galaaz 2.1.7 → 2.1.9

data/blogs/ruby_plot/ruby_plot.tex

@@ -101,7 +101,7 @@
 \usepackage[utf8]{inputenc}
 
 \usepackage{geometry}
-\geometry{a4paper, top=1in}
+\geometry{a4paper, top=1.05in, headheight=30pt, headsep=14pt}
 
 % needed for kableExtra
 \usepackage{longtable}
@@ -122,29 +122,60 @@
 \usepackage{graphicx}
 
 \usepackage{fancyhdr}
-% set the header and foot style
-% style 'fancy' adds the section name on the header
-% and the page number on the footer
+% Header: small Galaaz mark (left); page number + section title (right),
+% matching classic LaTeX style: "4  AN EXTENSION TO THE EXAMPLE"
+% (upright page number, uppercase italic section name).
+% Logo paths cover repo blogs (../../sty/), installed ~/sty/, and local images/.
+% Blogs may delay headers with \renewcommand{\galaazheaderfrompage}{3} after this sty
+% (e.g. skip title/TOC and a logo splash page).
+\newcommand{\galaazheaderfrompage}{1}
+\newcommand{\galaazheaderlogo}{%
+  \raisebox{-0.12\height}{%
+    \IfFileExists{../../sty/galaaz-header.png}{%
+      \includegraphics[height=0.32in]{../../sty/galaaz-header.png}%
+    }{%
+      \IfFileExists{galaaz-header.png}{%
+        \includegraphics[height=0.32in]{galaaz-header.png}%
+      }{%
+        \IfFileExists{images/galaaz-header.png}{%
+          \includegraphics[height=0.32in]{images/galaaz-header.png}%
+        }{}%
+      }%
+    }%
+  }%
+}
+% Section title only in marks (no \thesection); page number is separate.
+\renewcommand{\sectionmark}[1]{\markboth{#1}{}}
+\renewcommand{\subsectionmark}[1]{}% keep the current section in the header
+\newcommand{\galaazmaybeheaderlogo}{%
+  \ifnum\value{page}<\galaazheaderfrompage\relax\else\galaazheaderlogo\fi}
+\newcommand{\galaazmayberighthead}{%
+  \ifnum\value{page}<\galaazheaderfrompage\relax
+  \else
+    \textup{\thepage}\hspace{1em}\textit{\MakeUppercase{\leftmark}}%
+  \fi
+}
 \pagestyle{fancy}
-
-% style 'fancyhf' leaves header and footer empty
-%\fancyhf{}
-
-% sets the left head element to \rightmark, which contains the
-% current section (\leftmark is the current chapter)
-%\fancyhead[L]{\rightmark} .
-
-% sets the right head element to the page number.
-% \fancyhead[R]{\thepage}
-
-% lets the head rule disappear.
-% \renewcommand{\headrulewidth}{0pt}
-% Possible selectors for the optional argument of \fancyhead/\fancyfoot
-% are L (left), C (center) or R (right) for the position of the element
-% and E (even) or O (odd) to distinguish even and odd pages. If you omit
-% E/O the element is set for all pages.
-
-% \usepackage{lipsum}
+\fancyhf{}
+\fancyhead[L]{\galaazmaybeheaderlogo}
+\fancyhead[R]{\galaazmayberighthead}
+\renewcommand{\headrulewidth}{0.3pt}
+\makeatletter
+\renewcommand{\headrule}{%
+  \ifnum\value{page}<\galaazheaderfrompage\relax
+  \else
+    \hrule\@height\headrulewidth\@width\headwidth
+    \vskip-\headrulewidth
+  \fi
+}
+\makeatother
+% First page often uses plain; same conditional header logic.
+\fancypagestyle{plain}{%
+  \fancyhf{}%
+  \fancyhead[L]{\galaazmaybeheaderlogo}%
+  \fancyhead[R]{\galaazmayberighthead}%
+  \renewcommand{\headrulewidth}{0.3pt}%
+}
 
