galaaz 0.4.5 → 0.4.6

data/blogs/galaaz_ggplot/galaaz_ggplot.md

@@ -1,99 +1,148 @@
-    ## [1] TRUE
-
-Introduction
-============
-
-Galaaz is a system for tightly coupling Ruby and R. Ruby is a powerful language, with a large community, a very large set of libraries and great for web development. However, it lacks libraries for data science, statistics, scientific plotting and machine learning. On the other hand, R is considered one of the most powerful languages for solving all of the above problems. Maybe the strongest competitor to R is Python with libraries such as NumPy, Panda, SciPy, SciKit-Learn and a couple more.
-
-With Galaaz we do not intend to re-implement any of the scientific libraries in R, we allow for very tight coupling between the two languages to the point that the Ruby developer does not need to know that there is an R engine running. For this to happen we use new technologies provided by Oracle, with GraalVM, TruffleRuby and FastR:
-
-     GraalVM is a universal virtual machine for running applications written in JavaScript,
-     Python 3, Ruby, R, JVM-based languages like Java, Scala, Kotlin, and LLVM-based languages
-     such as C and C++.
-
-     GraalVM removes the isolation between programming languages and enables interoperability in a
-     shared runtime. It can run either standalone or in the context of OpenJDK, Node.js,
-     Oracle Database, or MySQL.
-
-     GraalVM allows you to write polyglot applications with a seamless way to pass values from one
-     language to another. With GraalVM there is no copying or marshalling necessary as it is with
-     other polyglot systems. This lets you achieve high performance when language boundaries are
-     crossed. Most of the time there is no additional cost for crossing a language boundary at all.
-
-     Often developers have to make uncomfortable compromises that require them to rewrite
-     their software in other languages. For example:
+---
+title: "Ruby Plotting with Galaaz"
+subtitle: "An example of tightly coupling Ruby and R in GraalVM"
+author: "Rodrigo Botafogo"
+tags: [Galaaz, Ruby, R, TruffleRuby, FastR, GraalVM, ggplot2]
+date: "16 October 2018"
+output:
+  html_document:
+    self_contained: true
+    keep_md: true
+  pdf_document:
+    includes:
+      in_header: "../../sty/galaaz.sty"
+    keep_tex: yes
+    number_sections: yes
+    toc: true
+    toc_depth: 2
+  md_document:
+    variant: markdown_github
+fontsize: 11pt
+---
+
+
+
+# Introduction
+
+Galaaz is a system for tightly coupling Ruby and R.  Ruby is a powerful language, with
+a large community, a very large set of libraries and great for web development.  However,
+it lacks libraries for data science, statistics, scientific plotting and machine learning.
+On the other hand, R is considered one of the most powerful languages for solving all of the
+above problems.  Maybe the strongest competitor to R is Python with libraries such as NumPy,
+Panda, SciPy, SciKit-Learn and a couple more.
+
+With Galaaz we do not intend to re-implement any of the scientific libraries in R, we allow
+for very tight coupling between the two languages to the point that the Ruby developer does
+not need to know that there is an R engine running.  For this to happen we use new
+technologies provided by Oracle: GraalVM, TruffleRuby and FastR:
+
+     GraalVM is a universal virtual machine for running applications
+     written in JavaScript, Python 3, Ruby, R, JVM-based languages like Java,
+     Scala, Kotlin, and LLVM-based languages such as C and C++.
+
+     GraalVM removes the isolation between programming languages and enables
+     interoperability in a shared runtime. It can run either standalone or in
+     the context of OpenJDK, Node.js, Oracle Database, or MySQL.
+
+     GraalVM allows you to write polyglot applications with a seamless way to
+     pass values from one language to another. With GraalVM there is no copying
+     or marshaling necessary as it is with other polyglot systems. This lets
+     you achieve high performance when language boundaries are crossed. Most
+     of the time there is no additional cost for crossing a language boundary
+     at all.
+
+     Often developers have to make uncomfortable compromises that require them
+     to rewrite their software in other languages. For example:
 
       * “That library is not available in my language. I need to rewrite it.” 
-      * “That language would be the perfect fit for my problem, but we cannot run it in our environment.” 
-      * “That problem is already solved in my language, but the language is too slow.”
+      * “That language would be the perfect fit for my problem, but we cannot
+        run it in our environment.” 
+      * “That problem is already solved in my language, but the language is
+        too slow.”
+    
+    With GraalVM we aim to allow developers to freely choose the right language
+    for the task at hand without making compromises.
+
+Interested readers should also check out the following sites:
 
