+
+```
+
+You can see the container, and the plot and the slider nested inside.
+This is going to be added to the body of the HTML page rendered by
+Shiny. The final HTML page will also contain all the JavaScript and CSS
+dependencies required to make the app interactive and styled properly.
+
+The Python UI uses the `ui` object imported from `shiny`. The setup is very
+similar to the R setup, but naming conventions are slightly different
+(`fixedPage` vs. `page_fixed`, `plotOutput` vs. `output_plot` and
+`sliderInput` vs. `input_slider`).
+
+```python
+app_ui = ui.page_fixed(
+ ui.panel_title("Old Faithful"),
+ ui.output_plot(id = "histogram"),
+ ui.input_slider(
+ id="n",
+ label="Number of bins:",
+ min=1,
+ max=50,
+ value=25,
+ ticks=True
+ ),
+)
+```
+
+Printing the `app_ui` in Python gives the following (slightly edited) HTML output:
+
+```html
+
+
+
+
+ + Old Faithful +
+
+
+
+
+
+
+
+
+
+
+```
+
+The only difference relative to the R output is that you can see the ``,
+`` and `` tags. Shiny will inject elements into the HTML head later.
+
+### The Server Function
+
+The server function contains the instructions for the reactivity needed
+for the Shiny app. The server function takes two arguments: `input` and
+`output` (sometimes also `session`). These reactive objects are created
+by Shiny and passed to the server function.
+
+`input` is used to pass the control values, in this case, `input$n`,
+the number of histogram bins:
+
+```R
+server <- function(input, output, session) {
+ output$histogram <- renderPlot(
+ alt = "Histogram of waiting times",
+ {
+ hist(
+ x,
+ breaks = seq(min(x), max(x),
+ length.out = input$n + 1
+ ),
+ freq = TRUE,
+ col = "#BB74DB",
+ border = "white",
+ main = "Histogram of waiting times",
+ xlab = "Waiting time to next eruption [mins]",
+ ylab = "Frequency"
+ )
+ box()
+ }
+ )
+}
+```
+
+The `output` object contains the reactive output objects, in our case the
+rendered plot. `input` and `output` together describe the state of the
+app. Changes in `input` (`input$n` here) will invalidate reactive objects that
+reference these reactive dependencies
+and cause the relevant render functions (`renderPlot()` here) to re-execute.
+
+We can see some differences in the Python version.
+Shiny for Python uses decorators (e.g. `@output`) instead of
+render functions and inputs are invoked as `input.n()`.
+(See the [Framework Comparisons](https://shiny.posit.co/py/docs/comp-r-shiny.html)
+section of the Shiny for Python documentation for a detailed overview of
+R vs. Python similarities and differences.)
+
+FIXME: KALVIN please explain here the `@output` part etc.
+
+```python
+def server(input, output, session):
+ @output
+ @render.plot(alt="Histogram of waiting times")
+ def histogram():
+ plt.hist(
+ x,
+ bins = input.n(),
+ density=False,
+ color="#BB74DB",
+ edgecolor="white")
+ plt.title("Histogram of waiting times")
+ plt.xlabel("Waiting time to next eruption [mins]")
+ plt.ylabel("Frequency")
+```
+
+The server function is called once for each Shiny session.
+A new session with a new websocket connection is created every time a web
+browser connects to the Shiny application.
+
+### Shiny Express
+
+Python for Shiny has two different syntax options, Shiny Core that you saw
+in the previous sections, and [Shiny Express](https://shiny.posit.co/py/docs/express-vs-core.html).
+Shiny Core drew inspiration from the original Shiny for R framework,
+but is _not_ a literal port of Shiny for R.
+Shiny Expressed was introduced quite recently, and is focused on making it
+easier for beginners to use Shiny, and might feel more natural to Python users.
+
+Shiny Core offers the separation between the UI and the server components,
+making it easier to organize code for larger Shiny apps.
+The server function declaration also helps separating code that should only
+run at startup vs. for the sessions.
+In Shiny Express, all of the code in the app file is executed for each session.
+
+There is only one Shiny syntax option in R.
+
+## Organizing Shiny Apps
+
+The previously presented `faithful` app is organized as a single file.
+The file contained all the globally scoped declarations at the top,
+the definition of the UI object and the server function, and ended
+with the Shiny app object. As Shiny apps grow from demo examples to full on
+data science projects, the increased complexity will necessitate the
+organization of the code. You can organize the code into multiple files,
+or even as a package. Let's see the most common patterns.
+
+### Single file
+
+When Shiny is organized in a single file, the convention is to name it `app.R`.
+This way your IDE (RStudio or VS Code) will recognize that it is a Shiny app.
+Apart from this convenience, the file can be named anything, e.g. `faithful_app.R`.
