galaaz 0.4.10 → 0.5.0

data/blogs/galaaz_ggplot/galaaz_ggplot.aux

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data/blogs/gknit/gknit.md

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----
-title: "How to do reproducible research in Ruby with gKnit"
-author:
-    - "Rodrigo Botafogo"
-    - "Daniel Mossé - University of Pittsburgh"
-tags: [Tech, Data Science, Ruby, R, GraalVM]
-date: "29/04/2019"
-bibliography: stats.bib
-output:
-  html_document:
-    self_contained: true
-    keep_md: true
-  pdf_document:
-    includes:
-      in_header: ["../../sty/galaaz.sty"]
-    number_sections: yes
----
-
-
-
-# Introduction
-
-The idea of "literate programming" was first introduced by Donald Knuth in the 
-1980's [@Knuth:literate_programming].
-The main intention of this approach was to develop software interspersing macro snippets,
-traditional source code, and a natural language such as English in a document 
-that could be compiled into
-executable code and at the same time easily read by a human developer. According to Knuth
-"The practitioner of 
-literate programming can be regarded as an essayist, whose main concern is with exposition 
-and excellence of style."
-
-The idea of literate programming evolved into the idea of reproducible research, in which
-all the data, software code, documentation, graphics etc. needed to reproduce the research
-and its reports could be included in a
-single document or set of documents that when distributed to peers could be rerun generating
-the same output and reports.
-
-The R community has put a great deal of effort in reproducible research.  In 2002, Sweave was
-introduced and it allowed mixing R code with Latex generating high quality PDF documents.  A
-Sweave document could include code, the results of executing the code, graphics and text 
-such that it contained the whole narrative to reproduce the research.  In
-2012, Knitr, developed by Yihui Xie from RStudio was released to replace Sweave and to
-consolidate in one single package the many extensions and add-on packages that
-were necessary for Sweave.
-
-With Knitr, __R markdown__ was also developed, an extension to the
-Markdown format.  With __R markdown__ and Knitr it is possible to generate reports in a multitude
-of formats such as HTML, markdown, Latex, PDF, dvi, etc.  __R markdown__ also allows the use of
-multiple programming languages such as R, Ruby, Python, etc. in the same document.  
-
-In __R markdown__, text is interspersed with
-code chunks that can be executed and both the code and its results can become
-part of the final report.  Although __R markdown__ allows multiple programming languages in the
-same document, only R and Python (with
-the reticulate package) can persist variables between chunks.  For other languages, such as
-Ruby, every chunk will start a new process and thus all data is lost between chunks, unless it
-is somehow stored in a data file that is read by the next chunk.
-
-Being able to persist data
-between chunks is critical for literate programming otherwise the flow of the narrative is lost
-by all the effort of having to save data and then reload it. Although this might, at first, seem like
-a small nuisance, not being able to persist data between chunks is a major issue. For example, let's
-take a look at the following simple example in which we want to show how to create a list and the
-use it.  Let's first assume that data cannot be persisted between chunks.  In the next chunk we
-create a list, then we would need to save it to file, but to save it, we need somehow to marshal the
-data into a binary format:
-
-
-```ruby
-lst = R.list(a: 1, b: 2, c: 3)
-lst.saveRDS("lst.rds")
-```
-then, on the next chunk, where variable 'lst' is used, we need to read back it's value
-
-
-```ruby
-lst = R.readRDS("lst.rds")
-puts lst
-```
-
-```
-## $a
-## [1] 1
-## 
-## $b
-## [1] 2
-## 
-## $c
-## [1] 3
-```
-
-Now, any single code has dozens of variables that we might want to use and reuse between chunks.
-Clearly, such an approach becomes quickly unmanageable. Probably, because of 
-this problem, it is very rare to see any __R markdown__ document in the Ruby community.
-
-When variables can be used accross chunks, then no overhead is needed:
-
-
-```ruby
-lst = R.list(a: 1, b: 2, c: 3)
-# any other code can be added here
-```
-
-
-```ruby
-puts lst
-```
-
-```
-## $a
-## [1] 1
-## 
-## $b
-## [1] 2
-## 
-## $c
-## [1] 3
-```
-
-In the Python community, the same effort to have code and text in an integrated environment
-started around the first decade of 2000. In 2006 iPython 0.7.2 was released.  In 2014,
-Fernando Pérez, spun off project Jupyter from iPython creating a web-based interactive
-computation environment.  Jupyter can now be used with many languages, including Ruby with the
-iruby gem (https://github.com/SciRuby/iruby).  In order to have multiple languages in a Jupyter
-notebook the SoS kernel was developed (https://vatlab.github.io/sos-docs/).
-
-# gKnitting a Document
-
-This document describes gKnit.  gKnit is based on knitr and __R markdown__ and can knit a document 
-written both in Ruby and/or R and output it in any of the available formats of __R markdown__.  gKnit
-allows ruby developers to do literate programming and reproducible research by allowing them to
-have in a single document, text and code.
