galaaz 0.4.10 → 2.0.0

data/blogs/oh_my/oh_my.tex

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+% usar portugues do Brasil
+% \usepackage[brazilian]{babel}
+\usepackage[utf8]{inputenc}
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+\geometry{a4paper, top=1in}
+
+% needed for kableExtra
+\usepackage{longtable}
+\usepackage{multirow}
+\usepackage[table]{xcolor}
+\usepackage{wrapfig}
+\usepackage{float}
+\usepackage{colortbl}
+\usepackage{pdflscape}
+\usepackage{tabu}
+\usepackage{threeparttable}
+\usepackage[normalem]{ulem}
+
+\usepackage{bbm}
+\usepackage{booktabs}
+\usepackage{expex}
+
+\usepackage{graphicx}
+
+\usepackage{fancyhdr}
+% set the header and foot style
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+% \usepackage{lipsum}
+
+% make available command lastpage
+\usepackage{lastpage}
+
+% default fontsize 11pt better to add
+% fontsize on the yaml header
+% \usepackage[fontsize=11pt]{scrextend}
+
+% comandos para formatar uma tabela
+\usepackage{array}
+\newcolumntype{L}[1]{>{\raggedright\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
+\newcolumntype{C}[1]{>{\centering\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
+\newcolumntype{R}[1]{>{\raggedleft\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
+
+% necessário if we need to import other latex documents
+\usepackage{import}
+
+% Command to import an R variable to latex
+\newcommand{\RtoLatex}[2]{\newcommand{#1}{#2}}
+
+% 
+%\newcommand{\atraso}[1]{\color{red} \textbf {Tempo desde a Assinatura do Contrato: #1 dias}}
+\usepackage{bookmark}
+\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
+\urlstyle{same}
+\hypersetup{
+  pdftitle={Extending R with classes{,} modules{,} procs{,} lambdas{,} oh my!},
+  pdfauthor={Rodrigo Botafogo; Daniel Mossé - University of Pittsburgh},
+  hidelinks,
+  pdfcreator={LaTeX via pandoc}}
+
+\title{Extending R with classes, modules, procs, lambdas, oh my!}
+\author{Rodrigo Botafogo \and Daniel Mossé - University of Pittsburgh}
+\date{November 19th, 2018 (narrative updated for Galaaz 2.0, 2026)}
+
+\begin{document}
+\maketitle
+
+{
+\setcounter{tocdepth}{2}
+\tableofcontents
+}
+\section{Introduction}\label{introduction}
+
+This paper introduces and compares Galaaz with R's S4. It is a shameless
+rip off of
+\href{https://cran.r-project.org/doc/contrib/Genolini-S4tutorialV0-5en.pdf}{``A
+`(not so)' Short Introduction to S4''} by Christophe Genolini and
+follows the same structure and examples presented there.
+
+Galaaz is a Ruby Gem (library) that allows very tight integration
+between Ruby and R.\\
+Its integration is tighter and more transparent than what one can get
+between RinRuby or similar solutions in Python, such as
+\href{https://pypi.python.org/pypi/PypeR/1.1.0}{PypeR},
+\href{http://rpy2.bitbucket.org/}{rpy2} and other similar solutions.
+
+\textbf{Galaaz 2.0} runs on
+\textbf{\href{https://www.jruby.org/}{JRuby}} and drives \textbf{GNU R}
+through a \textbf{bridge}, so Ruby code can create and manipulate R
+objects and call R functions while staying idiomatic Ruby. An earlier
+prototype used Oracle's \textbf{GraalVM} with \textbf{TruffleRuby} and
+\textbf{FastR}; that stack is historical and is \textbf{not} what
+current Galaaz targets.
+
+\section{Bases of Object Programming}\label{bases-of-object-programming}
+
+In this paper, we will start our discussion from Part II of ``The (not
+so) Short Introduction to S4'', which from now on we will reference as
+SS4 for ``short S4''. Interested readers are directed to this paper to
+understand the motivation and examples in that paper. In this paper we
+will present the S4 code from SS4 and then the same code in Ruby/Galaaz.