+The single file follows the following structure:
+
+```R
+# Load libraries
+library(shiny)
+
+# Define global variables
+x <- [...]
+
+# Define the UI
+app_ui <- [...]
+
+# Define the server
+server <- function(input, output, session) {
+ [...]
+}
+
+# Assemble the Shiny app
+shinyApp(ui = app_ui, server = server)
+```
+
+At the end of the file, we define the Shiny app using `shinyApp()`.
+To run the app in R, we either have to source the `app.R` or provide the
+file name as an argument to the `runApp()` function, e.g.
+`runApp("+ Old Faithful +
+
+
+
+
+
+
+ + diff --git a/book-source/_includes/logo.html b/book-source/_includes/logo.html new file mode 100644 index 0000000..ef82ca6 --- /dev/null +++ b/book-source/_includes/logo.html @@ -0,0 +1,3 @@ + +
+
diff --git a/book-source/_lint.R b/book-source/_lint.R
new file mode 100644
index 0000000..dae749a
--- /dev/null
+++ b/book-source/_lint.R
@@ -0,0 +1,20 @@
+lintr::lint_dir()
+library(lintr)
+dr <- "."
+rmd_files <- list.files(dir, pattern = "\\.Rmd$", full.names = TRUE)
+
+lint(
+ filename,
+ linters = NULL,
+ ...,
+ cache = FALSE,
+ parse_settings = TRUE,
+ text = NULL
+ )
+
+i <- 2
+lint(rmd_files[i], lintr::linters_with_defaults())
+lint(rmd_files[i], pkgpurl::default_linters)
+
+lint_dir(dir, pattern = "(?i)[.](rmd)$")
+
diff --git a/book-source/_output.yml b/book-source/_output.yml
new file mode 100755
index 0000000..ffd6257
--- /dev/null
+++ b/book-source/_output.yml
@@ -0,0 +1,43 @@
+# Modified from https://github.com/rstudio/bookdown/blob/master/inst/examples/_output.yml
+# To uncomment these lines to create a PDF version, we recommend activating
+# multiple cursors in RStudio using (on a Mac) Control + Option + A:
+# bookdown::pdf_book:
+# includes:
+# in_header: latex/preamble.tex
+# before_body: latex/before_body.tex
+# after_body: latex/after_body.tex
+# keep_tex: true
+# dev: "cairo_pdf"
+# latex_engine: xelatex
+# citation_package: natbib
+# template: null
+# pandoc_args: --top-level-division=chapter
+# toc_depth: 3
+# toc_unnumbered: false
+# toc_appendix: true
+# quote_footer: ["\\VA{", "}{}"]
+# highlight_bw: true
+bookdown::gitbook:
+ df_print: default
+ css: style.css
+ split_by: "chapter+number"
+ config:
+ toc:
+ collapse: section
+ scroll_highlight: true
+ edit:
+ link: https://github.com/analythium/hosting-shiny-book/edit/main/%s
+ includes:
+ in_header: _includes/analytics.html
+ before_body: _includes/logo.html
+# bookdown::bs4_book:
+# css: [css/style.css, css/style_gitbook.css]
+# repo: https://github.com/analythium/hosting-shiny-book
+# includes:
+# in_header: _includes/analytics.html
+# before_body: _includes/logo.html
+# after_body: _includes/footer.html
+# theme:
+# primary: "#DE633C"
+# fg: "#2b2121"
+# bg: "#ffffff"
diff --git a/book-source/bib/articles.bib b/book-source/bib/articles.bib
new file mode 100755
index 0000000..edeb9d9
--- /dev/null
+++ b/book-source/bib/articles.bib
@@ -0,0 +1,68 @@
+@article{Leisch2002,
+ author = {Leisch, Friedrich},
+ title = {Sweave, part I: Mixing R and LaTeX},
+ journal = {R News},
+ year = {2002},
+ note = {https://journal.r-project.org/articles/RN-2002-025/},
+ volume = {2},
+ issue = {3},
+ issn = {1609-3631},
+ pages = {28-31}
+}
+
+@article{rocker,
+ author = {Carl Boettiger and Dirk Eddelbuettel},
+ title = {{An Introduction to Rocker: Docker Containers for R}},
+ year = {2017},
+ journal = {{The R Journal}},
+ doi = {10.32614/RJ-2017-065},
+ url = {https://doi.org/10.32614/RJ-2017-065},
+ pages = {527--536},
+ volume = {9},
+ number = {2}
+}
+
+@article{Rockerverse,
+ author = {Daniel Nüst and Dirk Eddelbuettel and Dom Bennett and