-
-gKnit runs atop of GraalVM, and Galaaz (an integration 
-library between Ruby and R - see bellow).  In gKnit, Ruby variables are persisted between 
-chunks, making  it an ideal solution for literate programming in this language.  Also, 
-since it is based on  Galaaz, Ruby chunks can have access to R variables and Polyglot Programming 
-with Ruby and R is quite natural.
-
-Galaaz has already been describe in the following posts:
-
-* https://towardsdatascience.com/ruby-plotting-with-galaaz-an-example-of-tightly-coupling-ruby-and-r-in-graalvm-520b69e21021.  
-* https://medium.freecodecamp.org/how-to-make-beautiful-ruby-plots-with-galaaz-320848058857
-
-This is not a blog post on __R markdown__, and the interested user is directed to the following links
-for detailed information on its capabilities and use.
-
-* https://rmarkdown.rstudio.com/ or
-* https://bookdown.org/yihui/rmarkdown/ 
-
-In this post, we will describe just the main aspects of __R markdown__, so the user can start 
-gKnitting Ruby and R documents quickly.
-
-## The Yaml header
-
-An __R markdown__ document should start with a Yaml header and be stored in a file with 
-'.Rmd' extension. This document has the following header for gKitting an HTML document.
-
-```
----
-title: "How to do reproducible research in Ruby with gKnit"
-author: 
-    - "Rodrigo Botafogo"
-    - "Daniel Mossé - University of Pittsburgh"
-tags: [Tech, Data Science, Ruby, R, GraalVM]
-date: "20/02/2019"
-output:
-  html_document:
-    self_contained: true
-    keep_md: true
-  pdf_document:
-    includes:
-      in_header: ["../../sty/galaaz.sty"]
-    number_sections: yes
----
-```
-
-For more information on the options in the Yaml header, check https://bookdown.org/yihui/rmarkdown/html-document.html.
-
-## __R Markdown__ formatting
-
-Document formatting can be done with simple markups such as:
-
-### Headers
-
-```
-# Header 1
-
-## Header 2
-
-### Header 3
-
-```
-
-### Lists
-
-```
-Unordered lists:
-
-* Item 1
-* Item 2
-    + Item 2a
-    + Item 2b
-```
-
-```
-Ordered Lists
-
-1. Item 1
-2. Item 2
-3. Item 3
-    + Item 3a
-    + Item 3b
-```
-
-For more R markdown formatting go to https://rmarkdown.rstudio.com/authoring_basics.html.
-
-### R chunks
-
-Running and executing Ruby and R code is actually what really interests us is this blog.  
-Inserting a code chunk is done by adding code in a block delimited by three back ticks 
-followed by an open
-curly brace ('{') followed with the engine name (r, ruby, rb, include, ...), an 
-any optional chunk_label and options, as shown bellow:
-
-````
-```{engine_name [chunk_label], [chunk_options]}
-```
-````
-
-for instance, let's add an R chunk to the document labeled 'first_r_chunk'.  This is
-a very simple code just to create a variable and print it out, as follows:
-
-````
-```{r first_r_chunk}
-vec <- c(1, 2, 3)
-print(vec)
-```
-````
-
-If this block is added to an __R markdown__ document and gKnitted the result will be:
-
-
-```r
-vec <- c(1, 2, 3)
-print(vec)
-```
-
-```
-## [1] 1 2 3
-```
-
-Now let's say that we want to do some analysis in the code, but just print the result and not the
-code itself.  For this, we need to add the option 'echo = FALSE'.
-
-````
-```{r second_r_chunk, echo = FALSE}
-vec2 <- c(10, 20, 30)
-vec3 <- vec * vec2
-print(vec3)     
-```
-````
-Here is how this block will show up in the document. Observe that the code is not shown
-and we only see the execution result in a white box
-
-
-```
-## [1] 10 40 90
-```
-
-A description of the available chunk options can be found in https://yihui.name/knitr/.
-
-Let's add another R chunk with a function definition.  In this example, a vector 
-'r_vec' is created and
-a new function 'reduce_sum' is defined.  The chunk specification is
-
-````
-```{r data_creation}
-r_vec <- c(1, 2, 3, 4, 5)
-
-reduce_sum <- function(...) {
-  Reduce(sum, as.list(...))
-}
-```
-````
-
-and this is how it will look like once executed.  From now on, to be concise in the
-presentation we will not show chunk definitions any longer.
-
-
-
-```r
-r_vec <- c(1, 2, 3, 4, 5)
-
-reduce_sum <- function(...) {
-  Reduce(sum, as.list(...))
-}
-```
-
-We can, possibly in another chunk, access the vector and call the function as follows:
-
-
-```r
-print(r_vec)
-```
-
-```
-## [1] 1 2 3 4 5
-```
-
-```r
-print(reduce_sum(r_vec))
-```
-
-```
-## [1] 15
-```
-### R Graphics with ggplot
-
-In the following chunk, we create a bubble chart in R using ggplot and include it in 
-this document.  Note that there is no directive in the code to include the image, this
-occurs automatically.  The 'mpg' dataframe is natively available to R and to Galaaz as
-well.