+We will not comment on the S4 code, as all the comments can be found in
+SS4, we will only focus on the Ruby/Galaaz description.
+
+S4 defines classes by using the setClass function:
+
+\section{Classes Declaration}\label{classes-declaration}
+
+\begin{verbatim}
+# > setClass(
+# + Class="Trajectories",
+# + representation=representation(
+# + times = "numeric",
+# + traj = "matrix"
+# + )
+# + )
+\end{verbatim}
+
+\section{Instance Variables}\label{instance-variables}
+
+In Ruby a class is defined by the keyword `class'. Every class should
+start with a capital letter. S4 `slots' are called `instance variables'
+in Ruby. Differently from R's S4, instance variables in Ruby do not have
+type information. It should be clear though, that S4 type information is
+also not a ``compile'' time type, since R is not compiled. The type is
+checked at runtime. The same checking can be done in Ruby and we will do
+it later in this document.
+
+In the example bellow, we create class Trajectories with two instance
+variables, `times' and `matrix'. We will not go over the details of
+instance variables in Ruby, but here we created those variables with the
+keyword `attr\_reader' and a colom before the variables name:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{class} \DataTypeTok{Trajectories}
+  \OtherTok{attr\_reader} \WarningTok{:times}
+  \OtherTok{attr\_reader} \WarningTok{:matrix}
+\ControlFlowTok{end}
+\end{Highlighting}
+\end{Shaded}
+
+In order to create a new instance of object Trajectories we call method
+new on the class and we can store the result in a varible (not an
+instance variable) as bellow:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\OtherTok{@traj} \OperatorTok{=} \DataTypeTok{Trajectories}\AttributeTok{.new}
+\end{Highlighting}
+\end{Shaded}
+
+We now have in variable `@traj' a Trajectories object. In Ruby, printing
+variable `traj' will only print the class name of the object and not it
+contents as in R.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts} \OtherTok{@traj}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## #<RC::Trajectories:0x378c2595>
+\end{verbatim}
+
+To see the contents of an object, one needs to access its components
+using the `.' operator:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts} \OtherTok{@traj}\AttributeTok{.times}
+\end{Highlighting}
+\end{Shaded}
+
+\section{Constructor}\label{constructor}
+
+Since there is no content stored in `times' nor `matrix', nil is
+returned. In order to add a value in the variables, we need to add a
+constructor to the class Trajectories. In R, a constructor is build by
+default, in Ruby, this has to be created by adding a method called
+`initialize'. In the example bellow, we will create the initializer that
+accepts two values, a `times' value and a `matrix' value and they are
+used to initialize the value of the instance variables:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{class} \DataTypeTok{Trajectories}
+  
+  \OtherTok{attr\_reader} \WarningTok{:times}
+  \OtherTok{attr\_reader} \WarningTok{:matrix}
+
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# Initializes the Trajectories class.  Takes two parameters}
+  \CommentTok{\# @param times}
+  \CommentTok{\# @param matrix}
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  
+  \ControlFlowTok{def}\NormalTok{ initialize(times}\OperatorTok{:} \DecValTok{nil}\NormalTok{, }\WarningTok{matrix:} \DecValTok{nil}\NormalTok{)}
+    \OtherTok{@times} \OperatorTok{=}\NormalTok{ times}
+    \OtherTok{@matrix} \OperatorTok{=}\NormalTok{ matrix}
+  \ControlFlowTok{end}
+
+\ControlFlowTok{end}
+\end{Highlighting}
+\end{Shaded}
+
+Up to this point, everything described is pure Ruby code and has
+absolutely no relationship with R. We now want to create a Trajectories
+with a `times' vector. Ruby has a vector class and we could use this
+class to create a vector and add it to the `times' instance variable;
+however, in order to make use of R's functions, we want to create a R
+vector to add to `times'. In Galaaz, creating R objects is done using
+the corresponding R functions by just preceding them with `R.', i.e., R
+functions are all defined in Galaaz in the R namespace.