 % make available command lastpage
 \usepackage{lastpage}
@@ -165,8 +196,34 @@
 % Command to import an R variable to latex
 \newcommand{\RtoLatex}[2]{\newcommand{#1}{#2}}
 
+% Soft-wrap Pandoc highlighted code/output boxes (Shaded + Highlighting).
+% This runs after Pandoc's default \DefineVerbatimEnvironment{Highlighting}
+% (header includes come later in the generated .tex). Prefer manual line
+% breaks in Rmd sources; breaklines is a safety net for leftovers/output.
+% Requires TinyTeX/TeX Live package: tlmgr install fvextra
+\IfFileExists{fvextra.sty}{%
+  \usepackage{fvextra}%
+  \DefineVerbatimEnvironment{Highlighting}{Verbatim}{%
+    breaklines=true,
+    breakanywhere=true,
+    breakindent=1.5em,
+    fontsize=\small,
+    commandchars=\\\{\}%
+  }%
+}{%
+  % fancyvrb is already loaded by Pandoc; shrink code so more fits per line.
+  \DefineVerbatimEnvironment{Highlighting}{Verbatim}{%
+    fontsize=\small,
+    commandchars=\\\{\}%
+  }%
+}
+
 % 
 %\newcommand{\atraso}[1]{\color{red} \textbf {Tempo desde a Assinatura do Contrato: #1 dias}}
+% No header on title/TOC (p.1) or splash logo page (p.2);
+% logo + page number + section title from page 3 onward.
+% Load after galaaz.sty.
+\renewcommand{\galaazheaderfrompage}{3}
 \usepackage{bookmark}
 \IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
 \urlstyle{same}
@@ -187,6 +244,8 @@
 \setcounter{tocdepth}{2}
 \tableofcontents
 }
+\begin{center}\includegraphics[width=0.45\linewidth]{images/galaaz-lockup-stacked} \end{center}
+
 According to Wikipedia ``Ruby is a dynamic, interpreted, reflective,
 object-oriented, general-purpose programming language. It was designed
 and developed in the mid-1990s by Yukihiro''Matz'' Matsumoto in Japan.''
@@ -194,41 +253,42 @@ It reached high popularity with the development of Ruby on Rails (RoR)
 by David Heinemeier Hansson. RoR is a web application framework first
 released around 2005. It makes extensive use of Ruby's metaprogramming
 features. With RoR, Ruby became very popular. According to
-\href{https://www.tiobe.com/tiobe-index/ruby/}{Ruby's Tiobe index} it
-peeked in popularity around 2008, then declined until 2015 when it
-started picking up again. At the time of this writing (November 2018),
-the Tiobe index puts Ruby in 16th position as most popular language.
-
-Python, a language similar to Ruby, ranks 4th in the index. Java, C and
-C++ take the first three positions. Ruby is often criticized for its
+\href{https://www.tiobe.com/tiobe-index/ruby/}{Ruby's ranking in the
+TIOBE index} it \textbf{peaked} in popularity around 2008, then declined
+until 2015 when it started picking up again. As of the original
+publication date (November 2018), TIOBE placed Ruby around 16th among
+languages.
+
+Python, often grouped with Ruby as a high-level scripting language,
+ranked higher in that same snapshot. Ruby is often criticized for its
 focus on web applications. But Ruby can do
 \href{https://github.com/markets/awesome-ruby}{much more} than just web
-applications. Yet, for scientific computing, Ruby lags way behind Python
-and R. Python has Django framework for web, NumPy for numerical arrays,
-Pandas for data analysis. R is a free software environment for
-statistical computing and graphics with thousands of libraries for data
-analysis.
+applications. Yet, for scientific computing, Ruby lags behind Python and
+R. Python combines web frameworks such as Django with NumPy, pandas,
+SciPy, and \textbf{a very large ecosystem} of domain-specific packages.
+R is a free software environment for statistical computing and graphics
+with thousands of libraries for data analysis.
 
 Until recently, there was no real perspective for Ruby to bridge this
 gap. Implementing a complete scientific computing infrastructure would
 take too long.
 