-    With GraalVM we aim to allow developers to freely choose the right language for the task at
-    hand without making compromises.
+* [GraalVM Home](https://www.graalvm.org/)
+* [TruffleRuby](https://github.com/oracle/truffleruby)
+* [FastR](https://github.com/oracle/fastr)
+* [Faster R with FastR](https://medium.com/graalvm/faster-r-with-fastr-4b8db0e0dceb)
 
-What does Galaaz mean
----------------------
+## What does Galaaz mean
 
-Galaaz is the Portuguese name for "Galahad". From Wikipedia:
+Galaaz is the Portuguese name for "Galahad".  From Wikipedia:
 
-    Sir Galahad (/ˈɡæləhæd/; sometimes referred to as Galeas /ɡəˈliːəs/ or Galath /ˈɡæləθ/),
-    in Arthurian legend, is a knight of King Arthur's Round Table and one of the three
-    achievers of the Holy Grail. He is the illegitimate son of Sir Lancelot and Elaine of
-    Corbenic, and is renowned for his gallantry and purity as the most perfect of all knights.
-    Emerging quite late in the medieval Arthurian tradition, Sir Galahad first appears in the
-    Lancelot–Grail cycle, and his story is taken up in later works such as the Post-Vulgate
-    Cycle and Sir Thomas Malory's Le Morte d'Arthur. His name should not be mistaken with
-    Galehaut, a different knight from Arthurian legend. 
+    Sir Galahad (sometimes referred to as Galeas or Galath),
+    in Arthurian legend, is a knight of King Arthur's Round Table and one
+    of the three achievers of the Holy Grail. He is the illegitimate son
+    of Sir Lancelot and Elaine of Corbenic, and is renowned for his
+    gallantry and purity as the most perfect of all knights. Emerging quite
+    late in the medieval Arthurian tradition, Sir Galahad first appears in the
+    Lancelot–Grail cycle, and his story is taken up in later works such as
+    the Post-Vulgate Cycle and Sir Thomas Malory's Le Morte d'Arthur.
+    His name should not be mistaken with Galehaut, a different knight from
+    Arthurian legend. 
 
-Galaaz Demo
-===========
+# Galaaz Demo
 
-Prerequisites
--------------
+## Prerequisites
 
--   GraalVM (>= rc7)
--   TruffleRuby
--   FastR
+* GraalVM (>= rc7)
+* TruffleRuby
+* FastR
 
-The following R packages will be automatically installed when necessary, but could be installed prior to the demo if desired:
+The following R packages will be automatically installed when necessary, but could be installed prior
+to the demo if desired:
 
--   ggplot2
--   gridExtra
+* ggplot2
+* gridExtra
 
-Installation of R packages requires a development environment. In Linux, the gnu compiler and tools should be enough. I am not sure what is needed on the Mac.
+Installation of R packages requires a development environment.  In Linux, the gnu compiler and
+tools should be enough.  I am not sure what is needed on the Mac.
 
 In order to run the 'specs' the following Ruby package is necessary:
 
--   gem install rspec
+* gem install rspec
 
-Preparation
------------
+## Preparation
 
--   gem install galaaz
+* gem install galaaz
 
-Running the demo
-----------------
+## Running the demo
 
-The ggplot for this demos was extracted from: <http://r-statistics.co/Top50-Ggplot2-Visualizations-MasterList-R-Code.html>.
+The ggplot for this demos was extracted from: http://r-statistics.co/Top50-Ggplot2-Visualizations-MasterList-R-Code.html.
 
 On the console do
 
     > galaaz master_list:scatter_plot
 
-Running other demos
--------------------
+## Running other demos
 
 Doing on the console
 
     > galaaz -T
 
-will show a list with all available demos. To run any of the demos in the list, substitute the call to 'rake' to 'galaaz'. For instance, one of the examples in the list is 'rake sthda:bar'. In order to run this example just do 'galaaz sthda:bar'. Doing 'galaaz sthda:all' will run all demos in the sthda cathegory. Some of the examples require 'rspec' do be available. To install 'rspec' just do 'gem install rspec'.
+will show a list with all available demos.  To run any of the demos in the list,
+substitute the call to
+'rake' to 'galaaz'.  For instance, one of the examples in the list is 'rake sthda:bar'.
+In order to run
+this example just do 'galaaz sthda:bar'.  Doing 'galaaz sthda:all' will run all demos in the sthda
+cathegory.  Some of the examples require 'rspec' do be available.  To install 'rspec' just do
+'gem install rspec'.
 