+
+Since Galaaz is Ruby and not R, some syntax adjustments are sometimes
+necessary. For instance, in R, a range is represented as `(1:4)', in
+Ruby, the same range is represented as `(1..4)'. When passing arguments
+to an R function in R one uses the `=' sign after the slot name; in R,
+one uses the `:' operator after parameter's name as we can see bellow:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# Create a Trajectories passing a times vector, but no matrix parameter}
+\OtherTok{@traj} \OperatorTok{=} \DataTypeTok{Trajectories}\AttributeTok{.new}\NormalTok{(}\WarningTok{times:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DecValTok{2}\NormalTok{, }\DecValTok{3}\NormalTok{, }\DecValTok{4}\NormalTok{))}
+
+\CommentTok{\# Create a Trajectories with times and matrix}
+\OtherTok{@traj2} \OperatorTok{=} \DataTypeTok{Trajectories}\AttributeTok{.new}\NormalTok{(}\WarningTok{times:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DecValTok{3}\NormalTok{), }\WarningTok{matrix:} \ConstantTok{R}\AttributeTok{.matrix}\NormalTok{((}\DecValTok{1}\OperatorTok{..}\DecValTok{4}\NormalTok{), }\WarningTok{ncol:} \DecValTok{2}\NormalTok{))}
+\end{Highlighting}
+\end{Shaded}
+
+\section{Access to Instance Variables (to reach a
+slot)}\label{access-to-instance-variables-to-reach-a-slot}
+
+In order to access data in an instance variable the operator `.' is
+used. In R, a similar result is obtained by use of the `@' operator, but
+SS4 does not recommend its use. In Galaaz, the `.' operator is the
+recommended way of accessing an instance variable.
+
+Now that we have created two trajectories, let's try to print its
+instance variables to see that everything is fine:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts} \OtherTok{@traj}\AttributeTok{.times}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1] 1 2 3 4
+\end{verbatim}
+
+We now have the expected value. Note that the `times' vector is printed
+exactly as it would if we were using GNU R. Let's now take a look at
+variable `traj2':
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts} \OtherTok{@traj2}\AttributeTok{.times}
+\FunctionTok{puts}
+\FunctionTok{puts} \OtherTok{@traj2}\AttributeTok{.matrix}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1] 1 3
+## 
+##      [,1] [,2]
+## [1,]    1    3
+## [2,]    2    4
+\end{verbatim}
+
+Let's now build the same examples as in SS4: Three hospitals take part
+in a study. The Pitié Salpêtriere (which has not yet returned its data
+file, shame on them!), Cochin and Saint-Anne. We first show the code in
+R and the corresponding Galaaz:
+
+\begin{verbatim}
+> trajPitie <- new(Class="Trajectories")
+> trajCochin <- new(
++     Class= "Trajectories",
++     times=c(1,3,4,5),
++     traj=rbind (
++         c(15,15.1, 15.2, 15.2),
++         c(16,15.9, 16,16.4),
++         c(15.2, NA, 15.3, 15.3),
++         c(15.7, 15.6, 15.8, 16)
++     )
++ )
+> trajStAnne <- new(
++     Class= "Trajectories",
++     times=c(1: 10, (6: 16) *2),
++     traj=rbind(
++         matrix (seq (16,19, length=21), ncol=21, nrow=50, byrow=TRUE),
++         matrix (seq (15.8, 18, length=21), ncol=21, nrow=30, byrow=TRUE)
++     )+rnorm (21*80,0,0.2)
++ )
+\end{verbatim}
+
+This same code in Galaaz becomes:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\OtherTok{@trajPitie} \OperatorTok{=} \DataTypeTok{Trajectories}\AttributeTok{.new}
+
