RJafroc

What is this repository for?

  • This repository serves as the software companion to my book: Chakraborty DP: Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples. Taylor-Francis LLC; 2017.
  • Full documentation (the updated book plus the software) is currently under preparation and will be posted to https://dpc10ster.github.io/RJafrocBook/
  • Software documentation (the functions used in the software, vignettes and the update history) is at https://dpc10ster.github.io/RJafroc/

Relation to the Windows software

Update History

Branch designations

  • The current tested version of the software is on the master branch.
  • The developer branch is for development/experimental work.
  • The software documentation website is pushed from the master branch.
  • RJafroc book has its own GitHub repository.

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

How do I get set up?

Three options are given below, in increasing order of complexity. The first method downloads from CRAN, the second from GitHub and the third downloads all source files from GitHub and then installs the software. I recommend the first or second methods.

1. Install from CRAN

  • Install R and RStudio.
  • Create an empty directory, e.g., myProject. In my computer it is /Users/Dev/Downloads/myProject.
  • Open RStudio by clicking on the myProject.Rproj file.
  • Starting from RStudio > Packages > Install > RJafroc.
  • library(RJafroc).
  • This loads the CRAN package and all functions on the cran2 branch become avaialable.
  • For documentation of functions and vignettes, go to https://dpc10ster.github.io/RJafroc/. It may be helpful to have both windows open (RStudio and the above website) simulataneously.
  • The CRAN version will not include more recent updates on the master branch. To access them use the next suggested method, below.
  • 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.

2. Install 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 by clicking on the myProject.Rproj file.
  • 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.

3. Download the RJafroc source files 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).
  • Do not write any of your files to the RJafroc directory!
  • 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, outside of the RJafroc folder. 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

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

  • 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.

Who do I talk to?