+ Robrecht Cannoodt and Dav Clark and Gergely Daróczi and
+ Mark Edmondson and Colin Fay and Ellis Hughes and Lars
+ Kjeldgaard and Sean Lopp and Ben Marwick and Heather Nolis
+ and Jacqueline Nolis and Hong Ooi and Karthik Ram and Noam
+ Ross and Lori Shepherd and Péter Sólymos and Tyson Lee
+ Swetnam and Nitesh Turaga and Charlotte Van Petegem and
+ Jason Williams and Craig Willis and Nan Xiao},
+ title = {{The Rockerverse: Packages and Applications for
+ Containerisation with R}},
+ year = {2020},
+ journal = {{The R Journal}},
+ doi = {10.32614/RJ-2020-007},
+ url = {https://doi.org/10.32614/RJ-2020-007},
+ pages = {437--461},
+ volume = {12},
+ number = {1}
+}
+
+@INPROCEEDINGS{Eng_2021,
+ author={Eng, Kalvin and Hindle, Abram},
+ booktitle={2021 IEEE/ACM 18th International Conference on Mining Software Repositories (MSR)},
+ title={Revisiting Dockerfiles in Open Source Software Over Time},
+ year={2021},
+ volume={},
+ number={},
+ pages={449-459},
+ keywords={Education;Containers;Tools;Market research;Cognition;History;Data mining;Git;GitHub;Docker},
+ doi={10.1109/MSR52588.2021.00057}
+}
+
+@article{Eng_2024,
+ title={Patterns of multi-container composition for service orchestration with Docker Compose},
+ volume={29},
+ ISSN={1573-7616},
+ url={http://dx.doi.org/10.1007/s10664-024-10462-8},
+ DOI={10.1007/s10664-024-10462-8},
+ number={3},
+ journal={Empirical Software Engineering},
+ publisher={Springer Science and Business Media LLC},
+ author={Eng, Kalvin and Hindle, Abram and Stroulia, Eleni},
+ year={2024}
+}
diff --git a/book-source/bib/books.bib b/book-source/bib/books.bib
new file mode 100755
index 0000000..e3c4d92
--- /dev/null
+++ b/book-source/bib/books.bib
@@ -0,0 +1,124 @@
+@book{Rodrigues2023,
+ title = {Building reproducible analytical pipelines with {R}},
+ author = {Bruno Rodrigues},
+ year = {2023},
+ url = {https://raps-with-r.dev/}
+}
+
+@book{Wickham2021,
+ title = {Mastering {Shiny}},
+ author = {Hadley Wickham},
+ year = {2021},
+ publisher = {O'Reilly Media, Inc.},
+ isbn = {9781492047339},
+ url = {https://mastering-shiny.org/}
+}
+
+@book{Fay2021,
+ title = {Engineering Production-Grade {Shiny} Apps},
+ author = {Colin Fay and Sébastien Rochette and Vincent Guyader and Cervan Girard},
+ year = {2021},
+ publisher = {Chapman & Hall},
+ isbn = {9780367466022 },
+ url = {https://engineering-shiny.org/}
+}
+
+@book{coene2021javascript,
+ title={Javascript for R},
+ author={Coene, J.},
+ isbn={9781000408171},
+ lccn={2021008502},
+ series={Chapman \& Hall/CRC The R Series},
+ url={https://books.google.ch/books?id=ntUxEAAAQBAJ},
+ year={2021},
+ publisher={CRC Press}
+}
+
+@book{Granjon2022,
+ title = {Outstanding User Interfaces with Shiny},
+ author = {David Granjon},
+ year = {2022},
+ publisher = {Chapman & Hall},
+ isbn = {9780367643652},
+ url = {https://unleash-shiny.rinterface.com/}
+}
+
+@book{Gold2024,
+ title = {DevOps for Data Science},
+ author = {Alex Gold},
+ year = {2024},
+ publisher = {Chapman & Hall},
+ isbn = {9781032100340},
+ url = {https://do4ds.com/}
+}
+
+
+@book{usedtor2016,
+ title = {Getting Used to R, {RStudio}, and R Markdown},
+ author = {Chester Ismay and Patrick C. Kennedy},
+ year = {2016},
+ url = {https://rbasics.netlify.com}
+}
+
+@book{wilkinson2005,
+ title = {The Grammar of Graphics (Statistics and Computing)},
+ author = {Leland Wilkinson},
+ year = {2005},
+ edition = {First},
+ publisher = {Springer-Verlag},
+ address = {Secaucus, NJ},
+ isbn = {978-0387245447}
+}
+
+@Book{xie2015,
+ author = {Yihui Xie},
+ title = {Dynamic Documents with {R} and knitr},