+\OtherTok{@trajCochin} \OperatorTok{=} \DataTypeTok{Trajectories}\AttributeTok{.new}\NormalTok{(}\WarningTok{times:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{1}\NormalTok{,}\DecValTok{3}\NormalTok{,}\DecValTok{4}\NormalTok{,}\DecValTok{5}\NormalTok{),}
+                               \WarningTok{matrix:} \ConstantTok{R}\AttributeTok{.rbind}\NormalTok{(}
+                               \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{15}\NormalTok{,}\FloatTok{15.1}\NormalTok{, }\FloatTok{15.2}\NormalTok{, }\FloatTok{15.2}\NormalTok{),}
+                               \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{16}\NormalTok{,}\FloatTok{15.9}\NormalTok{, }\DecValTok{16}\NormalTok{,}\FloatTok{16.4}\NormalTok{),}
+                               \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\FloatTok{15.2}\NormalTok{, }\ConstantTok{R}\OperatorTok{::}\ConstantTok{NA}\NormalTok{, }\FloatTok{15.3}\NormalTok{, }\FloatTok{15.3}\NormalTok{),}
+                               \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\FloatTok{15.7}\NormalTok{, }\FloatTok{15.6}\NormalTok{, }\FloatTok{15.8}\NormalTok{, }\DecValTok{16}\NormalTok{)))}
+
+\OtherTok{@trajStAnne} \OperatorTok{=}
+  \DataTypeTok{Trajectories}\AttributeTok{.new}\NormalTok{(}\WarningTok{times:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{((}\DecValTok{1}\OperatorTok{..}\DecValTok{10}\NormalTok{), }\ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{6}\OperatorTok{..}\DecValTok{16}\NormalTok{) }\OperatorTok{*} \DecValTok{2}\NormalTok{),}
+                   \WarningTok{matrix:}\NormalTok{ (}\ConstantTok{R}\AttributeTok{.rbind}\NormalTok{(}
+                             \ConstantTok{R}\AttributeTok{.matrix}\NormalTok{(}\ConstantTok{R}\AttributeTok{.seq}\NormalTok{(}\DecValTok{16}\NormalTok{, }\DecValTok{19}\NormalTok{, }\WarningTok{length:} \DecValTok{21}\NormalTok{), }\WarningTok{ncol:} \DecValTok{21}\NormalTok{,}
+                                      \WarningTok{nrow:} \DecValTok{50}\NormalTok{, }\WarningTok{byrow:} \DecValTok{true}\NormalTok{),}
+                             \ConstantTok{R}\AttributeTok{.matrix}\NormalTok{(}\ConstantTok{R}\AttributeTok{.seq}\NormalTok{(}\FloatTok{15.8}\NormalTok{, }\DecValTok{18}\NormalTok{, }\WarningTok{length:} \DecValTok{21}\NormalTok{), }\WarningTok{ncol:} \DecValTok{21}\NormalTok{,}
+                                      \WarningTok{nrow:} \DecValTok{30}\NormalTok{, }\WarningTok{byrow:} \DecValTok{true}\NormalTok{)) }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.rnorm}\NormalTok{(}\DecValTok{21}\OperatorTok{*}\DecValTok{80}\NormalTok{, }\DecValTok{0}\NormalTok{, }\FloatTok{0.2}\NormalTok{)))}
+\end{Highlighting}
+\end{Shaded}
+
+Let's check that the `times' and `matrix' instance variables were
+correctly set:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts} \OtherTok{@trajCochin}\AttributeTok{.times}
+\FunctionTok{puts}
+\FunctionTok{puts} \OtherTok{@trajCochin}\AttributeTok{.matrix}
+\FunctionTok{puts}
+\FunctionTok{puts} \OtherTok{@trajStAnne}\AttributeTok{.times}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1] 1 3 4 5
+## 
+##          [,1] [,2] [,3] [,4]
+## g2_v2114 15.0 15.1 15.2 15.2
+## g2_v2115 16.0 15.9 16.0 16.4
+## g2_v2116 15.2   NA 15.3 15.3
+## g2_v2117 15.7 15.6 15.8 16.0
+## 
+##  [1]  1  2  3  4  5  6  7  8  9 10 12 14 16 18 20 22 24 26 28 30 32
+\end{verbatim}
+
+We will not at this time print trajStAnne.matrix, since this is a huge
+matrix and the result would just take too much space. Later we will
+print just a partial view of the matrix.