-
-For the reader not knowledgeable of ggplot, ggplot is a graphics library based on "the
-grammar of graphics" [@Wilkinson:grammar_of_graphics]. The idea of the grammar of graphics
-is to build a graphics by adding layers to the plot.  More information can be found in
-https://towardsdatascience.com/a-comprehensive-guide-to-the-grammar-of-graphics-for-effective-visualization-of-multi-dimensional-1f92b4ed4149.
-
-In the plot bellow the 'mpg' dataset from base R is used. "The data concerns city-cycle fuel 
-consumption in miles per gallon, to be predicted in terms of 3 multivalued discrete and 5 
-continuous attributes." (Quinlan, 1993)
-
-First, the 'mpg' dataset if filtered to extract only cars from the following manumactures: Audi, Ford,
-Honda, and Hyundai and stored in the 'mpg_select' variable.  Then, the selected dataframe is passed
-to the ggplot function specifying in the aesthetic method (aes) that 'displacement' (disp) should
-be plotted in the 'x' axis and 'city mileage' should be on the 'y' axis.  In the 'labs' layer we
-pass the 'title' and 'subtitle' for the plot.  To the basic plot 'g', geom\_jitter is added, that
-plots cars from the same manufactures with the same color (col=manufactures) and the size of the
-car point equal its high way consumption (size = hwy).  Finally, a last layer is plotter containing
-a linear regression line (method = "lm") for every manufacturer.
-
-
-```r
-# load package and data
-library(ggplot2)
-data(mpg, package="ggplot2")
-
-mpg_select <- mpg[mpg$manufacturer %in% c("audi", "ford", "honda", "hyundai"), ]
-
-# Scatterplot
-theme_set(theme_bw())  # pre-set the bw theme.
-g <- ggplot(mpg_select, aes(displ, cty)) + 
-  labs(subtitle="mpg: Displacement vs City Mileage",
-       title="Bubble chart")
-
-g + geom_jitter(aes(col=manufacturer, size=hwy)) + 
-  geom_smooth(aes(col=manufacturer), method="lm", se=F)
-```
-
-![](/home/rbotafogo/desenv/galaaz/blogs/gknit/gknit_files/figure-html/bubble-1.png)<!-- -->
-
-### Ruby chunks
-
-
-Including a Ruby chunk is just as easy as including an R chunk in the document: just 
-change the name of the engine to 'ruby'.  It is also possible to pass chunk options
-to the Ruby engine; however, this version does not accept all the options that are
-available to R chunks.  Future versions will add those options.
-
-````
-```{ruby first_ruby_chunk}
-```
-````
-
-In this example, the ruby chunk is called 'first_ruby_chunk'.  One important 
-aspect of chunk labels is that they cannot be duplicated.  If a chunk label is 
-duplicated, gKnit will stop with an error.
-
-In the following chunk, variable 'a', 'b' and 'c' are standard Ruby variables 
-and 'vec' and 'vec2' are two vectors created  by calling the 'c' method on the 
-R module.
-
-In Galaaz, the R module allows us to access R functions transparently.  The 'c' 
-function in R, is a function that concatenates its arguments making a vector.
-
-It 
-should be clear that there is no requirement in gknit to call or use any R 
-functions.  gKnit will knit standard Ruby code, or even general text without 
-any code.
-
-
-```ruby
-a = [1, 2, 3]
-b = "US$ 250.000"
-c = "The 'outputs' function"
-
-vec = R.c(1, 2, 3)
-vec2 = R.c(10, 20, 30)
-```
-
-In the next block, variables 'a', 'vec' and 'vec2' are used and printed.
-
-
-```ruby
-puts a
-puts vec * vec2
-```
-
-```
-## 1
-## 2
-## 3
-## [1] 10 40 90
-```
-
-Note that 'a' is a standard Ruby Array and 'vec' and 'vec2' are vectors that behave accordingly,
-where multiplication works as expected.
-
-
-### Accessing R from Ruby
-
-One of the nice aspects of Galaaz on GraalVM, is that variables and functions defined in R, can
-be easily accessed from Ruby.  This next chunk, reads data from R and uses the 'reduce_sum'
-function defined previously.  To access an R variable from Ruby the '~' function should be
-applied to the Ruby symbol representing the R variable.  Since the R variable is called 'r_vec',
-in Ruby, the symbol to acess it is ':r_vec' and thus '~:r_vec' retrieves the value of the
-variable.
-
-
-```ruby
-puts ~:r_vec
-```
-
-```
-## [1] 1 2 3 4 5
-```
-
-In order to call an R function, the 'R.' module is used as follows
-
-
-```ruby
-puts R.reduce_sum(~:r_vec)
-```
-
-```
-## [1] 15
-```
-
-### Ruby Plotting
-
-We have seen an example of plotting with R.  Plotting with Ruby does not require
-anything different from plotting with R.  In the following example, we plot a 
-diverging bar graph using the 'mtcars' dataframe from R.  This data was extracted 
-from the 1974 Motor Trend US magazine, and comprises fuel consumption and 10 aspects 
-of automobile design and performance for 32 automobiles (1973–74 models).  The 
-ten aspects are:
-
-* mpg:	Miles/(US) gallon
-* cyl:	Number of cylinders
-* disp:	Displacement (cu.in.)
