This book is based on R Markdown and bookdown (https://github.com/rstudio/bookdown).

Detailed instructions for the approach used for building a book are available from https://bookdown.org/yihui/bookdown/build-the-book.html. See also https://bookdown.org/yihui/bookdown-demo/.

DataSense

Files are for a booklet that I have titled "The Skeptical Data Analyst Think again — examples that inform and educate". It brings together, and updates and revises, notes for a Victoria University of Wellington 2017 Continuing Education cours. The earlier brief notes have been supplemented with explanatory text, and further examples added, with the aim of creating self-contained document that can stand on its own.

Setup required, for processing the several chapters

The normal way to get started with R and RStudio is:

1. Download and install R from, e.g., https://cran.stat.auckland.ac.nz/ or http://cran.ms.unimelb.edu.au/
   • Usually it is just a matter of clicking on the downloaded file and following instructions.
   • [Installation using brew can lead to later problems, and is not recommended.]
2. Use of the RStudio Integrated Development Environment is recommended. Download RStudio Desktop from https://www.rstudio.com/products/rstudio/download/ Click on the downloaded file and follow instructions.
3. Install R packages knitr, bookdown, rmarkdown, ggplot2, gridExtra, histdata, mgcv, lattice, xtable GGally, latticeExtra, car, MASS, DAAG, GDAdata, corrplot. This can be done either from the R command line or from the RStudio GUI. You will be prompted to install various dependencies as installation proceeds. Compiled versions (which may not always be the most recent version) should in all cases be all you require.
   • If a needed package has been missed, this will become obvious when you try to process the Rmd file.
4. The setup for the document is specified in the YAML header in the file index.Rmd. Note also the files _bookdown.yml and _output.yml, which add some further setup commands that could alternatively be placed in the file index.Rmd. The setting new_session: yes has the consequence that chapters are processed independently in what is called the "Knit and Merge" (K-M) approach, as opposed to "Merge and Knit" (M-K).
5. Click on knit to preview an individual chapter, or to preview the output from index.Rmd. Click on the menu item Build, and then on Build Book to build the whole book.
   • The html file(s), and the pdf file, appear in the directory _book.
6. The YAML file _bookdown.yml lists in order, against the entry yml_files, the R markdown (.Rmd) files that are the source files that are processed to form the separate items (frontmatter, chapters, endmatter items) that, make up the book. Note the YAML entry before_chapter_script: eachChap.R, which lists an R script that is to be run before the Rmd file for each chapter is processed.
7. The YAML file _output.yml specifies the several formats of output file that are required. For PDF output, this includes information about table of contents (toc), toc depth, the latex engine (e.g., xelatex rather than tinytex), the graphics device, and so on. Under includes:, note in_header: preamble.tex. This specifies latex file header packages, etc.
8. For PDF output, see the requirements noted at: https://bookdown.org/yihui/rmarkdown/installation.html#installation See also https://bookdown.org/yihui/rmarkdown/pdf-document.html
9. For html output, specify split_by: none to generate a single html file.
10. The directory _book/work/ holds the files tmat4.txt and termFunIndex.Rmd that are used in generating the index file book-index.ind.
    • In tmat4.txt each line is i) a row number ii) an index entry (the syntax a! b identifies entry a with subitem b) iii) one or two words which, if found on a page, will generate that entry iv) a further one or two words which (if not both NA) will be used to that entry.
    • See further, below, for details of how to use this code.

If ~/_notes/dataThoughts/book-index.ind has no entries, enter, from the Unix command line (this for Mac; Windows?) $ cp ~/_notes/dataThoughts/_book/work/book-index.ind \ ~/_notes/dataThoughts/book-index.ind

To generate a new index file, proceed thus:

• Enter, from the Unix command line in the _book/work/ subdirectory $ pdftotext -f 11 -l 102 -layout -eol unix
  ../dataSense-book.pdf dataSense-book.txt If necessary, change -l 96 to exclude the existing index.
• Open the file termFunIndex.Rmd, from the _book/work/ subdirectory, in RStudio.
• Run the code chunk termFuns that starts at line 14 (Position the cursor within the chunk, and press Cmd/Shift/Enter). This loads the functions 'locateTermandmakeTermIndex `.
• Run the code chunk mkind that starts at line 144.
  • If you run it using Cmd/Shift/Enter, it will be run as if in the _book/work/ subdirectory, which is the subdirectory from which you opened the termFunIndex.Rmd* file.
  • If you want to run it from the command line, note that you will then (unless you change directories) be running it from the ~/_notes/dataThoughts directory, and you have to adjust the file paths accordingly.