+
+\section{Default Values}\label{default-values}
+
+Default values are very useful and quite often used in Ruby programs.
+Although SS4 does not recommend its use, there are many cases in which
+default values are useful and make code simpler. We have already seen
+default values in this document, with the default being `nil'. This was
+necessary in order to be able to create our constructor and passing it
+the proper values.
+
+In the example bellow, a class TrajectoriesBis is created with default
+value 1 for times and a matrix with no elements in matrix.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{class} \DataTypeTok{TrajectoriesBis}
+
+  \OtherTok{attr\_reader} \WarningTok{:times}
+  \OtherTok{attr\_reader} \WarningTok{:matrix}
+
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# Initializes the Trajectories class.  Takes two parameters}
+  \CommentTok{\# @param times}
+  \CommentTok{\# @param matrix}
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+
+  \ControlFlowTok{def}\NormalTok{ initialize(times}\OperatorTok{:} \DecValTok{1}\NormalTok{, }\WarningTok{matrix:} \ConstantTok{R}\AttributeTok{.matrix}\NormalTok{(}\DecValTok{0}\NormalTok{))}
+    \OtherTok{@times} \OperatorTok{=}\NormalTok{ times}
+    \OtherTok{@matrix} \OperatorTok{=}\NormalTok{ matrix}
+  \ControlFlowTok{end}
+  
+\ControlFlowTok{end}
+
+\OtherTok{@traj\_bis} \OperatorTok{=} \DataTypeTok{TrajectoriesBis}\AttributeTok{.new}
+\end{Highlighting}
+\end{Shaded}
+
+Let's take a look at our new class:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts} \OtherTok{@traj\_bis}\AttributeTok{.times}
+\FunctionTok{puts}
+\FunctionTok{puts} \OtherTok{@traj\_bis}\AttributeTok{.matrix}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## 1
+## 
+##      [,1]
+## [1,]    0
+\end{verbatim}
+
+Note that `@traj\_bis.times' is the numeric 1, and what we actually want
+is a vector with {[}1{]} in it.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{class} \DataTypeTok{TrajectoriesBis}
+
+  \OtherTok{attr\_reader} \WarningTok{:times}
+  \OtherTok{attr\_reader} \WarningTok{:matrix}
+
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# Initializes the Trajectories class.  Takes two parameters}
+  \CommentTok{\# @param times [R::Vector] should be an R vector.}
+  \CommentTok{\# @param matrix [R::Matrix] should be an R matrix.}
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+
+  \CommentTok{\# Use R.c to convert number 1 to a vector}
+  \ControlFlowTok{def}\NormalTok{ initialize(times}\OperatorTok{:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\DecValTok{1}\NormalTok{), }\WarningTok{matrix:} \ConstantTok{R}\AttributeTok{.matrix}\NormalTok{(}\DecValTok{0}\NormalTok{))}
+    \OtherTok{@times} \OperatorTok{=}\NormalTok{ times}
+    \OtherTok{@matrix} \OperatorTok{=}\NormalTok{ matrix}
+  \ControlFlowTok{end}
+  
+\ControlFlowTok{end}
+
+\OtherTok{@traj\_bis} \OperatorTok{=} \DataTypeTok{TrajectoriesBis}\AttributeTok{.new}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts} \OtherTok{@traj\_bis}\AttributeTok{.times}
+\FunctionTok{puts}
+\FunctionTok{puts} \OtherTok{@traj\_bis}\AttributeTok{.matrix}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1] 1
+## 
+##      [,1]
+## [1,]    0
+\end{verbatim}
+
+\section{The Empty Object}\label{the-empty-object}
+
+When a Trajectories is created with new, and no argument is given, all
+its instance variables will have the default nil value. Since Ruby has
+no type information, then there is only one type (or actually no type)
+of nil. To check if a variable is empty, we check it against the nil
+value.