-* hp:	Gross horsepower
-* drat:	Rear axle ratio
-* wt:	Weight (1000 lbs)
-* qsec:	1/4 mile time
-* vs:	Engine (0 = V-shaped, 1 = straight)
-* am:	Transmission (0 = automatic, 1 = manual)
-* gear:	Number of forward gears
-* carb:	Number of carburetors
-
-
-
-```ruby
-# copy the R variable :mtcars to the Ruby mtcars variable
-mtcars = ~:mtcars
-
-# create a new column 'car_name' to store the car names so that it can be
-# used for plotting. The 'rownames' of the data frame cannot be used as
-# data for plotting
-mtcars.car_name = R.rownames(:mtcars)
-
-# compute normalized mpg and add it to a new column called mpg_z
-# Note that the mean value for mpg can be obtained by calling the 'mean'
-# function on the vector 'mtcars.mpg'.  The same with the standard
-# deviation 'sd'.  The vector is then rounded to two digits with 'round 2'
-mtcars.mpg_z = ((mtcars.mpg - mtcars.mpg.mean)/mtcars.mpg.sd).round 2
-
-# create a new column 'mpg_type'. Function 'ifelse' is a vectorized function
-# that looks at every element of the mpg_z vector and if the value is below
-# 0, returns 'below', otherwise returns 'above'
-mtcars.mpg_type = (mtcars.mpg_z < 0).ifelse("below", "above")
-
-# order the mtcar data set by the mpg_z vector from smaler to larger values
-mtcars = mtcars[mtcars.mpg_z.order, :all]
-
-# convert the car_name column to a factor to retain sorted order in plot
-mtcars.car_name = mtcars.car_name.factor levels: mtcars.car_name
-
-# let's look at the first records of the final data frame
-puts mtcars.head
-```
-
-```
-##                      mpg cyl disp  hp drat    wt  qsec vs am gear carb
-## Cadillac Fleetwood  10.4   8  472 205 2.93 5.250 17.98  0  0    3    4
-## Lincoln Continental 10.4   8  460 215 3.00 5.424 17.82  0  0    3    4
-## Camaro Z28          13.3   8  350 245 3.73 3.840 15.41  0  0    3    4
-## Duster 360          14.3   8  360 245 3.21 3.570 15.84  0  0    3    4
-## Chrysler Imperial   14.7   8  440 230 3.23 5.345 17.42  0  0    3    4
-## Maserati Bora       15.0   8  301 335 3.54 3.570 14.60  0  1    5    8
-##                                car_name mpg_z mpg_type
-## Cadillac Fleetwood   Cadillac Fleetwood -1.61    below
-## Lincoln Continental Lincoln Continental -1.61    below
-## Camaro Z28                   Camaro Z28 -1.13    below
-## Duster 360                   Duster 360 -0.96    below
-## Chrysler Imperial     Chrysler Imperial -0.89    below
-## Maserati Bora             Maserati Bora -0.84    below
-```
-
-
-```ruby
-require 'ggplot'
-
-puts mtcars.ggplot(E.aes(x: :car_name, y: :mpg_z, label: :mpg_z)) +
-     R.geom_bar(E.aes(fill: :mpg_type), stat: 'identity', width: 0.5) +
-     R.scale_fill_manual(name: 'Mileage',
-                         labels: R.c('Above Average', 'Below Average'),
-                         values: R.c('above': '#00ba38', 'below': '#f8766d')) +
-     R.labs(subtitle: "Normalised mileage from 'mtcars'",
-            title: "Diverging Bars") + 
-     R.coord_flip
-```
-
-
-![](/home/rbotafogo/desenv/galaaz/blogs/gknit/gknit_files/figure-html/diverging_bar.png)<!-- -->
-
-### Inline Ruby code
-
-When using a Ruby chunk, the code and the output are formatted in blocks as seen above.
-This formatting is not always desired.  Sometimes, we want to have the results of the
-Ruby evaluation included in the middle of a phrase. gKnit allows adding inline Ruby code 
-with the 'rb' engine.  The following chunk specification will 
-create and inline Ruby text:
-
-````
-This is some text with inline Ruby accessing variable 'b' which has value:
-```{rb puts b}
-```
-and is followed by some other text!
-````
-
-<div style="margin-bottom:30px;">
-</div>
-
-This is some text with inline Ruby accessing variable 'b' which has value:
-US$ 250.000
-and is followed by some other text!
-
-<div style="margin-bottom:30px;">
-</div>
-
-Note that it is important not to add any new line before of after the code
-block if we want everything to be in only one line, resulting in the following sentence 
-with inline Ruby code.
-
-
-### The 'outputs' function
-
-He have previously used the standard 'puts' method in Ruby chunks in order produce
-output.  The result of a 'puts', as seen in all previous chunks that use it,  is formatted 
-inside a white box that 
-follows the code block. Many times however, we would like to do some processing in the 
-Ruby chunk and have the result of this processing generate and output that is 
-"included" in the document as if we had typed it in __R markdown__ document.
-
-For example, suppose we want to create a new heading in our document, but the heading 
-phrase is the result of some code processing: maybe it's the first line of a file we are
-going to read.  Method 'outputs' adds its output as if typed in the __R markdown__ document. 