-\textbf{Galaaz 2.0} couples
-\textbf{\href{https://www.jruby.org/}{JRuby}} (Ruby on the JVM) with
-\textbf{GNU R}---the same R distribution used for data science
-everywhere. A \textbf{bridge} evaluates R from Ruby and exchanges data
-between the two processes so that, from Ruby, you call R functions and
-work with R objects using familiar Ruby syntax. In other words, a Ruby
-programmer can use the capabilities of R without memorizing all of R's
-syntax for day-to-day tasks.
+\textbf{Galaaz 2.0} supports
+\textbf{\href{https://www.jruby.org/}{JRuby}} or \textbf{CRuby} equally
+and drives \textbf{GNU R}---the same R distribution used for data
+science everywhere. A \textbf{bridge} evaluates R from Ruby and
+exchanges data between the two processes so that, from Ruby, you call R
+functions and work with R objects using familiar Ruby syntax. In other
+words, a Ruby programmer can use the capabilities of R without
+memorizing all of R's syntax for day-to-day tasks.
 
 An \textbf{earlier line of work} used Oracle's \textbf{GraalVM} with
 \textbf{TruffleRuby} and \textbf{FastR} so that Ruby and R could share
 one JVM runtime. That stack is \textbf{no longer} what Galaaz targets;
-today's Galaaz is developed and tested with \textbf{JRuby + GNU R} (see
-the project manual for setup and command-line tools).
+today's Galaaz is developed and tested with \textbf{JRuby or CRuby + GNU
+R} (see the project manual for setup and command-line tools).
 
-Library wrapping is a usual way of bringing features from one language
+Library wrapping is a common way to bring features from one language
 into another. To improve performance, Python often wraps more efficient
 C libraries. For the Python developer, the existence of such C libraries
 is hidden. The problem with library wrapping is that for any new
@@ -239,12 +299,12 @@ language in Ruby. Doing so, all thousands of R libraries are available
 immediately to Ruby developers without any new wrapping effort.
 
 To show the power of Galaaz, we show in this article how Ruby can use
-R's ggplot2 library tranparantly bringing to Ruby the power of high
-quality scientific plotting. We also show that migrating from R to Ruby
-with Galaaz is a matter of small syntactic changes. By using Ruby, the R
-developer can use all of Ruby's powerful object-oriented features. Also,
-with Ruby, it becomes much easier to move code from the analysis phase
-to the production phase.
+R's ggplot2 library \textbf{transparently}, bringing to Ruby the power
+of high-quality scientific plotting. We also show that migrating from R
+to Ruby with Galaaz is a matter of small syntactic changes. By using
+Ruby, the R developer can use all of Ruby's powerful object-oriented
+features. Also, with Ruby, it becomes much easier to move code from the
+analysis phase to the production phase.
 
 In this article we will explore the R ToothGrowth dataset. To
 illustrate, we will create some boxplots. A primer on boxplot is
@@ -261,15 +321,16 @@ special knowledge.
 
 \href{https://towardsdatascience.com/ruby-plotting-with-galaaz-an-example-of-tightly-coupling-ruby-and-r-in-graalvm-520b69e21021}{Here}
 is an older article (GraalVM-era Galaaz) with a scatter plot in Ruby;
-the \textbf{ideas} still apply under Galaaz 2.0 with JRuby and GNU R.
+the \textbf{ideas} still apply under Galaaz 2.0 with JRuby or CRuby and
+GNU R.
 
 \section{gKnit}\label{gknit}
 
 \emph{Knitr} is an application that converts text written in rmarkdown
 to many different output formats. For instance, a writer can convert an
-rmarkdown document to HTML, \(LaTex\), docx and many other formats.
-Rmarkdown documents can contain text and \emph{code chunks}. Knitr
-formats code chunks in a grayed box in the output document. It also
+rmarkdown document to HTML, LaTeX, Word, and many other formats. R
+Markdown documents can contain text and \emph{code chunks}. knitr
+formats code chunks in a shaded box in the output document. It also
 executes the code chunks and formats the output in a white box. Every
 line of output from the execution code is preceded by `\#\#'.
 