+ publisher = {Chapman and Hall/CRC},
+ address = {Boca Raton, Florida},
+ year = {2015},
+ edition = {2nd},
+ note = {ISBN 978-1498716963},
+ url = {http://yihui.name/knitr/}
+}
+
+@Book{AdvancedR,
+ author = {Wickham Hadley},
+ title = {Advanced R},
+ publisher = {Chapman and Hall/CRC},
+ address = {Boca Raton, Florida},
+ year = {2019},
+ edition = {2nd},
+ note = {ISBN 978-0815384571},
+ url = {https://adv-r.hadley.nz/}
+}
+
+@book{R4DS,
+author = {Wickham, Hadley and Grolemund, Garrett},
+title = {R for Data Science: Import, Tidy, Transform, Visualize, and Model Data},
+year = {2017},
+isbn = {1491910399},
+publisher = {O'Reilly Media, Inc.},
+adress = {Farnham, UK},
+edition = {1st}
+}
+
+@Book{rpkg-book,
+ author = {Wickham Hadley and Jennifer Bryan},
+ title = {R Packages},
+ publisher = {O'Reilly Media, Inc.},
+ adress = {Farnham, UK},
+ year = {2023},
+ edition = {2nd},
+ note = {ISBN 978-1098134945},
+ url = {https://r-pkgs.org/}
+}
+
+@Book{Knuth1992,
+ author = {Donald Knuth},
+ title = {Literate Programming},
+ publisher = {Center for the Study of Language and Information---CSLI},
+ adress = {Stanford, CA},
+ year = {1992},
+ note = {ISBN 978-0937073803}
+}
+
diff --git a/book-source/bib/libraries.bib b/book-source/bib/libraries.bib
new file mode 100755
index 0000000..31bb8cf
--- /dev/null
+++ b/book-source/bib/libraries.bib
@@ -0,0 +1,39 @@
+@article{Waskom2021,
+ doi = {10.21105/joss.03021},
+ url = {https://doi.org/10.21105/joss.03021},
+ year = {2021},
+ publisher = {The Open Journal},
+ volume = {6},
+ number = {60},
+ pages = {3021},
+ author = {Michael L. Waskom},
+ title = {seaborn: statistical data visualization},
+ journal = {Journal of Open Source Software}
+}
+
+@Article{Hunter2007,
+ Author = {Hunter, J. D.},
+ Title = {Matplotlib: A 2D graphics environment},
+ Journal = {Computing in Science \& Engineering},
+ Volume = {9},
+ Number = {3},
+ Pages = {90--95},
+ abstract = {Matplotlib is a 2D graphics package used for Python for
+ application development, interactive scripting, and publication-quality
+ image generation across user interfaces and operating systems.},
+ publisher = {IEEE COMPUTER SOC},
+ doi = {10.1109/MCSE.2007.55},
+ year = 2007
+}
+
+@article{scikit-learn,
+ title={Scikit-learn: Machine Learning in {P}ython},
+ author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
+ and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
+ and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
+ Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
+ journal={Journal of Machine Learning Research},
+ volume={12},
+ pages={2825--2830},
+ year={2011}
+}
diff --git a/book-source/bib/packages.bib b/book-source/bib/packages.bib
new file mode 100644
index 0000000..ee61a7d
--- /dev/null
+++ b/book-source/bib/packages.bib
@@ -0,0 +1,208 @@
+@Manual{R-base,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2024},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{R-shiny,
+ title = {shiny: Web Application Framework for R},
+ author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
+ year = {2024},
+ note = {R package version 1.8.1.1},
+ url = {https://CRAN.R-project.org/package=shiny},
+}
+
+@Manual{R-bookdown,
+ title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+ author = {Yihui Xie},
+ year = {2024},
+ note = {R package version 0.39,
+https://pkgs.rstudio.com/bookdown/},
+ url = {https://github.com/rstudio/bookdown},
+}
+
+@Manual{R-ggplot2,
+ title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
+ author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington and Teun {van den Brand}},
