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index.Rmd
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---
title: "The RJafroc Froc Book"
author: "Dev P. Chakraborty, PhD"
geometry: margin=2cm
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: html_document
documentclass: book
bibliography: [packages.bib, myRefs.bib]
biblio-style: apalike
link-citations: yes
github-repo: dpc10ster/RJafrocFrocBook
description: "Artificial intelligence and observer performance book based on RJafroc."
---
```{r include=FALSE}
# automatically create a bib database for R packages
knitr::write_bib(c(
.packages(), 'bookdown', 'knitr', 'rmarkdown', 'ggplot2', 'mvtnorm',
'binom', 'exactci', 'RJafroc', 'bbmle', 'Rmpfr'), 'packages.bib')
```
# (PART\*) Preamble {-}
# Please ignore preface
TBA
## Please ignore issues
<!-- Setting margins for pdf output currently does not work on GitHub actions -->
## Please ignore following sections
* They are intended for my convenience and will be deleted in final version
## TBA Rationale and Organization
* Intended as an online update to my print book [@chakraborty2017observer].
* All references in this book to `RJafroc` refer to the R package with that name (case sensitive) [@R-RJafroc].
* 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](https://cran.r-project.org/src/contrib/Archive/RJafroc/) 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.
+ The [RJafrocQuickStartBook](https://dpc10ster.github.io/RJafrocQuickStart/) book.
+ The [RJafrocRocBook](https://dpc10ster.github.io/RJafrocRocBook/) book.
+ **This book:** [RJafrocFrocBook](https://dpc10ster.github.io/RJafrocFrocBook/).
## TBA Acknowledgements
Dr. Xuetong Zhai
Dr. Peter Phillips
Online Latex Editor [at](https://latexeditor.lagrida.com/)
Dataset contributors: Nico especially \@ref(standalone-cad-radiologists)
## 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
## The pdf file of the book
Go [here](https://github.com/dpc10ster/RJafrocFrocBook/blob/gh-pages/RJafrocFrocBook.pdf) 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.
## 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`
## Please ignore: A note on the online distribution mechanism of the book
* In the hard-copy version of my book [@chakraborty2017observer] 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](https://github.com) and click on `Sign Up`.
## Please ignore: Structure of the book
## Please ignore Contributing to this book
I appreciate constructive feedback on this document. To do this raise an `Issue` on the `GitHub` [interface](https://github.com/dpc10ster/RJafrocFrocBook). 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.
## 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
## Please ignore: Chapters needing heavy edits
## Please ignore: Shelved vs. removed vs. parked folders needing heavy edits
* replace functions with \text{}; 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
## 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
### formatting
* sprintf("%.4f", proper formatting of numbers
* OpPtStr(, do:
### 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
### 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:
``` {r}
#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