@@ -283,7 +344,7 @@ With \emph{gKnit} Ruby code chunks can share data.
 \section{Exploring the Dataset}\label{exploring-the-dataset}
 
 Let's start by exploring our selected dataset. ToothGrowth is an R
-dataset. A dataset is like a simple excel spreadsheet, in which each
+dataset. A dataset is like a simple Excel spreadsheet, in which each
 column has only one type of data. For instance one column can have
 float, the other integer, and a third strings. This dataset analyzes the
 length of odontoblasts (cells responsible for tooth growth) in 60 guinea
@@ -293,17 +354,17 @@ or ascorbic acid (a form of vitamin C and coded as VC).
 
 The ToothGrowth dataset contains three columns: `len', `supp' and
 `dose'. Let's take a look at a few rows of this dataset. In Galaaz, R
-variables are accessed by using the corresponding Ruby symbol preceeded
-by the tilda (`\textasciitilde{}') function. Note in the following chunk
+variables are accessed by using the corresponding Ruby symbol with the
+tilde (\texttt{\textasciitilde{}}) operator. Note in the following chunk
 that `ToothGrowth' is the R variable and Ruby's `tooth\_growth' is
-assigned the value of `\textasciitilde:ToothGrowth'.
+assigned the value of `\textasciitilde R{[}:ToothGrowth{]}'.
 
 \begin{Shaded}
 \begin{Highlighting}[]
 \CommentTok{\# Read the R ToothGrowth variable and assign it to the}
 \CommentTok{\# Ruby instance variable tooth\_growth that will be }
 \CommentTok{\# available to all Ruby chunks in this document.}
-\NormalTok{tooth\_growth }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\WarningTok{:ToothGrowth}
+\NormalTok{tooth\_growth }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\ConstantTok{R}\KeywordTok{[}\WarningTok{:ToothGrowth}\KeywordTok{]}
 \CommentTok{\# print the first few elements of the dataset}
 \FunctionTok{puts}\NormalTok{ tooth\_growth}\AttributeTok{.head}
 \end{Highlighting}
@@ -340,7 +401,7 @@ The `dose' column contains a numeric value with either, 0.5, 1 or 2,
 although the first 6 rows as seen above only contain the 0.5 values.
 Even though those are number, they are better interpreted as a
 \href{https://swcarpentry.github.io/r-novice-inflammation/12-supp-factors/}{factor
-or cathegory}. So, let's convert our `dose' column from numeric to
+or category}. So, let's convert our `dose' column from numeric to
 `factor'. In R, the function `as.factor' is used to convert data in a
 vector to factors. To use this function from Galaaz the dot (`.') in the
 function name is substituted by '\_\_' (double underline). The function
@@ -431,7 +492,7 @@ R, this would be written as
 you the flexibility to use either
 \texttt{R.ggplot(\textless{}dataset\textgreater{},\ ...)} or
 \texttt{\textless{}dataset\textgreater{}.ggplot(...)}. In the graph
-specification bellow, we use the second notation that looks more like
+specification below, we use the second notation that looks more like
 Ruby.\\
 ggplot uses the `aes' method to specify x and y axes; in this case, the
 `dose' on the \(x\) axis and the `length' on the \(y\) axis: `E.aes(x:
@@ -447,7 +508,7 @@ For a boxplot, the geom is R.geom\_boxplot.
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/dose_len.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/dose_len.png}}
 
 Great! We've just managed to create and save our first plot in Ruby with
 only four lines of code. We can now easily see with this plot a clear
@@ -469,8 +530,8 @@ The parameter to the `facet\_grid' method is a
 
 In Galaaz we give programmers the flexibility to use two different ways
 to write formulas. In the first way, we use Ruby expressions and the
-`.til' function. The formula `x \textasciitilde{} y', becomes `:x.til
-:y'. More information on expressions can be found in
+`.til' function. The formula `x \textasciitilde{} y', becomes
+`R{[}:x{]}.til :y'. More information on expressions can be found in
 \href{https://www.rubydoc.info/gems/galaaz/}{Galaaz Manual}.
 