-The demo code
-=============
+# The demo code
 
-The following is the Ruby code and plot for the above example. There is a small difference between the code in the example and the code bellow. If the example is ran, the plot will appear on the screen, bellow, we generate an 'svg' image and then include it in this document. In order to generate and image, the R.svg device is used. To generate the plot on the screen, use the R.awt device, as commented on the code.
 
-``` galaaz
+The following is the Ruby code and plot for the above example.  There is a small difference between
+the code in the example and the code bellow.  If the example is ran, the plot will appear on the
+screen, bellow, we generate an 'svg' image and then include it in this document.  In order to
+generate and image, the R.svg device is used.  To generate the plot on the screen, use the R.awt
+device, as commented on the code.
+
+
+```ruby
 require 'galaaz'
 require 'ggplot'
 
@@ -126,11 +175,17 @@ R.dev__off               # R.dev__off turns off the device.  If using awt, the p
                          # window will be closed
 ```
 
-<img src="https://user-images.githubusercontent.com/3999729/46742999-87bc2480-cc7e-11e8-9f16-31c3437e4a58.PNG" alt="Midwest Plot" style="width:70.0%" />
+```
+## This is the fake output
+```
+
+
+![Midwest Plot](midwest.png){width=70%}
 
 In R, the code to generate this plot is the following
 
-``` r
+
+```r
 # install.packages("ggplot2")
 # load package and data
 options(scipen=999)  # turn-off scientific notation like 1e+48
@@ -154,29 +209,48 @@ gg <- ggplot(midwest, aes(x=area, y=poptotal)) +
 plot(gg)
 ```
 
-Note that both codes are very similar. The Ruby code requires the use of "R." before calling any functions, for instance R function 'geom\_point' becomes 'R.geom\_point' in Ruby. R named parameters such as (col = state, size = popdensity), become in Ruby (col: :state, size: :popdensity).
+Note that both codes are very similar.  The Ruby code requires the use of "R." before calling
+any functions,
+for instance R function 'geom_point' becomes 'R.geom_point' in Ruby.  R named parameters such as
+(col = state, size = popdensity), become in Ruby (col: :state, size: :popdensity).
+
+One last
+point that needs to be observed is the call to the 'aes' function.  In Ruby instead of doing
+'R.aes', we use 'E.aes'.  The explanation of why E.aes is needed is an advanced topic in R and
+depends on what is know as Non-standard Evaluation (NSE) in R.  In short, function 'aes' is lazily
+evaluated in R, i.e., in R when calling geom_point(aes(col=state, size=popdensity)), function
+geom_point receives as argument something similar to a string containing
+'aes(col=state, size=popdensity)', and the aes function will be evaluated inside the geom_point
+function.  In Ruby, there is no Lazy evaluation and doing R.aes would try to evaluate aes
+immediately.  In order to delay the evaluation of function aes we need to use E.aes.  The
+interested reader on NSE in R is directed to http://adv-r.had.co.nz/Computing-on-the-language.html.
 
-One last point that needs to be observed is the call to the 'aes' function. In Ruby instead of doing 'R.aes', we use 'E.aes'. The explanation of why E.aes is needed is an advanced topic in R and depends on what is know as Non-standard Evaluation (NSE) in R. In short, function 'aes' is lazily evaluated in R, i.e., in R when calling geom\_point(aes(col=state, size=popdensity)), function geom\_point receives as argument something similar to a string containing 'aes(col=state, size=popdensity)', and the aes function will be evaluated inside the geom\_point function. In Ruby, there is no Lazy evaluation and doing R.aes would try to evaluate aes immediately. In order to delay the evaluation of function aes we need to use E.aes. The interested reader on NSE in R is directed to <http://adv-r.had.co.nz/Computing-on-the-language.html>.
+# An extension to the example
 
-An extension to the example
-===========================
+If both codes are so similar, then why would one use Ruby instead of R and what good is galaaz
+after all?
 
-If both codes are so similar, then why would one use Ruby instead of R and what good is galaaz after all?
+Ruby is a modern OO language with numerous very useful constructs such as classes, modules, blocks,
+procs, etc.  The example above focus on the coupling of both languages, and does not show the
+use of other Ruby constructs.  In the following example, we will show a more complex example using
+other Ruby constructs.  This is certainly not a very well written and robust Ruby code, but
+it give the idea of how Ruby and R are strongly coupled.
 
-Ruby is a modern OO language with numerous very useful constructs such as classes, modules, blocks, procs, etc. The example above focus on the coupling of both languages, and does not show the use of other Ruby constructs. In the following example, we will show a more complex example using other Ruby constructs. This is certaily not a very well written and robust Ruby code, but it give the idea of how Ruby and R are stronglyg coupled.
+Let's imagine that we work in a corporation that has its plot themes.  So, it has defined a
+'CorpTheme' module.  Plots in this corporation should not have grids, numbers in labels should
+not use scientific notation and the preferred color is blue.
 
