Enable live code runs

[mitchellmanware]

After discussion on 08/07, we will re-enable live code runs for rendering the book. This will allow us to keep the code base up to date and ensure the code we publish as a tutorial runs as expected.

To ensure that the book renders in a reasonable time we can:

1. eval = FALSE for download chunks
2. save large data files as .rds. or .qs files

[mitchellmanware]

Testing run time with all code chunks eval = FALSE (on HPC)

> # all code chunks disabled
> tic()
> bookdown::render_book(".")
toc()
Rendering book in directory '.'

processing file: _main.Rmd
  |.............                                     |  26%                     [unnamed-chunk-41]                        |................                                  |  32% [unnamed-chunk-50]                      [unnamed-chunk-51]    |...................                               |  38%                     [unnamed-chunk-60]                        |......................                            |  44% [unnamed-chunk-69]                      [unnamed-chunk-70]    |.........................                         |  50%                     [unnamed-chunk-79]                        |............................                      |  56% [unnamed-chunk-88]                      [unnamed-chunk-89]    |...............................                   |  62%                     [unnamed-chunk-98]                        |..................................                |  68% [unnamed-chunk-107]                     [unnamed-chunk-108]   |.....................................             |  74%                     [unnamed-chunk-117]                                                                                                                                   hunk-156]
output file: _main.knit.md

/ddn/gs1/biotools/misc/bin/pandoc +RTS -K512m -RTS _main.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _main.html --lua-filter /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpBvM0nu/file3b72a47f0bd89 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 2 --template /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css style.css --mathjax --include-in-header /tmp/RtmpBvM0nu/rmarkdown-str3b72a45738f05b.html --include-after-body after_body.html --citeproc 

Output created: docs/index.html
[1] "/ddn/gs1/home/manwareme/chords/PCOR_bookdown_tools/docs/index.html"
Warning message:
In verify_rstudio_version() :
  Please install a newer version of the RStudio IDE: https://posit.co/download/rstudio-desktop/
> toc()
4.826 sec elapsed

[mitchellmanware]

Testing run time with 1. Getting Started eval = TRUE (on HPC)

> tic()
bookdown::render_book(".")
toc()
> bookdown::render_book(".")
Rendering book in directory '.'

processing file: _main.Rmd
  |.                                                 |   2%                     [unnamed-chunk-3]    |..                                                |   4% [unnamed-chunk-6]                        |...                                               |   6% [unnamed-chunk-9]                        |....                                              |   8% [unnamed-chunk-12]                       |.....                                             |  10%                     [unnamed-chunk-16]   |......                                            |  12%                     [unnamed-chunk-19]   |.......                                           |  14%                     [unnamed-chunk-22]   |........                                          |  16% [unnamed-chunk-25]                       |.........                                         |  18% [unnamed-chunk-28]                       |..........                                        |  20% [unnamed-chunk-31]                       |...........                                       |  22%                     [unnamed-chunk-35]   |............                                      |  24%                     [unnamed-chunk-38]   |.............                                     |  26%                     [unnamed-chunk-41]   |..............                                    |  28% [unnamed-chunk-44]                       |...............                                   |  30% [unnamed-chunk-47]                       |................                                  |  32% [unnamed-chunk-50]                       |.................                                 |  34%                     [unnamed-chunk-54]   |..................                                |  36%                     [unnamed-chunk-57]   |...................                               |  38%                     [unnamed-chunk-60]   |....................                              |  40% [unnamed-chunk-63]                       |.....................                             |  42% [unnamed-chunk-66]                       |......................                            |  44% [unnamed-chunk-69]                       |.......................                           |  46%                     [unnamed-chunk-73]   |........................                          |  48%                     [unnamed-chunk-76]   |.........................                         |  50%                     [unnamed-chunk-79]   |..........................                        |  52% [unnamed-chunk-82]                       |...........................                       |  54% [unnamed-chunk-85]                       |............................                      |  56% [unnamed-chunk-88]                       |.............................                     |  58%                     [unnamed-chunk-92]   |..............................                    |  60%                     [unnamed-chunk-95]   |...............................                   |  62%                     [unnamed-chunk-98]   |................................                  |  64% [unnamed-chunk-101]                      |.................................                 |  66% [unnamed-chunk-104]                      |..................................                |  68% [unnamed-chunk-107]                      |...................................               |  70%                     [unnamed-chunk-111]  |....................................              |  72%                     [unnamed-chunk-114]  |.....................................             |  74%                     [unnamed-chunk-117]  |......................................            |  76% [unnamed-chunk-120]                      |.......................................           |  78% [unnamed-chunk-123]                      |........................................          |  80%                     [unnamed-chunk-127]  |.........................................         |  82%                     [unnamed-chunk-130]  |..........................................        |  84%                     [unnamed-chunk-133]  |...........................................       |  86% [unnamed-chunk-136]                      |............................................      |  88% [unnamed-chunk-139]                      |.............................................     |  90% [unnamed-chunk-142]                      |..............................................    |  92%                     [unnamed-chunk-146]  |...............................................   |  94%                     [unnamed-chunk-149]  |................................................  |  96%                     [unnamed-chunk-152]  |................................................. |  98% [unnamed-chunk-155]                                                                                                                                  
output file: _main.knit.md

/ddn/gs1/biotools/misc/bin/pandoc +RTS -K512m -RTS _main.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _main.html --lua-filter /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpPA4YTO/file529d22241b4f7 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 2 --template /ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css style.css --mathjax --include-in-header /tmp/RtmpPA4YTO/rmarkdown-str529d2119d28d3.html --include-after-body after_body.html --citeproc 
> toc()
767.297 sec elapsed

[mitchellmanware]

@larapclark @szcc Rendering with the three introductory spatial analysis chapters running live code takes ~12.5 minutes. Since these are the some of the heaviest and longest chapters, I think we should continue with transitioning eval = FALSE to eval = TRUE code runs.

In these chapters, I have kept chunks where data is downloaded and/or unzipped as eval = TRUE, because there is no need to re-download and unzip the data at each run.