+
+\section{To See an Object}\label{to-see-an-object}
+
+Ruby has very strong meta-programming features, in particular, one can
+use introspection to see methods and instance variables from a given
+class. Method `instance\_variables' shows all the instance variables of
+an object:
+
+\begin{verbatim}
+puts @traj.instance_variables
+\end{verbatim}
+
+The description of all meta-programming features of Ruby is well beyond
+the scope of this document, but it is a very frequent a powerful feature
+of Ruby, that makes programming in Ruby a different experience than
+programming in other languages.
+
+\section{Methods}\label{methods}
+
+Methods are a fundamental feature of object oriented programming. We
+will now extend our class Trajectories to add methods to it. In SS4, a
+method `plot' is added to Trajectories. At this point, Renjin and Galaaz
+do not yet have plotting capabilities, so we will have to skip this
+method and go directly to the implementation of the `print' method.
+
+Bellow is the R code for method print:
+
+\begin{verbatim}
+> setMethod ("print","Trajectories",
++ function(x,...){
++ cat("*** Class Trajectories, method Print *** \\n")
++ cat("* Times ="); print (x@times)
++ cat("* Traj = \\n"); print (x@traj)
++ cat("******* End Print (trajectories) ******* \\n")
++ }
++ )
+\end{verbatim}
+
+Now the same code for class Trajectories in Galaaz. In general methods
+are defined in a class together with all the class definition. We will
+first use this approach. Later, we will show how to `reopen' a class to
+add new methods to it.
+
+In this example, we are defining a method named `print'. We have being
+using method `puts' to output data. There is a Ruby method that is more
+flexible than puts and that we need to use to implement our function:
+`print'. However, trying to use Ruby print inside the definition of
+Trajectories's print will not work, as Ruby will understand that as a
+recursive call to print. Ruby's print is defined inside the Kernel
+class, so, in order to call Ruby's print inside the definition of
+Trajectories's print we need to write `Kernel.print'.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{class} \DataTypeTok{Trajectories}
+  
+  \OtherTok{attr\_reader} \WarningTok{:times}
+  \OtherTok{attr\_reader} \WarningTok{:matrix}
+
+
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# Initializes the Trajectories class.  Takes two parameters}
+  \CommentTok{\# @param times [R::Vector] should be an R vector.}
+  \CommentTok{\# @param matrix [R::Matrix] should be an R matrix.}
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+
+  \ControlFlowTok{def}\NormalTok{ initialize(times}\OperatorTok{:} \DecValTok{nil}\NormalTok{, }\WarningTok{matrix:} \DecValTok{nil}\NormalTok{)}
+    \OtherTok{@times} \OperatorTok{=}\NormalTok{ times}
+    \OtherTok{@matrix} \OperatorTok{=}\NormalTok{ matrix}
+  \ControlFlowTok{end}
+
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# }
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  
+  \ControlFlowTok{def} \FunctionTok{print}
+    \FunctionTok{puts}\NormalTok{(}\StringTok{"*** Class Trajectories, method Print *** "}\NormalTok{)}
+    \DataTypeTok{Kernel}\AttributeTok{.print}\NormalTok{(}\StringTok{"times = "}\NormalTok{)}
+    \FunctionTok{puts} \OtherTok{@times}
+    \FunctionTok{puts}\NormalTok{(}\StringTok{"traj ="}\NormalTok{)}
+    \FunctionTok{puts} \OtherTok{@matrix}
+    \FunctionTok{puts}\NormalTok{(}\StringTok{"******* End Print (trajectories) ******* "}\NormalTok{)}
+  \ControlFlowTok{end}
+  
+\ControlFlowTok{end}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\OtherTok{@trajCochin}\AttributeTok{.print}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## *** Class Trajectories, method Print *** 
+## times = 1
+## 3
+## 4
+## 5
+## traj =
+##          [,1] [,2] [,3] [,4]
+## g2_v2114 15.0 15.1 15.2 15.2
+## g2_v2115 16.0 15.9 16.0 16.4
+## g2_v2116 15.2   NA 15.3 15.3
+## g2_v2117 15.7 15.6 15.8 16.0
+## ******* End Print (trajectories) *******
+\end{verbatim}
+
+For Cochin, the result is correct. For Saint-Anne, print will display
+too much information. So we need a second method.