-
-Take now a look at variable 'c' (it was defined in a previous block above) as 
-'c = "The 'outputs' function".  "The 'outputs' function" is actually the name of this
-section and it was created using the 'outputs' function inside a Ruby chunk.
-
-The ruby chunk to generate this heading is:
-
-````
-```{ruby heading}
-outputs "### #{c}"
-```
-````
-
-The three '###' is the way we add a Heading 3 in __R markdown__.
-
-
-### HTML Output from Ruby Chunks
-
-We've just seen the use of method 'outputs' to add text to the the __R markdown__ 
-document.  This technique can also be used to add HTML code to the document. In 
-__R markdown__, any html code typed directly in the document will be properly rendered.  
-Here, for instance, is a table definition in HTML and its output in the document:
-
-```
-<table style="width:100%">
-  <tr>
-    <th>Firstname</th>
-    <th>Lastname</th> 
-    <th>Age</th>
-  </tr>
-  <tr>
-    <td>Jill</td>
-    <td>Smith</td> 
-    <td>50</td>
-  </tr>
-  <tr>
-    <td>Eve</td>
-    <td>Jackson</td> 
-    <td>94</td>
-  </tr>
-</table>
-```
-<div style="margin-bottom:30px;">
-</div>
-
-<table style="width:100%">
-  <tr>
-    <th>Firstname</th>
-    <th>Lastname</th> 
-    <th>Age</th>
-  </tr>
-  <tr>
-    <td>Jill</td>
-    <td>Smith</td> 
-    <td>50</td>
-  </tr>
-  <tr>
-    <td>Eve</td>
-    <td>Jackson</td> 
-    <td>94</td>
-  </tr>
-</table>
-
-<div style="margin-bottom:30px;">
-</div>
-
-But manually creating HTML output is not always easy or desirable, specially
-if we intend the document to be rendered in other formats, for example, as Latex.
-Also, The above 
-table looks ugly.  The 'kableExtra' library is a great library for 
-creating beautiful tables. Take a look at https://cran.r-project.org/web/packages/kableExtra/vignettes/awesome_table_in_html.html
-
-In the next chunk, we output the 'mtcars' dataframe from R in a nicely formatted 
-table.  Note that we retrieve the mtcars dataframe by using '~:mtcars'.
-
-
-```ruby
-R.install_and_loads('kableExtra')
-outputs (~:mtcars).kable.kable_styling
-```
-
-<table class="table" style="margin-left: auto; margin-right: auto;">
- <thead>
-  <tr>
-   <th style="text-align:left;">   </th>
-   <th style="text-align:right;"> mpg </th>
-   <th style="text-align:right;"> cyl </th>
-   <th style="text-align:right;"> disp </th>
-   <th style="text-align:right;"> hp </th>
-   <th style="text-align:right;"> drat </th>
-   <th style="text-align:right;"> wt </th>
-   <th style="text-align:right;"> qsec </th>
-   <th style="text-align:right;"> vs </th>
-   <th style="text-align:right;"> am </th>
-   <th style="text-align:right;"> gear </th>
-   <th style="text-align:right;"> carb </th>
-  </tr>
- </thead>
-<tbody>
-  <tr>
-   <td style="text-align:left;"> Mazda RX4 </td>
-   <td style="text-align:right;"> 21.0 </td>
-   <td style="text-align:right;"> 6 </td>
-   <td style="text-align:right;"> 160.0 </td>
-   <td style="text-align:right;"> 110 </td>
-   <td style="text-align:right;"> 3.90 </td>
-   <td style="text-align:right;"> 2.620 </td>
-   <td style="text-align:right;"> 16.46 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Mazda RX4 Wag </td>
-   <td style="text-align:right;"> 21.0 </td>
-   <td style="text-align:right;"> 6 </td>
-   <td style="text-align:right;"> 160.0 </td>
-   <td style="text-align:right;"> 110 </td>
-   <td style="text-align:right;"> 3.90 </td>
-   <td style="text-align:right;"> 2.875 </td>
-   <td style="text-align:right;"> 17.02 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Datsun 710 </td>
-   <td style="text-align:right;"> 22.8 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 108.0 </td>
-   <td style="text-align:right;"> 93 </td>
-   <td style="text-align:right;"> 3.85 </td>
-   <td style="text-align:right;"> 2.320 </td>
-   <td style="text-align:right;"> 18.61 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 1 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Hornet 4 Drive </td>
-   <td style="text-align:right;"> 21.4 </td>
-   <td style="text-align:right;"> 6 </td>
-   <td style="text-align:right;"> 258.0 </td>
-   <td style="text-align:right;"> 110 </td>
-   <td style="text-align:right;"> 3.08 </td>
-   <td style="text-align:right;"> 3.215 </td>
-   <td style="text-align:right;"> 19.44 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 1 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Hornet Sportabout </td>
-   <td style="text-align:right;"> 18.7 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 360.0 </td>
-   <td style="text-align:right;"> 175 </td>
-   <td style="text-align:right;"> 3.15 </td>
-   <td style="text-align:right;"> 3.440 </td>
-   <td style="text-align:right;"> 17.02 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Valiant </td>
-   <td style="text-align:right;"> 18.1 </td>
-   <td style="text-align:right;"> 6 </td>
-   <td style="text-align:right;"> 225.0 </td>
-   <td style="text-align:right;"> 105 </td>
-   <td style="text-align:right;"> 2.76 </td>
-   <td style="text-align:right;"> 3.460 </td>
-   <td style="text-align:right;"> 20.22 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 1 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Duster 360 </td>
-   <td style="text-align:right;"> 14.3 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 360.0 </td>
-   <td style="text-align:right;"> 245 </td>
-   <td style="text-align:right;"> 3.21 </td>
-   <td style="text-align:right;"> 3.570 </td>