+ year = {2024},
+ note = {R package version 3.5.1,
+https://github.com/tidyverse/ggplot2},
+ url = {https://ggplot2.tidyverse.org},
+}
+
+@Manual{R-kableExtra,
+ title = {kableExtra: Construct Complex Table with kable and Pipe Syntax},
+ author = {Hao Zhu},
+ year = {2024},
+ note = {R package version 1.4.0,
+https://github.com/haozhu233/kableExtra},
+ url = {http://haozhu233.github.io/kableExtra/},
+}
+
+@Manual{R-knitr,
+ title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+ author = {Yihui Xie},
+ year = {2024},
+ note = {R package version 1.46},
+ url = {https://yihui.org/knitr/},
+}
+
+@Manual{R-rmarkdown,
+ title = {rmarkdown: Dynamic Documents for R},
+ author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
+ year = {2024},
+ note = {R package version 2.27, https://pkgs.rstudio.com/rmarkdown/},
+ url = {https://github.com/rstudio/rmarkdown},
+}
+
+@Book{bookdown2016,
+ title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
+ author = {Yihui Xie},
+ publisher = {Chapman and Hall/CRC},
+ address = {Boca Raton, Florida},
+ year = {2016},
+ isbn = {978-1138700109},
+ url = {https://bookdown.org/yihui/bookdown},
+}
+
+@Book{ggplot22016,
+ author = {Hadley Wickham},
+ title = {ggplot2: Elegant Graphics for Data Analysis},
+ publisher = {Springer-Verlag New York},
+ year = {2016},
+ isbn = {978-3-319-24277-4},
+ url = {https://ggplot2.tidyverse.org},
+}
+
+@Book{knitr2015,
+ title = {Dynamic Documents with {R} and knitr},
+ author = {Yihui Xie},
+ publisher = {Chapman and Hall/CRC},
+ address = {Boca Raton, Florida},
+ year = {2015},
+ edition = {2nd},
+ note = {ISBN 978-1498716963},
+ url = {https://yihui.org/knitr/},
+}
+
+@InCollection{knitr2014,
+ booktitle = {Implementing Reproducible Computational Research},
+ editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
+ title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
+ author = {Yihui Xie},
+ publisher = {Chapman and Hall/CRC},
+ year = {2014},
+ note = {ISBN 978-1466561595},
+}
+
+@Book{rmarkdown2018,
+ title = {R Markdown: The Definitive Guide},
+ author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
+ publisher = {Chapman and Hall/CRC},
+ address = {Boca Raton, Florida},
+ year = {2018},
+ isbn = {9781138359338},
+ url = {https://bookdown.org/yihui/rmarkdown},
+}
+
+@Book{rmarkdown2020,
+ title = {R Markdown Cookbook},
+ author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
+ publisher = {Chapman and Hall/CRC},
+ address = {Boca Raton, Florida},
+ year = {2020},
+ isbn = {9780367563837},
+ url = {https://bookdown.org/yihui/rmarkdown-cookbook},
+}
+
+@Manual{R-e107,
+ title = {e1071: Misc Functions of the Department of Statistics, Probability
+Theory Group (Formerly: E1071), TU Wien},
+ author = {David Meyer and Evgenia Dimitriadou and Kurt Hornik and Andreas Weingessel and Friedrich Leisch},
+ year = {2023},
+ note = {R package version 1.7-14},
+ url = {https://CRAN.R-project.org/package=e1071},
+}
+
+@Manual{R-httpuv,
+ title = {httpuv: HTTP and WebSocket Server Library},
+ author = {Joe Cheng and Winston Chang and Steve Reid and James Brown and Bob Trower and Alexander Peslyak},
+ year = {2024},
+ note = {R package version 1.6.15},
+ url = {https://CRAN.R-project.org/package=httpuv},
+}
+
+@Manual{R-rhino,
+ title = {rhino: A Framework for Enterprise Shiny Applications},
+ author = {Kamil Żyła and Jakub Nowicki and Leszek Siemiński and Marek Rogala and Recle Vibal and Tymoteusz Makowski and Rodrigo Basa},
+ year = {2024},
+ note = {R package version 1.7.0},
+ url = {https://CRAN.R-project.org/package=rhino},
+}
+
