RJafroc

What is this repository for?

  • Modeling, Analysis, Validation and Visualization of ROC/FROC/LROC studies.
  • Extends and replaces Windows JAFROC software at http://www.devchakraborty.com.
  • I know the Windows software is much easier to use, so I am keeping it online for now, but I cannot maintain or extend it.
  • This repository also serves as the Online Appendix to my book: Chakraborty DP: Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples. Taylor-Francis LLC; 2017.

Update History

Branch designations

The complete (all vignettes and tests) and most current and tested version of the software is on the master branch. The development branch is for ongoing development/experimental work. When finished and tested, the development branch should be merged with master, then file-size-limited and merged to CRAN branch, and then submitted to CRAN. The website is pushed from master branch.

Documentation (articles or vignettes) is available at https://dpc10ster.github.io/RJafroc/

Highly recommended in order to familiarize oneself with the code. It has some QuickStart vignettes that will enable one already familiar with the Windows software to run the R code.

My wiki is at https://github.com/dpc10ster/RJafroc/wiki

This is under development and may be dropped in future in favor of an online book, or extended vignettes.

A CRAN version of RJafroc has been published

Thanks to help from Dr. Peter Phillips, version 1.2.0 of RJafroc has passed CRAN tests. This version is on the cran branch.

Those already familiar with installing R packages from GitHub can ignore the following directions

How do I get set up?

Short version: install directly from GitHub using package devtools

  • Install R and RStudio.
  • Create an empty directory, e.g., myProject. In my computer it is /Users/Dev/Downloads/myProject.
  • Open RStudio.
  • Starting from RStudio > File > New Project > Existing Directory > Select myProject > Create Project.
  • Oila! You should see myProject.RProj in the Files menu.
  • Install the devtools package as shown below:
  • Starting from RStudio > Packages > Install > devtools.
  • Load devtools as shown below:
library(devtools)
  • Install RJafroc directly from GitHub (this is where devtools is used):
install_github("dpc10ster/rjafroc")
  • Hit Enter on any prompts…
  • Lots of activity and compilation of C++ code ….
  • Load RJafroc as shown below:
library(RJafroc)
  • Test the installation:
cbmPlot <- PlotCbmFit(c(1, 2), c(0.5, 0.5))
print(cbmPlot)
  • You should see two ROC plots in the Plots window.
  • Preliminary documentation (vignettes) is available at https://dpc10ster.github.io/RJafroc/.
  • Be sure to study these examples and make full use of the online documentation.
  • Put your data and other files, if any, in myProject.
  • TBA

Long version: download the RJafroc package and install from the downloaded files

  • Clone this repository to a directory anywhere on your computer. On my computer it is in /Users/Dev/Downloads/rjafroc. Rename the folder if necessary to match my example.
  • I find the GitHub desktop app useful in mananging my downloads/uploads from Git.
  • Install R and RStudio.
  • Navigate to the rjafroc directory.
  • Open RJafroc.Rproj. This will open RStudio.
  • Navigate to File menu (lower-right window) and click on DESCRIPTION file.
  • Install all packages listed under Imports, e.g.,
    openxlsx, ggplot2, stringr, tools, utils, stats, bbmle, binom, mvtnorm, dplyr, numDeriv, Rcpp
  • For example, to install the first two above-listed packages, use the following command at the Console prompt:
install.packages(c("openxlsx", "ggplot2"))
  • Click on Build > Install and Restart (upper right panel). If errors result from missing packages, install those packages.
  • A successful Install and Restart will result in the following line in the Console window:
library(RJafroc)
  • Thats it! RJafroc has been installed to your computer and is visible to any other R project in any directory.
  • You will not need to access the RJafroc folder again (unless you reinstall a new version of the software).
  • All necessary files of the installation are in a hidden directory that you do not normally need to worry about.
  • Create an empty directory, e.g., myProject. In my computer it is /Users/Dev/Downloads/myProject.
  • Starting from RStudio > File > New Project > Existing Directory > myProject > Create Project.
  • Oila! You should see myProject.RProj in the Files menu.
  • Click on Packages and scroll down to find RJafroc, and check the box next to it. This results in RJafroc being loaded to the current workspace. The following line appears in the Console window (this is the hidden directory referrred to above).
  library("RJafroc", lib.loc="/Library/Frameworks/R.framework/Versions/3.5/Resources/library")
  • Click on RJafroc in the packages window. A help window opens up. I find it convenient to put this in its own window by clicking the “out” arrow button (hover message: Show in new window). You can access all documentation from here.
  • Test the installation:
cbmPlot <- PlotCbmFit(c(1, 2), c(0.5, 0.5))
print(cbmPlot)
  • You should see two ROC plots in the Plots window.
  • Preliminary documentation (vignettes) is available at https://dpc10ster.github.io/RJafroc/.
  • Put your data and other files, if any, in myProject.
  • TBA

Contibutor guidelines

  • As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.

  • We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.

  • Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.

  • Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.

  • Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.

  • These guidelines are adapted from content on the devtools GitHub page.

Who do I talk to?