Chapter 1 Please ignore preface

TBA

1.1 Please ignore issues

1.2 Please ignore following sections

  • They are intended for my convenience and will be deleted in final version

1.3 TBA Rationale and Organization

  • Intended as an online update to my print book (Chakraborty 2017).
  • All references in this book to RJafroc refer to the R package with that name (case sensitive) (Chakraborty and Zhai 2022).
  • Since its publication in 2017 RJafroc, on which the R code examples in the print book depend, has evolved considerably causing many of the examples to “break” if one uses the most current version of RJafroc. The code will still run if one uses RJafroc 0.0.1 but this is inconvenient and misses out on many of the software improvements made since the print book appeared.
  • This gives me the opportunity to update the print book.
  • The online book has been divided into 3 books.

1.4 TBA Acknowledgements

Dr. Xuetong Zhai

Dr. Peter Phillips

Online Latex Editor at

Dataset contributors: Nico especially 11

1.5 TBA Nearly finished chapters

  • Chapter 1 The FROC paradigm and search
  • Chapter 2 Empirical plots from FROC data
  • Chapter 3 Visual Search
  • Chapter 4 The radiological search model (RSM)
  • Chapter 5 ROC curve implications of the RSM
  • Chapter 6 Search and classification performances
  • Chapter 7 RSM fitting
  • Chapter 8 Three proper ROC fits
  • Chapter 9 Standalone CAD vs. Radiologists
  • Chapter 10 Optimal operating point
  • Chapter 11 Optimal operating point appendices

1.6 The pdf file of the book

Go here and then click on Download to get the RJafrocFrocBook.pdf file. The pdf version may not be as aesthetically pleasing as the HTML version, in particular the layout of figures and tables is sometimes disjointed from the citing text.

1.7 Please ignore: TBA How much finished HMF

  • HMF approximately 30%
  • This book is currently (as of August 2022) in preparation.
  • Parts labeled TBA and TODOLAST need to be updated on final revision.
  • Un-comment links like \@ref(froc-paradigm-solar-analogy) etc. Search for \@ref

1.8 Please ignore: A note on the online distribution mechanism of the book

  • In the hard-copy version of my book (Chakraborty 2017) the online distribution mechanism was BitBucket.
  • BitBucket allows code sharing within a closed group of a few users (e.g., myself and a grad student).
  • Since the purpose of open-source code is to encourage collaborations, this was, in hindsight, an unfortunate choice. Moreover, as my experience with R-packages grew, it became apparent that the vast majority of R-packages are shared on GitHub, not BitBucket.
  • For these reasons I have switched to GitHub. All previous instructions pertaining to BitBucket are obsolete.
  • In order to access GitHub material one needs to create a (free) GitHub account.
  • Go to this link and click on Sign Up.

1.9 Please ignore: Structure of the book

1.10 Please ignore Contributing to this book

I appreciate constructive feedback on this document. To do this raise an Issue on the GitHub interface. Click on the Issues tab under dpc10ster/RJafrocFrocBook, then click on New issue. When done this way, contributions from users automatically become part of the GitHub documentation/history of the book.

1.11 Please ignore: Is this book relevant to you and what are the alternatives?

  • Diagnostic imaging system evaluation
  • Detection
  • Detection combined with localization
  • Detection combined with localization and classification
  • Optimization of Artificial Intelligence (AI) algorithms
  • CV
  • Alternatives

1.12 Please ignore: Chapters needing heavy edits

1.13 Please ignore: Shelved vs. removed vs. parked folders needing heavy edits

  • replace functions with ; eg. erf and exp in all of document
  • Also for TPF, FPF etc.
  • Temporarily shelved 17c-rsm-evidence.Rmd in removed folder
  • Now 17-b is breaking; possibly related to changes in RJafroc: had to do with recent changes to RJafroc code - RSM_xFROC etc requiring intrinsic parameters; fixed 17-b
  • parked has dependence of ROC/FROC performance on threshold

1.14 Please ignore: Coding aids (for me)

  • weird error with knitr not responding to changes in Rmd file: traced to upper case lower case confusion: 13A-empirical1.Rmd which should be 13a-empirical1.Rmd

1.14.1 formatting

  • sprintf(“%.4f”, proper formatting of numbers
  • OpPtStr(, do:

1.14.2 tables

  • https://github.com/haozhu233/kableExtra/issues/624
  • kbl(dfA, caption = “….”, booktabs = TRUE, escape = FALSE) %>% collapse_rows(columns = c(1, 3), valign = “middle”) %>% kable_styling(latex_options = c(“basic”, “scale_down”, “HOLD_position”), row_label_position = “c”)
  • ```{r, attr.source = “.numberLines”}
  • kbl(x12, caption = “Summary of optimization results using wAFROC-AUC.”, booktabs = TRUE, escape = FALSE) %>% collapse_rows(columns = c(1), valign = “middle”) %>% kable_styling(latex_options = c(“basic”, “scale_down”, “HOLD_position”), row_label_position = “c”)
  • \(\text{exp} \left ( -\lambda' \right )\) space before dollar sign generates a pdf error
  • FP errors generated by GitHub actions due to undefined labels: Error: Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available). In addition: Warning message: In verify_rstudio_version() : Please install or upgrade Pandoc to at least version 1.17.2; or if you are using RStudio, you can just install RStudio 1.0+. Execution halted

1.14.3 tinytex problems

  • dont update in response to messages; breaks everything
  • DONT DO THIS: When tinytex::install_tinytex() hangs up try
  • DONT DO THIS: tinytex::install_tinytex(repository = “http://mirrors.tuna.tsinghua.edu.cn/CTAN/”, version = “latest”)
  • Getting very long builds: looping certain commands
  • First uninstall tinytex then reinstall:
#uninstall_tinytex(force = FALSE, dir = tinytex_root())
#tinytex::install_tinytex()
  • get very long build first time with looping certain commands
  • fixed on subsequent pdf builds

REFERENCES

Chakraborty, Dev P. 2017. Observer Performance Methods for Diagnostic Imaging: Foundations, Modeling, and Applications with R-Based Examples. Boca Raton, FL: CRC Press.

Chakraborty, Dev, and Xuetong Zhai. 2022. RJafroc: Artificial Intelligence Systems and Observer Performance. https://dpc10ster.github.io/RJafroc/.