-Let's imagine that we work in a corporation that has its plot themes. So, it has defined a 'CorpTheme' module. Plots in this corporation should not have grids, numbers in labels should not use scientific notation and the prefered color is blue.
 
-``` galaaz
+```ruby
 # corp_theme.rb
 # defines the corporate theme for all plots
     
 module CorpTheme
 
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
   # Defines the plot theme (visualization).  In this theme we remove major and minor
   # grids, borders and background.  We also turn-off scientific notation.
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
   
   def self.global_theme
     
@@ -205,9 +279,14 @@ module CorpTheme
 end
 ```
 
+```
+## This is the fake output
+```
+
 We now define a ScatterPlot class:
 
-``` galaaz
+
+```ruby
 # ScatterPlot.rb
 # creates a scatter plot and allow some configuration
     
@@ -219,40 +298,40 @@ class ScatterPlot
   attr_accessor :x_label
   attr_accessor :y_label
   
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
   # Initialize the plot with the data and the x and y variables
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
 
   def initialize(data, x:, y:)
     @data = data
     @x = x
     @y = y
   end
-
-  #--------------------------------------------------------------------------------------
+  
+  #---------------------------------------------------------------------------------
   # Define groupings by color and size
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
 
   def group_by(color:, size:)
     @color_by = color
     @size_by = size
   end
 
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
   # Add a smoothing line, and if confidence is true the add a confidence interval, if
   # false does not add the confidence interval
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
 
   def add_smoothing_line(method:, confidence: true)
     @method = method
     @confidence = confidence
   end
   
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
   # Creates the graph title, properly formated for this theme
   # @param title [String] The title to add to the graph
   # @return textGrob that can be included in a graph
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
 
   def graph_params(title: "", subtitle: "", caption: "", x_label: "", y_label: "")
     R.labs(
@@ -264,9 +343,9 @@ class ScatterPlot
     )
   end
 
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
   # Prepare the plot's points
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
 
   def points
     params = {}
@@ -275,9 +354,9 @@ class ScatterPlot
     R.geom_point(E.aes(params))
   end
       
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
   # Plots the scatterplot
-  #--------------------------------------------------------------------------------------
+  #---------------------------------------------------------------------------------
 
   def plot(device = 'awt')
     device == 'awt' ? R.awt : R.svg
@@ -303,9 +382,14 @@ class ScatterPlot
 end
 ```
 
+```
+## This is the fake output
+```
+
 And this is the final code for making the scatter plot with the midwest data
 
-``` galaaz
+
+```ruby
 require 'galaaz'
 require 'ggplot'
 
@@ -318,10 +402,30 @@ sp.y_label = "Population"
 sp.group_by(color: :state, size: :popdensity)    # try sp.group_by(color: :state)
 # available methods: "lm", "glm", "loess", "gam"
 sp.add_smoothing_line(method: "glm") 
-sp.plot('svg')
+# sp.plot('svg')
+puts sp
+```
 