-   <td style="text-align:right;"> 15.84 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Merc 240D </td>
-   <td style="text-align:right;"> 24.4 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 146.7 </td>
-   <td style="text-align:right;"> 62 </td>
-   <td style="text-align:right;"> 3.69 </td>
-   <td style="text-align:right;"> 3.190 </td>
-   <td style="text-align:right;"> 20.00 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Merc 230 </td>
-   <td style="text-align:right;"> 22.8 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 140.8 </td>
-   <td style="text-align:right;"> 95 </td>
-   <td style="text-align:right;"> 3.92 </td>
-   <td style="text-align:right;"> 3.150 </td>
-   <td style="text-align:right;"> 22.90 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Merc 280 </td>
-   <td style="text-align:right;"> 19.2 </td>
-   <td style="text-align:right;"> 6 </td>
-   <td style="text-align:right;"> 167.6 </td>
-   <td style="text-align:right;"> 123 </td>
-   <td style="text-align:right;"> 3.92 </td>
-   <td style="text-align:right;"> 3.440 </td>
-   <td style="text-align:right;"> 18.30 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Merc 280C </td>
-   <td style="text-align:right;"> 17.8 </td>
-   <td style="text-align:right;"> 6 </td>
-   <td style="text-align:right;"> 167.6 </td>
-   <td style="text-align:right;"> 123 </td>
-   <td style="text-align:right;"> 3.92 </td>
-   <td style="text-align:right;"> 3.440 </td>
-   <td style="text-align:right;"> 18.90 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Merc 450SE </td>
-   <td style="text-align:right;"> 16.4 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 275.8 </td>
-   <td style="text-align:right;"> 180 </td>
-   <td style="text-align:right;"> 3.07 </td>
-   <td style="text-align:right;"> 4.070 </td>
-   <td style="text-align:right;"> 17.40 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 3 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Merc 450SL </td>
-   <td style="text-align:right;"> 17.3 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 275.8 </td>
-   <td style="text-align:right;"> 180 </td>
-   <td style="text-align:right;"> 3.07 </td>
-   <td style="text-align:right;"> 3.730 </td>
-   <td style="text-align:right;"> 17.60 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 3 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Merc 450SLC </td>
-   <td style="text-align:right;"> 15.2 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 275.8 </td>
-   <td style="text-align:right;"> 180 </td>
-   <td style="text-align:right;"> 3.07 </td>
-   <td style="text-align:right;"> 3.780 </td>
-   <td style="text-align:right;"> 18.00 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 3 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Cadillac Fleetwood </td>
-   <td style="text-align:right;"> 10.4 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 472.0 </td>
-   <td style="text-align:right;"> 205 </td>
-   <td style="text-align:right;"> 2.93 </td>
-   <td style="text-align:right;"> 5.250 </td>
-   <td style="text-align:right;"> 17.98 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Lincoln Continental </td>
-   <td style="text-align:right;"> 10.4 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 460.0 </td>
-   <td style="text-align:right;"> 215 </td>
-   <td style="text-align:right;"> 3.00 </td>
-   <td style="text-align:right;"> 5.424 </td>
-   <td style="text-align:right;"> 17.82 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Chrysler Imperial </td>
-   <td style="text-align:right;"> 14.7 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 440.0 </td>
-   <td style="text-align:right;"> 230 </td>
-   <td style="text-align:right;"> 3.23 </td>
-   <td style="text-align:right;"> 5.345 </td>
-   <td style="text-align:right;"> 17.42 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Fiat 128 </td>
-   <td style="text-align:right;"> 32.4 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 78.7 </td>
-   <td style="text-align:right;"> 66 </td>
-   <td style="text-align:right;"> 4.08 </td>
-   <td style="text-align:right;"> 2.200 </td>
-   <td style="text-align:right;"> 19.47 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 1 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Honda Civic </td>
-   <td style="text-align:right;"> 30.4 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 75.7 </td>
-   <td style="text-align:right;"> 52 </td>
-   <td style="text-align:right;"> 4.93 </td>
-   <td style="text-align:right;"> 1.615 </td>
-   <td style="text-align:right;"> 18.52 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Toyota Corolla </td>
-   <td style="text-align:right;"> 33.9 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 71.1 </td>
-   <td style="text-align:right;"> 65 </td>
-   <td style="text-align:right;"> 4.22 </td>
-   <td style="text-align:right;"> 1.835 </td>
-   <td style="text-align:right;"> 19.90 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 1 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Toyota Corona </td>
-   <td style="text-align:right;"> 21.5 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 120.1 </td>
-   <td style="text-align:right;"> 97 </td>
-   <td style="text-align:right;"> 3.70 </td>
-   <td style="text-align:right;"> 2.465 </td>
-   <td style="text-align:right;"> 20.01 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 1 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Dodge Challenger </td>