+
+Show is the default R method used to show an object when its name is
+written in the console. We thus define `show' by taking into account the
+size of the object: if there are too many trajectories, `show' posts
+only part of them.
+
+Here is the R code for method `show':
+
+\begin{verbatim}
+> setMethod("show","Trajectories",
++ function(object){
++ cat("*** Class Trajectories, method Show *** \\n")
++ cat("* Times ="); print(object@times)
++ nrowShow <- min(10,nrow(object@traj))
++ ncolShow <- min(10,ncol(object@traj))
++ cat("* Traj (limited to a matrix 10x10) = \\n")
++ print(formatC(object@traj[1:nrowShow,1:ncolShow]),quote=FALSE)
++ cat("******* End Show (trajectories) ******* \\n")
++ }
++ )
+\end{verbatim}
+
+Now, let's write it with Galaaz. This time though, we will not rewrite
+the whole Trajectories class, but just reopen it to add this specific
+method. The next example has many interesting features of Galaaz, some
+we have already seen, others will be described now:
+
+\begin{itemize}
+\item
+  As we have already seen, to call an R function one uses the R.
+  notation. There is however another way: when the first argument to the
+  R function is an R object such as a matrix, a list, a vector, etc. we
+  can use `.' notation to call the function. This makes the function
+  look like a method of the object. For instance, R.nrow(@matrix), can
+  be called by doing @matrix.nrow;
+\item
+  In R, every number is converted to a vector and this can be done with
+  method R.i. Converting a vector with only one number back to a number
+  can be done with method `.gz'. So if @num is an R vector that holds a
+  number, then @num.gz is a number that can be used normally with Ruby
+  methods;
+\item
+  R functions and Ruby methods can be used freely in Galaaz. We show
+  bellow two different ways of getting the minimum of a number, either
+  by calling R.min or by getting the minimum of an array, with the min
+  method;
+\item
+  Galaaz allows for method `chaining'. Method chaining, also known as
+  named parameter idiom, is a common syntax for invoking multiple method
+  calls in object-oriented programming languages. Each method returns an
+  object, allowing the calls to be chained together in a single
+  statement without requiring variables to store the intermediate
+  results. For instance @matrix.nrow.gz, which returns the number of
+  rows of the matrix as a number;
+\item
+  Ranges in Ruby are represented by (x..y), where x is the beginning of
+  the range and y its end. An R matrix can be indexed by range,
+  \href{mailto:object@traj}{\nolinkurl{object@traj}}{[}1:nrowShow,1:ncolShow{]},
+  the same result is obtained in Galaaz by indexing @matrix
+  {[}(1..nrow\_show), (1..ncol\_show){]}. Observe that this statement is
+  then chained with the format function and with the pp method to print
+  the matrix.