-# require input from the user so that the script does not end removing the plot from
-# the screen
 ```
+## This is the fake output
+```
+
+![Midwest Plot with 'glm' function and modified theme](scatter_plot.png){width=70%}
+
+# Conclusion
+
+R is a very powerful language for statistical analysis, data analytics, machine learning, plotting
+and many other scientific applications with a very large package ecosystem.  However R is often
+considered hard to learn and lacking modern computer languages constructs such as object oriented
+classes, modules, lambdas, etc.  For this reason, many developers have started or switched from R
+to Python.
+
+With Galaaz, R programmers can almost transparently migrate from R to Ruby, since syntax is
+almost identical and they have fastR as the R engine.  FastR, by most benchmarks, can be orders of
+magnitude faster than Gnu R.  Further, by using Galaaz the R developer can start (slowly if needed)
+using all of Ruby's constructs and libraries that nicely complement R packages.
 
-![Midwest Plot with 'glm' function and modified theme](https://user-images.githubusercontent.com/3999729/47120345-a903ae80-d244-11e8-9be3-a0db13cf51ab.PNG)
+For the Ruby developer, Galaaz allows the immediate use of R functions completely transparently. As
+shown in the second example above, class ScatterPlot completely hides all the details an R calls
+from the Ruby developer, furthermore Galaaz is powered by TruffleRuby that can also be orders of
+magnitude faster than MRI Ruby.

data/blogs/galaaz_ggplot/galaaz_ggplot.tex

@@ -38,37 +38,37 @@
 \usepackage{framed}
 \definecolor{shadecolor}{RGB}{248,248,248}
 \newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
-\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
-\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
-\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
+\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
 \newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
-\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
-\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\BuiltInTok}[1]{#1}
 \newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
-\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
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-\newcommand{\ImportTok}[1]{#1}
 \newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
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 \newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
-\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
-\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
-\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
 \newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
-\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
-\newcommand{\BuiltInTok}[1]{#1}
+\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
+\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
 \newcommand{\ExtensionTok}[1]{#1}
+\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\ImportTok}[1]{#1}
+\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\NormalTok}[1]{#1}
+\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
+\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
 \newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
-\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
 \newcommand{\RegionMarkerTok}[1]{#1}
-\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
 \newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
-\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
-\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
-\newcommand{\NormalTok}[1]{#1}
 \usepackage{graphicx,grffile}
 \makeatletter
 \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
@@ -204,7 +204,8 @@
 \setcounter{tocdepth}{2}
 \tableofcontents
 }
-\section{Introduction}\label{introduction}
+\hypertarget{introduction}{%
+\section{Introduction}\label{introduction}}
 
 Galaaz is a system for tightly coupling Ruby and R. Ruby is a powerful
 language, with a large community, a very large set of libraries and
@@ -264,7 +265,8 @@ Interested readers should also check out the following sites:
   R with FastR}
 \end{itemize}
 
-\subsection{What does Galaaz mean}\label{what-does-galaaz-mean}
+\hypertarget{what-does-galaaz-mean}{%
+\subsection{What does Galaaz mean}\label{what-does-galaaz-mean}}
 
 Galaaz is the Portuguese name for ``Galahad''. From Wikipedia:
 
@@ -281,9 +283,11 @@ His name should not be mistaken with Galehaut, a different knight from
 Arthurian legend. 