 Another way of writing a formula is to use the `formula' function with
@@ -479,10 +540,11 @@ the actual formula as a string. The formula
 \texttt{R.formula("x\ \textasciitilde{}\ y")}. For more complex
 formulas, the use of the `formula' function is preferred.
 
-The formula \texttt{:all.til\ :supp} indicates to the `facet\_grid'
-function that it needs to facet the plot based on the \texttt{supp}
-variable and split the plot vertically. Changing the formula to
-\texttt{:supp.til\ :all} would split the plot horizontally.
+The formula \texttt{R{[}:all{]}.til\ :supp} indicates to the
+`facet\_grid' function that it needs to facet the plot based on the
+\texttt{supp} variable and split the plot vertically. Changing the
+formula to \texttt{R{[}:supp{]}.til\ :all} would split the plot
+horizontally.
 
 \begin{Shaded}
 \begin{Highlighting}[]
@@ -490,13 +552,13 @@ variable and split the plot vertically. Changing the formula to
 
 \NormalTok{bp }\OperatorTok{=}\NormalTok{ base\_tooth }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.geom\_boxplot} \OperatorTok{+}
       \CommentTok{\# Split in vertical direction}
-      \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\WarningTok{:all}\AttributeTok{.til} \OperatorTok{:}\NormalTok{supp)}
+      \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:all}\KeywordTok{]}\AttributeTok{.til} \OperatorTok{:}\NormalTok{supp)}
 
 \FunctionTok{puts}\NormalTok{ bp}
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facet_by_delivery.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/facet_by_delivery.png}}
 
 It now becomes clear that although both methods of delivery have a
 direct impact on tooth growth, method (OJ) is non-linear having a higher
@@ -521,7 +583,7 @@ this command each `dose' factor gets its own color.
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_by_delivery_color.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/facets_by_delivery_color.png}}
 
 Facetting helps us compare the general trends for each delivery method.
 Adding color allow us to compare specifically how each dosage impacts
@@ -567,7 +629,7 @@ experiment. For that, add the function `R.geom\_point' to the plot.
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_with_points.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/facets_with_points.png}}
 
 Now we can see the actual distribution of all the 60 subjects. Actually,
 this is not totally true. We have a hard time seing all 60 subjects. It
@@ -589,7 +651,7 @@ making them even easier to see.
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_with_jitter.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/facets_with_jitter.png}}
 
 Now we can see all 60 points in the graph. We have here a much higher
 information density and we can see outliers and subjects distribution.
@@ -629,14 +691,15 @@ order of the colors in the plot.
 \begin{Shaded}
 \begin{Highlighting}[]
 \NormalTok{bp }\OperatorTok{=}\NormalTok{ bp }\OperatorTok{+}
-     \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}\WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{),}
-                          \WarningTok{breaks:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"2"}\NormalTok{,}\StringTok{"1"}\NormalTok{,}\StringTok{"0.5"}\NormalTok{))}
+     \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}
+       \WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{),}
+       \WarningTok{breaks:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"2"}\NormalTok{, }\StringTok{"1"}\NormalTok{, }\StringTok{"0.5"}\NormalTok{))}
 
 \FunctionTok{puts}\NormalTok{ bp}
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_by_delivery_color2.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/facets_by_delivery_color2.png}}
 
 \subsection{Violin Plot and Jitter}\label{violin-plot-and-jitter}
 
@@ -660,17 +723,19 @@ dot represents the median average value.
 