+@Manual{R-box,
+ title = {box: Write Reusable, Composable and Modular R Code},
+ author = {Konrad Rudolph},
+ year = {2024},
+ note = {R package version 1.2.0},
+ url = {https://CRAN.R-project.org/package=box},
+}
+
+@Manual{R-golem,
+ title = {golem: A Framework for Robust Shiny Applications},
+ author = {Colin Fay and Vincent Guyader and Sébastien Rochette and Cervan Girard},
+ year = {2023},
+ note = {R package version 0.4.1},
+ url = {https://CRAN.R-project.org/package=golem},
+}
+
+@Manual{R-leprechaun,
+ title = {leprechaun: Create Simple 'Shiny' Applications as Packages},
+ author = {John Coene},
+ year = {2022},
+ note = {R package version 1.0.0},
+ url = {https://CRAN.R-project.org/package=leprechaun},
+}
+
+@Manual{R-roxygen2,
+ title = {roxygen2: In-Line Documentation for R},
+ author = {Hadley Wickham and Peter Danenberg and Gábor Csárdi and Manuel Eugster},
+ year = {2024},
+ note = {R package version 7.3.1},
+ url = {https://CRAN.R-project.org/package=roxygen2},
+}
+
+@Manual{R-shinytest2,
+ title = {shinytest2: Testing for Shiny Applications},
+ author = {Barret Schloerke},
+ year = {2024},
+ note = {R package version 0.3.2},
+ url = {https://CRAN.R-project.org/package=shinytest2},
+}
+
+@Manual{R-flexdashboard,
+ title = {flexdashboard: R Markdown Format for Flexible Dashboards},
+ author = {Garrick Aden-Buie and Carson Sievert and Richard Iannone and JJ Allaire and Barbara Borges},
+ year = {2023},
+ note = {R package version 0.6.2},
+ url = {https://CRAN.R-project.org/package=flexdashboard},
+}
+
+@Manual{R-reticulate,
+ title = {reticulate: Interface to 'Python'},
+ author = {Kevin Ushey and JJ Allaire and Yuan Tang},
+ year = {2024},
+ note = {R package version 1.37.0},
+ url = {https://CRAN.R-project.org/package=reticulate},
+}
+
+@Manual{R-languageserver,
+ title = {languageserver: Language Server Protocol},
+ author = {Randy Lai},
+ year = {2023},
+ note = {R package version 0.3.16},
+ url = {https://CRAN.R-project.org/package=languageserver},
+}
diff --git a/book-source/css/style.css b/book-source/css/style.css
new file mode 100755
index 0000000..fa6f438
--- /dev/null
+++ b/book-source/css/style.css
@@ -0,0 +1,42 @@
+.learncheck {
+ padding: 1em 1em 1em 1em;
+ margin-bottom: 10px;
+ background: #9ED3AD 5px center/3em no-repeat;
+}
+
+.announcement {
+ padding: 1em 1em 1em 1em;
+ margin-bottom: 10px;
+ background: #F6D328 5px center/3em no-repeat;
+}
+
+.review {
+ padding: 1em 1em 1em 1em;
+ margin-bottom: 10px;
+ background: #9ED3AD 1px center/1em no-repeat;
+}
+
+
+p.caption {
+ color: #777;
+ margin-top: 10px;
+}
+p code {
+ white-space: inherit;
+}
+pre {
+ word-break: normal;
+ word-wrap: normal;
+}
+pre code {
+ white-space: inherit;
+}
+p.flushright {
+ text-align: right;
+}
+blockquote > p:last-child {
+ text-align: right;
+}
+blockquote > p:first-child {
+ text-align: inherit;
+}
diff --git a/book-source/css/style_gitbook.css b/book-source/css/style_gitbook.css
new file mode 100644
index 0000000..cbb47de
--- /dev/null
+++ b/book-source/css/style_gitbook.css
@@ -0,0 +1,128 @@
+/* Special text */
+.advert {
+ color: #FF8929;
+ font-style: italic;
+}
+.codecommand, .codebox code {
+ background-color: #E0E0E0;
+ font-family: monospace;
+}
+.Large {
+ font-size: 2rem;
+}
+.exercise, .exo {
+ color: #00BA10;
+ font-size: 1.1rem;
+}
+.math.inline {
+ background-color: aliceblue;
+}
+
+/* Special backgrounds*/
+.blueShaded {
+ background-color: #D6E8F5;
+ font-family: monospace;
+}
+.blueShaded pre:not([class]) {
+ background-color: #D6E8F5;
+}
+.redbox {
+ background-color: #FF7F7F;
+ padding: 2px 5px;
+}
+