 \end{verbatim}
 
-\section{Galaaz Demo}\label{galaaz-demo}
+\hypertarget{galaaz-demo}{%
+\section{Galaaz Demo}\label{galaaz-demo}}
 
-\subsection{Prerequisites}\label{prerequisites}
+\hypertarget{prerequisites}{%
+\subsection{Prerequisites}\label{prerequisites}}
 
 \begin{itemize}
 \tightlist
@@ -318,7 +322,8 @@ In order to run the `specs' the following Ruby package is necessary:
   gem install rspec
 \end{itemize}
 
-\subsection{Preparation}\label{preparation}
+\hypertarget{preparation}{%
+\subsection{Preparation}\label{preparation}}
 
 \begin{itemize}
 \tightlist
@@ -326,7 +331,8 @@ In order to run the `specs' the following Ruby package is necessary:
   gem install galaaz
 \end{itemize}
 
-\subsection{Running the demo}\label{running-the-demo}
+\hypertarget{running-the-demo}{%
+\subsection{Running the demo}\label{running-the-demo}}
 
 The ggplot for this demos was extracted from:
 \url{http://r-statistics.co/Top50-Ggplot2-Visualizations-MasterList-R-Code.html}.
@@ -337,7 +343,8 @@ On the console do
 > galaaz master_list:scatter_plot
 \end{verbatim}
 
-\subsection{Running other demos}\label{running-other-demos}
+\hypertarget{running-other-demos}{%
+\subsection{Running other demos}\label{running-other-demos}}
 
 Doing on the console
 
@@ -352,7 +359,8 @@ example just do `galaaz sthda:bar'. Doing `galaaz sthda:all' will run
 all demos in the sthda cathegory. Some of the examples require `rspec'
 do be available. To install `rspec' just do `gem install rspec'.
 
-\section{The demo code}\label{the-demo-code}
+\hypertarget{the-demo-code}{%
+\section{The demo code}\label{the-demo-code}}
 
 The following is the Ruby code and plot for the above example. There is
 a small difference between the code in the example and the code bellow.
@@ -361,44 +369,9 @@ generate an `svg' image and then include it in this document. In order
 to generate and image, the R.svg device is used. To generate the plot on
 the screen, use the R.awt device, as commented on the code.
 
-\begin{Shaded}
-\begin{Highlighting}[]
-\NormalTok{require }\StringTok{'galaaz'}
-\NormalTok{require }\StringTok{'ggplot'}
-
-\CommentTok{# load package and data}
-\NormalTok{R.options(}\StringTok{scipen: }\DecValTok{999}\NormalTok{)  }\CommentTok{# turn-off scientific notation like 1e+48}
-\NormalTok{R.theme_set(R.theme_bw)  }\CommentTok{# pre-set the bw theme.}
-
-\NormalTok{midwest = ~}\StringTok{:midwest}
-\CommentTok{# midwest <- read.csv("http://goo.gl/G1K41K")  # bkup data source}
-
-\CommentTok{# R.awt  # run the awt device if the plot should show on the screen}
-\NormalTok{R.svg    }\CommentTok{# run the svg device if an image should be generated}
-
-\CommentTok{# Scatterplot}
-\NormalTok{gg = midwest.ggplot(E.aes(}\StringTok{x: :area}\NormalTok{, }\StringTok{y: :poptotal}\NormalTok{)) + }
-\NormalTok{     R.geom_point(E.aes(}\StringTok{col: :state}\NormalTok{, }\StringTok{size: :popdensity}\NormalTok{)) + }
-\NormalTok{     R.geom_smooth(}\StringTok{method: "loess"}\NormalTok{, }\StringTok{se: }\DecValTok{false}\NormalTok{) + }
-\NormalTok{     R.xlim(R.c(}\DecValTok{0}\NormalTok{, }\FloatTok{0.1}\NormalTok{)) + }
-\NormalTok{     R.ylim(R.c(}\DecValTok{0}\NormalTok{, }\DecValTok{500000}\NormalTok{)) + }
-\NormalTok{     R.labs(}\StringTok{subtitle: "Area Vs Population"}\NormalTok{, }
-            \StringTok{y: "Population"}\NormalTok{, }
-            \StringTok{x: "Area"}\NormalTok{, }
-            \StringTok{title: "Scatterplot"}\NormalTok{, }
-            \StringTok{caption: "Source: midwest"}\NormalTok{)}
-
-\NormalTok{R.png(}\StringTok{'midwest.png'}\NormalTok{)     }\CommentTok{# this line is not necessary with the awt device}
-\NormalTok{puts gg}
-
-\NormalTok{R.dev__off               }\CommentTok{# R.dev__off turns off the device.  If using awt, the plot}
-                         \CommentTok{# window will be closed}
-\end{Highlighting}
-\end{Shaded}
-
 \begin{figure}
 \centering
-\includegraphics[width=0.70000\textwidth]{midwest.png}
+\includegraphics[width=0.7\textwidth,height=\textheight]{midwest.png}
 \caption{Midwest Plot}
 \end{figure}
 
@@ -450,7 +423,9 @@ order to delay the evaluation of function aes we need to use E.aes. The
 interested reader on NSE in R is directed to
 \url{http://adv-r.had.co.nz/Computing-on-the-language.html}.
 
-\section{An extension to the example}\label{an-extension-to-the-example}
+\hypertarget{an-extension-to-the-example}{%
+\section{An extension to the
+example}\label{an-extension-to-the-example}}
 