-   <td style="text-align:right;"> 15.5 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 318.0 </td>
-   <td style="text-align:right;"> 150 </td>
-   <td style="text-align:right;"> 2.76 </td>
-   <td style="text-align:right;"> 3.520 </td>
-   <td style="text-align:right;"> 16.87 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> AMC Javelin </td>
-   <td style="text-align:right;"> 15.2 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 304.0 </td>
-   <td style="text-align:right;"> 150 </td>
-   <td style="text-align:right;"> 3.15 </td>
-   <td style="text-align:right;"> 3.435 </td>
-   <td style="text-align:right;"> 17.30 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Camaro Z28 </td>
-   <td style="text-align:right;"> 13.3 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 350.0 </td>
-   <td style="text-align:right;"> 245 </td>
-   <td style="text-align:right;"> 3.73 </td>
-   <td style="text-align:right;"> 3.840 </td>
-   <td style="text-align:right;"> 15.41 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Pontiac Firebird </td>
-   <td style="text-align:right;"> 19.2 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 400.0 </td>
-   <td style="text-align:right;"> 175 </td>
-   <td style="text-align:right;"> 3.08 </td>
-   <td style="text-align:right;"> 3.845 </td>
-   <td style="text-align:right;"> 17.05 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 3 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Fiat X1-9 </td>
-   <td style="text-align:right;"> 27.3 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 79.0 </td>
-   <td style="text-align:right;"> 66 </td>
-   <td style="text-align:right;"> 4.08 </td>
-   <td style="text-align:right;"> 1.935 </td>
-   <td style="text-align:right;"> 18.90 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 1 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Porsche 914-2 </td>
-   <td style="text-align:right;"> 26.0 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 120.3 </td>
-   <td style="text-align:right;"> 91 </td>
-   <td style="text-align:right;"> 4.43 </td>
-   <td style="text-align:right;"> 2.140 </td>
-   <td style="text-align:right;"> 16.70 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 5 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Lotus Europa </td>
-   <td style="text-align:right;"> 30.4 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 95.1 </td>
-   <td style="text-align:right;"> 113 </td>
-   <td style="text-align:right;"> 3.77 </td>
-   <td style="text-align:right;"> 1.513 </td>
-   <td style="text-align:right;"> 16.90 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 5 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Ford Pantera L </td>
-   <td style="text-align:right;"> 15.8 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 351.0 </td>
-   <td style="text-align:right;"> 264 </td>
-   <td style="text-align:right;"> 4.22 </td>
-   <td style="text-align:right;"> 3.170 </td>
-   <td style="text-align:right;"> 14.50 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 5 </td>
-   <td style="text-align:right;"> 4 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Ferrari Dino </td>
-   <td style="text-align:right;"> 19.7 </td>
-   <td style="text-align:right;"> 6 </td>
-   <td style="text-align:right;"> 145.0 </td>
-   <td style="text-align:right;"> 175 </td>
-   <td style="text-align:right;"> 3.62 </td>
-   <td style="text-align:right;"> 2.770 </td>
-   <td style="text-align:right;"> 15.50 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 5 </td>
-   <td style="text-align:right;"> 6 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Maserati Bora </td>
-   <td style="text-align:right;"> 15.0 </td>
-   <td style="text-align:right;"> 8 </td>
-   <td style="text-align:right;"> 301.0 </td>
-   <td style="text-align:right;"> 335 </td>
-   <td style="text-align:right;"> 3.54 </td>
-   <td style="text-align:right;"> 3.570 </td>
-   <td style="text-align:right;"> 14.60 </td>
-   <td style="text-align:right;"> 0 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 5 </td>
-   <td style="text-align:right;"> 8 </td>
-  </tr>
-  <tr>
-   <td style="text-align:left;"> Volvo 142E </td>
-   <td style="text-align:right;"> 21.4 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 121.0 </td>
-   <td style="text-align:right;"> 109 </td>
-   <td style="text-align:right;"> 4.11 </td>
-   <td style="text-align:right;"> 2.780 </td>
-   <td style="text-align:right;"> 18.60 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 1 </td>
-   <td style="text-align:right;"> 4 </td>
-   <td style="text-align:right;"> 2 </td>
-  </tr>
-</tbody>
-</table>
-
-### Including Ruby files in a chunk
-
-R is a language that was created to be easy and fast for statisticians to use.  As far
-as I know, it was not a
-language to be used for developing large systems.  Of course, there are large systems and
-libraries in R, but the focus of the language is for developing statistical models and
-distribute that to peers.
-
-Ruby on the other hand, is a language for large software development.  Systems written in
-Ruby will have dozens, hundreds or even thousands of files.  To document a 
-large system with literate programming, we cannot expect the developer to add all the 
-files in a single '.Rmd' file.  gKnit provides the 'include' chunk engine to include 
-a Ruby file as if it had being typed in the '.Rmd' file.
