnsfmSp" FOM is described in the paper by Popescu. The "ROI" FOM is described in the paper by Obuchowski et al.

** The Song A2 figure of merit is computationally very intensive.

Value

An c(I, J) array, where the row names are the IDs of the treatments and column names are the IDs of the readers.

References

Chakraborty, D. P., & Berbaum, K. S. (2004). Observer studies involving detection and localization: modeling, analysis, and validation. Medical Physics, 31(8), 1-18.

Song T, Bandos AI, Rockette HE, Gur D (2008) On comparing methods for discriminating between actually negative and actually positive subjects with FROC type data. Medical Physics 35: 1547-1558.

Popescu, L. M. (2011). Nonparametric signal detectability evaluation using an exponential transformation of the FROC curve. Medical Physics, 38(10), 5690.

Obuchowski, N. A., Lieber, M. L., & Powell, K. A. (2000). Data Analysis for Detection and Localization of Multiple Abnormalities with Application to Mammography. Academic Radiology, 553-554.

Examples

FigureOfMerit(dataset = rocData, fom = "Wilcoxon")

FigureOfMerit(dataset = frocData)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RJafroc)
Loading required package: tools
Loading required package: xlsx
Loading required package: rJava
Loading required package: xlsxjars
Loading required package: ggplot2
Loading required package: stringr
Loading required package: shiny
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/RJafroc/FigureOfMerit.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FigureOfMerit
> ### Title: Calculate figure of merit
> ### Aliases: FigureOfMerit
> 
> ### ** Examples
> 
> FigureOfMerit(dataset = rocData, fom = "Wilcoxon")
          Rdr - 0   Rdr - 1   Rdr - 2   Rdr - 3   Rdr - 4
Trt - 0 0.9196457 0.8587762 0.9038647 0.9731079 0.8297907
Trt - 1 0.9478261 0.9053140 0.9217391 0.9993559 0.9299517
> 
> FigureOfMerit(dataset = frocData)
         Rdr - 1   Rdr - 3   Rdr - 4   Rdr - 5
Trt - 4 0.809410 0.7423955 0.6935350 0.8285865
Trt - 5 0.748139 0.6815555 0.6545135 0.7704165
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>