+/* Document formatting*/
+body {
+ font-family: "Noto Sans", sans-serif;
+ /* font-size: 1.5rem; */
+ text-align: justify;
+}
+
+h3 {
+ font-style: italic;
+}
+
+/* Figures */
+.figure {
+ margin-bottom: 1.5em;
+}
+
+/* Custom specific to my bookdown template */
+.body-inner {
+/* background-color: #1e73be;*/
+ background-color: #f6f6f6;
+}
+.book .book-body .page-wrapper .page-inner {
+ max-width: 1025px;
+}
+.book .book-body .page-wrapper .page-inner section {
+ padding: 5px 3em;
+}
+.book .book-body .page-wrapper .page-inner section.normal p.caption {
+ margin: 0 10%;
+ text-align: center;
+ font-size: 1.4rem;
+}
+
+.page-inner {
+ max-width: 1025px;
+ margin-left: auto;
+ margin-right: auto;
+ background-color: white;
+ /* padding: 1em 30px 15px; */
+ }
+
+.book .book-body .navigation {
+ font-size: 70px;
+ color: #ccc;
+ text-align: center;
+}
+
+#content a, .book .book-body .page-wrapper .page-inner section.normal a {
+ color: #DE633C;
+}
+
+
+/* thinkr.css
+.container-fluid.main-container {
+ margin-top: 80px;
+}
+h1.title {
+ margin-top: 80px;
+}
+.container-fluid.main-container h1.title {
+ margin-top: 0px;
+}
+*/
+.logos {
+ position: fixed;
+ top: 50px;
+ width: 100px;
+ left: 330px;
+ z-index: 1;
+}
+.logos img {
+ margin: 5px auto; /* Modified for gitbook */
+ display: block;
+ height: 60px;
+}
+a {
+ color: #15b7d6;
+}
+h1 {
+ color: #DE633C;
+}
+h2 {
+ color: #15b7d6;
+}
+.sidebar h2 {
+ color: black;
+}
+
+/* Footer with logo */
+footer {
+ text-align: center;
+}
+footer img {
+ max-height: 40px;
+}
diff --git a/book-source/data/bananas.csv b/book-source/data/bananas.csv
new file mode 100644
index 0000000..9167f24
--- /dev/null
+++ b/book-source/data/bananas.csv
@@ -0,0 +1,121 @@
+"fruit","day","ripeness","green","yellow","brown"
+"fruit_14",0,"Under",0.387,0.592,0.021
+"fruit_14",1,"Ripe",0.149,0.844,0.007
+"fruit_14",2,"Ripe",0.117,0.801,0.082
+"fruit_14",4,"Ripe",0.09,0.771,0.139
+"fruit_14",5,"Ripe",0.113,0.774,0.113
+"fruit_14",6,"Ripe",0.165,0.767,0.068
+"fruit_14",7,"Very",0.144,0.646,0.21
+"fruit_14",8,"Very",0.183,0.55,0.267
+"fruit_14",9,"Very",0.21,0.429,0.361
+"fruit_14",10,"Very",0.108,0.319,0.573
+"fruit_14",11,"Very",0.099,0.296,0.605
+"fruit_14",12,"Over",0.081,0.208,0.711
+"fruit_14",13,"Over",0.097,0.168,0.735
+"fruit_14",14,"Over",0.066,0.121,0.813
+"fruit_14",15,"Over",0.062,0.075,0.863
+"fruit_14",16,"Over",0.056,0.044,0.9
+"fruit_14",17,"Over",0.051,0.041,0.908
+"fruit_14",18,"Over",0.044,0.034,0.922
+"fruit_14",19,"Over",0.043,0.033,0.924
+"fruit_14",20,"Over",0.044,0.024,0.932
+"fruit_15",0,"Under",0.568,0.425,0.007
+"fruit_15",1,"Under",0.295,0.691,0.014
+"fruit_15",2,"Ripe",0.27,0.693,0.037
+"fruit_15",4,"Ripe",0.168,0.687,0.145
+"fruit_15",5,"Ripe",0.157,0.704,0.139
+"fruit_15",6,"Ripe",0.186,0.724,0.09
+"fruit_15",7,"Ripe",0.158,0.657,0.185
+"fruit_15",8,"Very",0.176,0.626,0.198
+"fruit_15",9,"Very",0.208,0.528,0.264
+"fruit_15",10,"Very",0.168,0.422,0.41
+"fruit_15",11,"Very",0.135,0.451,0.414
+"fruit_15",12,"Very",0.108,0.431,0.461
+"fruit_15",13,"Very",0.153,0.362,0.485
+"fruit_15",14,"Over",0.104,0.373,0.523
+"fruit_15",15,"Over",0.11,0.242,0.648
+"fruit_15",16,"Over",0.101,0.206,0.693
+"fruit_15",17,"Over",0.083,0.172,0.745
+"fruit_15",18,"Over",0.076,0.137,0.787
+"fruit_15",19,"Over",0.074,0.097,0.829
+"fruit_15",20,"Over",0.072,0.061,0.867
+"fruit_21",0,"Under",0.402,0.566,0.032
+"fruit_21",1,"Ripe",0.149,0.82,0.031
+"fruit_21",2,"Ripe",0.095,0.887,0.018
+"fruit_21",4,"Ripe",0.076,0.885,0.039
+"fruit_21",5,"Ripe",0.054,0.901,0.045
+"fruit_21",6,"Ripe",0.064,0.886,0.05
+"fruit_21",7,"Very",0.074,0.81,0.116