 \begin{Shaded}
 \begin{Highlighting}[]
-\NormalTok{violin }\OperatorTok{=}\NormalTok{ base\_tooth }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.geom\_violin}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:dose}\NormalTok{)) }\OperatorTok{+} 
-   \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\WarningTok{:all}\AttributeTok{.til} \OperatorTok{:}\NormalTok{supp) }\OperatorTok{+}
+\NormalTok{violin }\OperatorTok{=}\NormalTok{ base\_tooth }\OperatorTok{+}
+   \ConstantTok{R}\AttributeTok{.geom\_violin}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:dose}\NormalTok{)) }\OperatorTok{+}
+   \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:all}\KeywordTok{]}\AttributeTok{.til} \OperatorTok{:}\NormalTok{supp) }\OperatorTok{+}
    \ConstantTok{R}\AttributeTok{.geom\_jitter}\NormalTok{(}\WarningTok{shape:} \DecValTok{23}\NormalTok{, }\WarningTok{color:} \StringTok{"cyan3"}\NormalTok{, }\WarningTok{size:} \DecValTok{1}\NormalTok{) }\OperatorTok{+}
-   \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}\WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{),}
-                       \WarningTok{breaks:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"2"}\NormalTok{,}\StringTok{"1"}\NormalTok{,}\StringTok{"0.5"}\NormalTok{))}
+   \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}
+     \WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{),}
+     \WarningTok{breaks:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"2"}\NormalTok{, }\StringTok{"1"}\NormalTok{, }\StringTok{"0.5"}\NormalTok{))}
 
 \FunctionTok{puts}\NormalTok{ violin}
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/violin_with_jitter.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/violin_with_jitter.png}}
 
 This plot is an alternative to the original boxplot. For the final
 presentation, it is important to think which graphics will be best
@@ -710,7 +775,7 @@ we defined a caption variable using Ruby's Here Doc style).
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_with_decorations.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/facets_with_decorations.png}}
 
 \subsection{The Corp Theme}\label{the-corp-theme}
 
@@ -732,42 +797,43 @@ axis and written in `bold'.
 \ControlFlowTok{module} \DataTypeTok{CorpTheme}
 