 If both codes are so similar, then why would one use Ruby instead of R
 and what good is galaaz after all?
@@ -468,177 +443,19 @@ So, it has defined a `CorpTheme' module. Plots in this corporation
 should not have grids, numbers in labels should not use scientific
 notation and the preferred color is blue.
 
-\begin{Shaded}
-\begin{Highlighting}[]
-\CommentTok{# corp_theme.rb}
-\CommentTok{# defines the corporate theme for all plots}
-    
-\KeywordTok{module} \DataTypeTok{CorpTheme}
-
-  \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{#---------------------------------------------------------------------------------}
-  
-  \KeywordTok{def} \DecValTok{self}\NormalTok{.global_theme}
-    
-\NormalTok{    R.options(}\StringTok{scipen: }\DecValTok{999}\NormalTok{)  }\CommentTok{# turn-off scientific notation like 1e+48}
-    
-    \CommentTok{# remove major grids}
-\NormalTok{    global_theme = R.theme(}\StringTok{panel__grid__major: }\NormalTok{E.element_blank())}
-    \CommentTok{# remove minor grids}
-\NormalTok{    global_theme = global_theme + R.theme(}\StringTok{panel__grid__minor: }\NormalTok{E.element_blank)}
-    \CommentTok{# remove border}
-\NormalTok{    global_theme = global_theme + R.theme(}\StringTok{panel__border: }\NormalTok{E.element_blank)}
-    \CommentTok{# remove background}
-\NormalTok{    global_theme = global_theme + R.theme(}\StringTok{panel__background: }\NormalTok{E.element_blank)}
-    \CommentTok{# Change axis font}
-\NormalTok{    global_theme = global_theme +}
-\NormalTok{                   R.theme(}\StringTok{axis__text: }\NormalTok{E.element_text(}\StringTok{size: }\DecValTok{8}\NormalTok{, }\StringTok{color: "#000080"}\NormalTok{))}
-    \CommentTok{# change color of axis titles}
-\NormalTok{    global_theme = global_theme +}
-\NormalTok{                   R.theme(}\StringTok{axis__title: }\NormalTok{E.element_text(}
-                             \StringTok{color: "#000080"}\NormalTok{, }
-                             \StringTok{face: "bold"}\NormalTok{,}
-                             \StringTok{size: }\DecValTok{8}\NormalTok{,}
-                             \StringTok{hjust: }\DecValTok{1}\NormalTok{))}
-  \KeywordTok{end}
-   
-\KeywordTok{end}
-\end{Highlighting}
-\end{Shaded}
-
 We now define a ScatterPlot class:
 
-\begin{Shaded}
-\begin{Highlighting}[]
-\CommentTok{# ScatterPlot.rb}
-\CommentTok{# creates a scatter plot and allow some configuration}
-    
-\KeywordTok{class} \DataTypeTok{ScatterPlot}
-
-  \OtherTok{attr_accessor} \StringTok{:title}
-  \OtherTok{attr_accessor} \StringTok{:subtitle}
-  \OtherTok{attr_accessor} \StringTok{:caption}
-  \OtherTok{attr_accessor} \StringTok{:x_label}
-  \OtherTok{attr_accessor} \StringTok{:y_label}
-  
-  \CommentTok{#---------------------------------------------------------------------------------}
-  \CommentTok{# Initialize the plot with the data and the x and y variables}
-  \CommentTok{#---------------------------------------------------------------------------------}
-
-  \KeywordTok{def}\NormalTok{ initialize(data, x:, y:)}
-    \OtherTok{@data}\NormalTok{ = data}
-    \OtherTok{@x}\NormalTok{ = x}
-    \OtherTok{@y}\NormalTok{ = y}
-  \KeywordTok{end}
-  
-  \CommentTok{#---------------------------------------------------------------------------------}
-  \CommentTok{# Define groupings by color and size}
-  \CommentTok{#---------------------------------------------------------------------------------}
-
-  \KeywordTok{def}\NormalTok{ group_by(color:, size:)}
-    \OtherTok{@color_by}\NormalTok{ = color}
-    \OtherTok{@size_by}\NormalTok{ = size}
-  \KeywordTok{end}
-
-  \CommentTok{#---------------------------------------------------------------------------------}
-  \CommentTok{# Add a smoothing line, and if confidence is true the add a confidence interval, if}
-  \CommentTok{# false does not add the confidence interval}
-  \CommentTok{#---------------------------------------------------------------------------------}
-
-  \KeywordTok{def}\NormalTok{ add_smoothing_line(method:, }\StringTok{confidence: }\DecValTok{true}\NormalTok{)}
-    \OtherTok{@method}\NormalTok{ = method}
-    \OtherTok{@confidence}\NormalTok{ = confidence}
-  \KeywordTok{end}
-  
-  \CommentTok{#---------------------------------------------------------------------------------}
-  \CommentTok{# Creates the graph title, properly formated for this theme}
-  \CommentTok{# @param title [String] The title to add to the graph}
-  \CommentTok{# @return textGrob that can be included in a graph}