+\end{itemize}
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{class} \DataTypeTok{Trajectories}
+
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\#}
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+
+  \ControlFlowTok{def}\NormalTok{ show}
+    \FunctionTok{puts}\NormalTok{(}\StringTok{"*** Class Trajectories, method Show *** "}\NormalTok{)}
+    \DataTypeTok{Kernel}\AttributeTok{.print}\NormalTok{(}\StringTok{"times = "}\NormalTok{)}
+    \FunctionTok{puts} \OtherTok{@times}
+\NormalTok{    nrow\_show }\OperatorTok{=} \KeywordTok{[}\DecValTok{10}\NormalTok{, }\OtherTok{@matrix}\AttributeTok{.nrow} \OperatorTok{\textless{}\textless{}} \DecValTok{0}\KeywordTok{]}\AttributeTok{.min}
+\NormalTok{    ncol\_show }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.min}\NormalTok{(}\DecValTok{10}\NormalTok{, }\OtherTok{@matrix}\AttributeTok{.ncol}\NormalTok{) }\OperatorTok{\textless{}\textless{}} \DecValTok{0}
+    \FunctionTok{puts}\NormalTok{(}\StringTok{"* Traj (limited to a matrix 10x10) = "}\NormalTok{)}
+    \FunctionTok{puts} \OtherTok{@matrix}\KeywordTok{[}\NormalTok{(}\DecValTok{1}\OperatorTok{..}\NormalTok{nrow\_show), (}\DecValTok{1}\OperatorTok{..}\NormalTok{ncol\_show)}\KeywordTok{]}\AttributeTok{.format}\NormalTok{(}\WarningTok{digits:} \DecValTok{2}\NormalTok{, }\WarningTok{nsmall:} \DecValTok{2}\NormalTok{)}
+    \FunctionTok{puts}\NormalTok{(}\StringTok{"******* End Show (trajectories) ******* "}\NormalTok{)}
+  \ControlFlowTok{end}
+  
+\ControlFlowTok{end}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\OtherTok{@trajStAnne}\AttributeTok{.show}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## parse error
+\end{verbatim}
+
+\begin{verbatim}
+## /home/rbotafogo/desenv_linux/galaaz/lib/new_bridge/session_client.rb:268:in 'eval_r'
+## /home/rbotafogo/desenv_linux/galaaz/lib/R_interface/new_bridge_adapter.rb:231:in 'eval_r_with_result'
+## /home/rbotafogo/desenv_linux/galaaz/lib/R_interface/rsupport.rb:359:in 'exec_function'
+## /home/rbotafogo/desenv_linux/galaaz/lib/R_interface/rsupport.rb:618:in 'process_missing_dispatch'
+## /home/rbotafogo/desenv_linux/galaaz/lib/R_interface/rsupport.rb:468:in 'process_missing'
+## /home/rbotafogo/desenv_linux/galaaz/lib/R_interface/robject.rb:404:in 'method_missing'
+## /home/rbotafogo/desenv_linux/galaaz/lib/util/exec_ruby.rb:180:in 'show'
+## /home/rbotafogo/desenv_linux/galaaz/lib/util/exec_ruby.rb:170:in 'exec_ruby'
+## org/jruby/RubyKernel.java:1268:in 'eval'
+## /home/rbotafogo/desenv_linux/galaaz/lib/util/exec_ruby.rb:169:in 'exec_ruby'
+## /home/rbotafogo/desenv_linux/galaaz/lib/gknit/knitr_engine.rb:777:in 'block in initialize'
+## org/jruby/RubyBasicObject.java:2695:in 'instance_eval'
+## org/jruby/RubyBasicObject.java:2723:in 'instance_eval'
+## /home/rbotafogo/desenv_linux/galaaz/lib/gknit/knitr_engine.rb:748:in 'block in initialize'
+## /home/rbotafogo/desenv_linux/galaaz/lib/R_interface/new_bridge_adapter.rb:358:in 'block in register_callback_proc_stub'
+## /home/rbotafogo/desenv_linux/galaaz/lib/new_bridge/session_client.rb:413:in 'block in handle_call'
+\end{verbatim}
+
+Our show method has the same problem as SS4, i.e., if an empty
+trajectories object is created and we try to `show' it, it will generate
+an error. Let's see it:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\OtherTok{@empty\_traj} \OperatorTok{=} \DataTypeTok{Trajectories}\AttributeTok{.new}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\OtherTok{@empty\_traj}\AttributeTok{.show}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## undefined method 'nrow' for nil
+\end{verbatim}
+
+\end{document}