   \ConstantTok{R}\AttributeTok{.install\_and\_loads} \VerbatimStringTok{\textquotesingle{}RColorBrewer\textquotesingle{}}
-  
-  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
-  \CommentTok{\# face can be  (1=plain, 2=bold, 3=italic, 4=bold{-}italic)}
-  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
-  
+
+  \CommentTok{\# {-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# face: 1=plain, 2=bold, 3=italic, 4=bold{-}italic}
+  \CommentTok{\# {-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+
   \ControlFlowTok{def} \DecValTok{self}\AttributeTok{.text\_element}\NormalTok{(size, }\WarningTok{face:} \StringTok{"plain"}\NormalTok{, }\WarningTok{hjust:} \DecValTok{nil}\NormalTok{)}
-    \ConstantTok{E}\AttributeTok{.element\_text}\NormalTok{(}\WarningTok{color:} \StringTok{"\#000080"}\NormalTok{, }
+    \ConstantTok{E}\AttributeTok{.element\_text}\NormalTok{(}\WarningTok{color:} \StringTok{"\#000080"}\NormalTok{,}
                    \WarningTok{face:}\NormalTok{ face,}
                    \WarningTok{size:}\NormalTok{ size,}
-           \WarningTok{hjust:}\NormalTok{ hjust)}
+                   \WarningTok{hjust:}\NormalTok{ hjust)}
   \ControlFlowTok{end}
-  
-  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
-  \CommentTok{\# Defines the plot theme (visualization).  In this theme we remove major and minor}
-  \CommentTok{\# grids, borders and background.  We also turn{-}off scientific notation.}
-  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
-  
+
+  \CommentTok{\# {-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# Plot theme: no major/minor grids or borders; optional}
+  \CommentTok{\# background for facets; turn off scientific notation.}
+  \CommentTok{\# {-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+
   \ControlFlowTok{def} \DecValTok{self}\AttributeTok{.global\_theme}\NormalTok{(faceted }\OperatorTok{=} \DecValTok{false}\NormalTok{)}
-    
+
     \ConstantTok{R}\AttributeTok{.options}\NormalTok{(}\WarningTok{scipen:} \DecValTok{999}\NormalTok{)  }\CommentTok{\# turn{-}off scientific notation like 1e+48}
-    \CommentTok{\#    R.theme\_set(R.theme\_bw)}
-    
+    \CommentTok{\# R.theme\_set(R.theme\_bw)}
+
     \CommentTok{\# remove major grids}
 \NormalTok{    gb }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_grid\_\_major:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{())}
     \CommentTok{\# remove minor grids}
 \NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_grid\_\_minor:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{)}
-    \CommentTok{\# gb = R.theme(panel\_\_grid\_\_minor: E.element\_blank)}
     \CommentTok{\# remove border}
 \NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_border:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{)}
-    \CommentTok{\# remove background. When working with faceted graphs, the background makes}
-    \CommentTok{\# it easier to see each facet, so leave it}
-\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_background:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{) }\ControlFlowTok{if} \OperatorTok{!}\NormalTok{faceted}
+    \CommentTok{\# Keep background on faceted plots (helps separate facets)}
+    \ControlFlowTok{if} \OperatorTok{!}\NormalTok{faceted}
+\NormalTok{      gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_background:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{)}
+    \ControlFlowTok{end}
     \CommentTok{\# Change axis font}
 \NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{axis\_\_text:}\NormalTok{ text\_element(}\DecValTok{8}\NormalTok{))}
     \CommentTok{\# change axis title font}
-\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{axis\_\_title:}\NormalTok{ text\_element(}\DecValTok{10}\NormalTok{, }\WarningTok{face:} \StringTok{"bold"}\NormalTok{, }\WarningTok{hjust:} \DecValTok{1}\NormalTok{))}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}
+      \WarningTok{axis\_\_title:}\NormalTok{ text\_element(}\DecValTok{10}\NormalTok{, }\WarningTok{face:} \StringTok{"bold"}\NormalTok{, }\WarningTok{hjust:} \DecValTok{1}\NormalTok{))}
     \CommentTok{\# change font of title}
 \NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{title:}\NormalTok{ text\_element(}\DecValTok{12}\NormalTok{, }\WarningTok{face:} \StringTok{"bold"}\NormalTok{))}
     \CommentTok{\# change font of subtitle}
@@ -776,7 +842,7 @@ axis and written in `bold'.
 \NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{plot\_\_caption:}\NormalTok{ text\_element(}\DecValTok{8}\NormalTok{))}
 
   \ControlFlowTok{end}
-   
+
 \ControlFlowTok{end}
 \end{Highlighting}
 \end{Shaded}
@@ -799,7 +865,7 @@ Here is our final boxplot, without jitter.
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/final_box_plot.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/final_box_plot.png}}
 
 And here is the final violin plot, with jitter and the same look and
 feel of the corporate boxplot.
@@ -810,7 +876,7 @@ feel of the corporate boxplot.
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/final_violin_plot.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/final_violin_plot.png}}
 
 \subsection{Another View}\label{another-view}
 
@@ -826,9 +892,12 @@ of graphics}.
 \DocumentationTok{Each animal received one of three dose levels of vitamin C.}
 \ControlFlowTok{EOT}
 