+"fruit_21",8,"Very",0.111,0.689,0.2
+"fruit_21",9,"Very",0.154,0.598,0.248
+"fruit_21",10,"Very",0.104,0.398,0.498
+"fruit_21",11,"Over",0.099,0.352,0.549
+"fruit_21",12,"Over",0.087,0.269,0.644
+"fruit_21",13,"Over",0.081,0.188,0.731
+"fruit_21",14,"Over",0.054,0.145,0.801
+"fruit_21",15,"Over",0.052,0.107,0.841
+"fruit_21",16,"Over",0.045,0.056,0.899
+"fruit_21",17,"Over",0.042,0.051,0.907
+"fruit_21",18,"Over",0.038,0.038,0.924
+"fruit_21",19,"Over",0.043,0.032,0.925
+"fruit_21",20,"Over",0.039,0.018,0.943
+"fruit_22",0,"Under",0.837,0.145,0.018
+"fruit_22",1,"Under",0.197,0.797,0.006
+"fruit_22",2,"Ripe",0.129,0.828,0.043
+"fruit_22",4,"Ripe",0.108,0.863,0.029
+"fruit_22",5,"Ripe",0.049,0.919,0.032
+"fruit_22",6,"Ripe",0.048,0.925,0.027
+"fruit_22",7,"Ripe",0.054,0.894,0.052
+"fruit_22",8,"Ripe",0.069,0.84,0.091
+"fruit_22",9,"Very",0.09,0.778,0.132
+"fruit_22",10,"Very",0.063,0.666,0.271
+"fruit_22",11,"Very",0.072,0.622,0.306
+"fruit_22",12,"Very",0.065,0.542,0.393
+"fruit_22",13,"Very",0.078,0.488,0.434
+"fruit_22",14,"Over",0.068,0.396,0.536
+"fruit_22",15,"Over",0.077,0.339,0.584
+"fruit_22",16,"Over",0.073,0.26,0.667
+"fruit_22",17,"Over",0.074,0.205,0.721
+"fruit_22",18,"Over",0.07,0.153,0.777
+"fruit_22",19,"Over",0.081,0.115,0.804
+"fruit_22",20,"Over",0.09,0.071,0.839
+"fruit_23",0,"Under",0.339,0.641,0.02
+"fruit_23",1,"Ripe",0.156,0.836,0.008
+"fruit_23",2,"Ripe",0.142,0.832,0.026
+"fruit_23",4,"Ripe",0.106,0.861,0.033
+"fruit_23",5,"Ripe",0.061,0.908,0.031
+"fruit_23",6,"Ripe",0.055,0.915,0.03
+"fruit_23",7,"Ripe",0.098,0.83,0.072
+"fruit_23",8,"Very",0.111,0.783,0.106
+"fruit_23",9,"Very",0.16,0.683,0.157
+"fruit_23",10,"Very",0.1,0.499,0.401
+"fruit_23",11,"Very",0.119,0.385,0.496
+"fruit_23",12,"Very",0.099,0.33,0.571
+"fruit_23",13,"Over",0.142,0.262,0.596
+"fruit_23",14,"Over",0.107,0.209,0.684
+"fruit_23",15,"Over",0.104,0.159,0.737
+"fruit_23",16,"Over",0.099,0.113,0.788
+"fruit_23",17,"Over",0.087,0.083,0.83
+"fruit_23",18,"Over",0.066,0.075,0.859
+"fruit_23",19,"Over",0.074,0.068,0.858
+"fruit_23",20,"Over",0.066,0.037,0.897
+"fruit_26",0,"Under",0.178,0.813,0.009
+"fruit_26",1,"Ripe",0.083,0.909,0.008
+"fruit_26",2,"Ripe",0.05,0.924,0.026
+"fruit_26",4,"Ripe",0.046,0.9,0.054
+"fruit_26",5,"Ripe",0.061,0.885,0.054
+"fruit_26",6,"Ripe",0.095,0.845,0.06
+"fruit_26",7,"Very",0.124,0.695,0.181
+"fruit_26",8,"Very",0.169,0.577,0.254
+"fruit_26",9,"Very",0.216,0.463,0.321
+"fruit_26",10,"Over",0.086,0.345,0.569
+"fruit_26",11,"Over",0.095,0.317,0.588
+"fruit_26",12,"Over",0.069,0.26,0.671
+"fruit_26",13,"Over",0.092,0.199,0.709
+"fruit_26",14,"Over",0.06,0.182,0.758
+"fruit_26",15,"Over",0.052,0.143,0.805
+"fruit_26",16,"Over",0.056,0.084,0.86
+"fruit_26",17,"Over",0.059,0.071,0.87
+"fruit_26",18,"Over",0.048,0.051,0.901
+"fruit_26",19,"Over",0.058,0.037,0.905
+"fruit_26",20,"Over",0.054,0.023,0.923
diff --git a/book-source/data/test.csv b/book-source/data/test.csv
new file mode 100644
index 0000000..898fd68
--- /dev/null
+++ b/book-source/data/test.csv
@@ -0,0 +1,2 @@
+x,y
+"a",1
diff --git a/book-source/hostingshiny.Rproj b/book-source/hostingshiny.Rproj
new file mode 100644
index 0000000..fd31270
--- /dev/null
+++ b/book-source/hostingshiny.Rproj
@@ -0,0 +1,18 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: XeLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Website
diff --git a/book-source/images/01/devops-cycle.drawio b/book-source/images/01/devops-cycle.drawio
new file mode 100644
index 0000000..8c9c770
--- /dev/null
+++ b/book-source/images/01/devops-cycle.drawio
@@ -0,0 +1,112 @@
+