-  \CommentTok{#---------------------------------------------------------------------------------}
-
-  \KeywordTok{def}\NormalTok{ graph_params(}\StringTok{title: ""}\NormalTok{, }\StringTok{subtitle: ""}\NormalTok{, }\StringTok{caption: ""}\NormalTok{, }\StringTok{x_label: ""}\NormalTok{, }\StringTok{y_label: ""}\NormalTok{)}
-\NormalTok{    R.labs(}
-      \StringTok{title: }\NormalTok{title, }
-      \StringTok{subtitle: }\NormalTok{subtitle, }
-      \StringTok{caption: }\NormalTok{caption,}
-      \StringTok{y_label: }\NormalTok{y_label, }
-      \StringTok{x_label: }\NormalTok{x_label, }
-\NormalTok{    )}
-  \KeywordTok{end}
-
-  \CommentTok{#---------------------------------------------------------------------------------}
-  \CommentTok{# Prepare the plot's points}
-  \CommentTok{#---------------------------------------------------------------------------------}
-
-  \KeywordTok{def}\NormalTok{ points}
-\NormalTok{    params = \{\}}
-\NormalTok{    params[}\StringTok{:col}\NormalTok{] = }\OtherTok{@color_by} \KeywordTok{if} \OtherTok{@color_by}
-\NormalTok{    params[}\StringTok{:size}\NormalTok{] = }\OtherTok{@size_by} \KeywordTok{if} \OtherTok{@size_by}
-\NormalTok{    R.geom_point(E.aes(params))}
-  \KeywordTok{end}
-      
-  \CommentTok{#---------------------------------------------------------------------------------}
-  \CommentTok{# Plots the scatterplot}
-  \CommentTok{#---------------------------------------------------------------------------------}
-
-  \KeywordTok{def}\NormalTok{ plot(device = }\StringTok{'awt'}\NormalTok{)}
-\NormalTok{    device == }\StringTok{'awt'}\NormalTok{ ? R.awt : R.svg}
-   
-\NormalTok{    gg = }\OtherTok{@data}\NormalTok{.ggplot(E.aes(}\StringTok{x: }\OtherTok{@x}\NormalTok{, }\StringTok{y: }\OtherTok{@y}\NormalTok{)) +}
-\NormalTok{      points + }
-\NormalTok{      R.geom_smooth(}\StringTok{method: }\OtherTok{@method}\NormalTok{, }\StringTok{se: }\OtherTok{@confidence}\NormalTok{) +}
-\NormalTok{      R.xlim(R.c(}\DecValTok{0}\NormalTok{, }\FloatTok{0.1}\NormalTok{)) +}
-\NormalTok{      R.ylim(R.c(}\DecValTok{0}\NormalTok{, }\DecValTok{500000}\NormalTok{)) + }
-\NormalTok{      graph_params(}\StringTok{title: }\OtherTok{@title}\NormalTok{,}
-                   \StringTok{subtitle: }\OtherTok{@subtitle}\NormalTok{, }
-                   \StringTok{y_label: }\OtherTok{@y_label}\NormalTok{, }
-                   \StringTok{x_label: }\OtherTok{@x_label}\NormalTok{, }
-                   \StringTok{caption: }\OtherTok{@caption}\NormalTok{) +}
-      \DataTypeTok{CorpTheme}\NormalTok{.global_theme}
-
-\NormalTok{    R.png(}\StringTok{'scatter_plot.png'}\NormalTok{) }\KeywordTok{if}\NormalTok{ !(device == }\StringTok{'awt'}\NormalTok{)}
-\NormalTok{    puts gg}
-\NormalTok{    R.dev__off}
-    
-  \KeywordTok{end}
-  
-\KeywordTok{end}
-\end{Highlighting}
-\end{Shaded}
-
 And this is the final code for making the scatter plot with the midwest
 data
 
-\begin{Shaded}
-\begin{Highlighting}[]
-\NormalTok{require }\StringTok{'galaaz'}
-\NormalTok{require }\StringTok{'ggplot'}
-
-\NormalTok{sp = }\DataTypeTok{ScatterPlot}\NormalTok{.new(~}\StringTok{:midwest}\NormalTok{, }\StringTok{x: :area}\NormalTok{, }\StringTok{y: :poptotal}\NormalTok{)}
-\NormalTok{sp.title = }\StringTok{"Midwest Dataset - Scatterplot"}
-\NormalTok{sp.subtitle = }\StringTok{"Area Vs Population"}
-\NormalTok{sp.caption = }\StringTok{"Source: midwest"}
-\NormalTok{sp.x_label = }\StringTok{"Area"}
-\NormalTok{sp.y_label = }\StringTok{"Population"}
-\NormalTok{sp.group_by(}\StringTok{color: :state}\NormalTok{, }\StringTok{size: :popdensity}\NormalTok{)    }\CommentTok{# try sp.group_by(color: :state)}
-\CommentTok{# available methods: "lm", "glm", "loess", "gam"}
-\NormalTok{sp.add_smoothing_line(}\StringTok{method: "glm"}\NormalTok{) }
-\NormalTok{sp.plot(}\StringTok{'svg'}\NormalTok{)}
-
-\CommentTok{# require input from the user so that the script does not end removing the plot from}
-\CommentTok{# the screen}
-\end{Highlighting}
-\end{Shaded}
-
 \begin{figure}
 \centering
-\includegraphics[width=0.70000\textwidth]{scatter_plot.png}
+\includegraphics[width=0.7\textwidth,height=\textheight]{scatter_plot.png}
 \caption{Midwest Plot with `glm' function and modified theme}
 \end{figure}
 
-\section{Conclusion}\label{conclusion}
+\hypertarget{conclusion}{%
+\section{Conclusion}\label{conclusion}}
 
 R is a very powerful language for statistical analysis, data analytics,
 machine learning, plotting and many other scientific applications with a