-\NormalTok{bp }\OperatorTok{=}\NormalTok{ tooth\_growth}\AttributeTok{.ggplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{x:} \WarningTok{:supp}\NormalTok{, }\WarningTok{y:} \WarningTok{:len}\NormalTok{, }\WarningTok{group:} \WarningTok{:supp}\NormalTok{)) }\OperatorTok{+} 
-     \ConstantTok{R}\AttributeTok{.geom\_boxplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:supp}\NormalTok{)) }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\WarningTok{:all}\AttributeTok{.til} \OperatorTok{:}\NormalTok{dose) }\OperatorTok{+}
-     \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}\WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{)) }\OperatorTok{+}
+\NormalTok{bp }\OperatorTok{=}\NormalTok{ tooth\_growth}\AttributeTok{.ggplot}\NormalTok{(}
+       \ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{x:} \WarningTok{:supp}\NormalTok{, }\WarningTok{y:} \WarningTok{:len}\NormalTok{, }\WarningTok{group:} \WarningTok{:supp}\NormalTok{)) }\OperatorTok{+}
+     \ConstantTok{R}\AttributeTok{.geom\_boxplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:supp}\NormalTok{)) }\OperatorTok{+}
+     \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\ConstantTok{R}\KeywordTok{[}\WarningTok{:all}\KeywordTok{]}\AttributeTok{.til} \OperatorTok{:}\NormalTok{dose) }\OperatorTok{+}
+     \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}
+       \WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{)) }\OperatorTok{+}
      \ConstantTok{R}\AttributeTok{.labs}\NormalTok{(}\WarningTok{title:} \StringTok{"Tooth Growth:  Length by Dose"}\NormalTok{,}
             \WarningTok{subtitle:} \StringTok{"Faceted by dose"}\NormalTok{,}
             \WarningTok{x:} \StringTok{"Delivery method"}\NormalTok{, }\WarningTok{y:} \StringTok{"Teeth length"}\NormalTok{,}
@@ -839,7 +908,7 @@ of graphics}.
 \end{Highlighting}
 \end{Shaded}
 
-\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facet_by_dose.png}}
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/ruby_plot_files/figure-latex/facet_by_dose.png}}
 
 \section{Conclusion}\label{conclusion}
 
@@ -856,15 +925,16 @@ enormous endeavour and would probably never be accomplished. Today's
 data scientists would certainly stick with either Python or R. Now, both
 the Ruby and R communities can benefit from this marriage:
 \textbf{Galaaz 2.0} uses \textbf{standard GNU R} for statistics and
-graphics and \textbf{JRuby} for application code, threading, and the JVM
-ecosystem. We presented the process to couple Ruby and R; the coupling
-is implemented by the Galaaz bridge and \textbf{gKnit} for literate
-documents, not by a single GraalVM polyglot runtime.
+graphics and \textbf{JRuby or CRuby} for application code (prefer
+\textbf{JRuby} when you want real threads and the JVM ecosystem). We
+presented the process to couple Ruby and R; the coupling is implemented
+by the Galaaz bridge and \textbf{gKnit} for literate documents, not by a
+single GraalVM polyglot runtime.
 
 For performance, expect \textbf{ordinary GNU R} behaviour for model
-fitting and plotting, while \textbf{JRuby} gives \textbf{real parallel
-threads} on the Ruby side and access to Java libraries when you need
-them.
+fitting and plotting, while \textbf{JRuby} can give \textbf{real
+parallel threads} on the Ruby side and access to Java libraries when you
+need them.
 
 This article has shown how to improve a plot step-by-step. Starting from
 a very simple boxplot with all default configurations, we moved slowly
@@ -885,10 +955,8 @@ Rubyist trying to write articles, blogs or documentation for Ruby.
 \begin{itemize}
 \tightlist
 \item
-  \textbf{JRuby} --- Ruby on the JVM
-  (\href{https://www.jruby.org/}{jruby.org})
-\item
-  A \textbf{JDK} compatible with your JRuby version
+  \textbf{JRuby} and a compatible \textbf{JDK}, \emph{or} \textbf{CRuby
+  3.3+}
 \item
   \textbf{GNU R} --- \texttt{R} on your \texttt{PATH}, with
   compilers/tools available if packages must be built from source
@@ -933,8 +1001,9 @@ required.
   In Ruby code:
   \texttt{require\ \textquotesingle{}galaaz\textquotesingle{}}
 \item
-  For running scripts with the correct JRuby and JVM options, use
-  \textbf{\texttt{bin/galaaz-jruby}} as described in the manual.
+  Run Ruby with \textbf{\texttt{bin/galaaz-ruby}} (either engine) or
+  \textbf{\texttt{bin/galaaz-jruby}} when you need JRuby JVM flags (see
+  the manual).
 \end{itemize}
 
 \end{document}