-
-To include a file, the following chunk should be created, where <filename> is the name of
-the file to be included and where the extension, if it is '.rb', does not need to be added.
-If the 'relative' option is not included, then it is treated as TRUE.  When 'relative' is
-true, ruby's 'require\_relative' semantics is used to load the file, when false, Ruby's 
-\$LOAD_PATH is searched to find the file and it is 'require'd.
-
-````
-```{include <filename>, relative = <TRUE/FALSE>}
-```
-````
-
-Bellow we include file 'model.rb', which is in the same directory of this blog.  
-This code uses R 'caret' package to split a dataset in a train and test sets.
-The 'caret' package is a very important a useful package for doing Data Analysis,
-it has hundreds of functions for all steps of the Data Analysis workflow.  To
-use 'caret' just to split a dataset is like using the proverbial cannon to 
-kill the fly.  We use it here only to show that integrating Ruby and R and 
-using even a very complex package as 'caret' is trivial with Galaaz.
-
-A word of advice: the 'caret' package has lots of dependencies and installing
-it in a Linux system is a time consuming operation.  Method 'R.install_and_loads'
-will install the package if it is not already installed and can take a while.
-
-````
-```{include model}
-```
-````
-
-
-```include
-require 'galaaz'
-
-# Loads the R 'caret' package.  If not present, installs it 
-R.install_and_loads 'caret'
-
-class Model
-  
-  attr_reader :data
-  attr_reader :test
-  attr_reader :train
-
-  #==========================================================
-  #
-  #==========================================================
-  
-  def initialize(data, percent_train:, seed: 123)
-
-    R.set__seed(seed)
-    @data = data
-    @percent_train = percent_train
-    @seed = seed
-    
-  end
-
-  #==========================================================
-  #
-  #==========================================================
-
-  def partition(field)
-
-    train_index =
-      R.createDataPartition(@data.send(field), p: @percet_train,
-                            list: false, times: 1)
-    @train = @data[train_index, :all]
-    @test = @data[-train_index, :all]
-    
-  end
-  
-end
-
-```
-
-
-```ruby
-mtcars = ~:mtcars
-model = Model.new(mtcars, percent_train: 0.8)
-model.partition(:mpg)
-puts model.train.head
-puts model.test.head
-```
-
-```
-##                    mpg cyl  disp  hp drat    wt  qsec vs am gear carb
-## Datsun 710        22.8   4 108.0  93 3.85 2.320 18.61  1  1    4    1
-## Hornet 4 Drive    21.4   6 258.0 110 3.08 3.215 19.44  1  0    3    1
-## Hornet Sportabout 18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2
-## Merc 240D         24.4   4 146.7  62 3.69 3.190 20.00  1  0    4    2
-## Merc 280          19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4
-## Merc 280C         17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4
-##                mpg cyl  disp  hp drat    wt  qsec vs am gear carb
-## Mazda RX4     21.0   6 160.0 110 3.90 2.620 16.46  0  1    4    4
-## Mazda RX4 Wag 21.0   6 160.0 110 3.90 2.875 17.02  0  1    4    4
-## Valiant       18.1   6 225.0 105 2.76 3.460 20.22  1  0    3    1
-## Duster 360    14.3   8 360.0 245 3.21 3.570 15.84  0  0    3    4
-## Merc 230      22.8   4 140.8  95 3.92 3.150 22.90  1  0    4    2
-## Merc 450SE    16.4   8 275.8 180 3.07 4.070 17.40  0  0    3    3
-```
-
-### Documenting Gems
-
-gKnit also allows developers to document and load files that are not in the same directory
-of the '.Rmd' file.
-
-Here is an example of loading the 'find.rb' file from TruffleRuby. In this example, relative
-is set to FALSE, so Ruby will look for the file in its $LOAD\_PATH, and the user does not
-need to no it's directory.
-
-````
-```{include find, relative = FALSE}
-```
-````
-
-
-```include
-# frozen_string_literal: true
-#
-# find.rb: the Find module for processing all files under a given directory.
-#
-
-#
-# The +Find+ module supports the top-down traversal of a set of file paths.
-#
-# For example, to total the size of all files under your home directory,
-# ignoring anything in a "dot" directory (e.g. $HOME/.ssh):
-#
-#   require 'find'
-#
-#   total_size = 0
-#
-#   Find.find(ENV["HOME"]) do |path|
-#     if FileTest.directory?(path)
-#       if File.basename(path)[0] == ?.
-#         Find.prune       # Don't look any further into this directory.
-#       else
-#         next
-#       end
-#     else
-#       total_size += FileTest.size(path)
-#     end
-#   end
-#
-module Find
-
-  #
-  # Calls the associated block with the name of every file and directory listed
-  # as arguments, then recursively on their subdirectories, and so on.
-  #
-  # Returns an enumerator if no block is given.
-  #
-  # See the +Find+ module documentation for an example.
-  #
-  def find(*paths, ignore_error: true) # :yield: path
-    block_given? or return enum_for(__method__, *paths, ignore_error: ignore_error)
-
-    fs_encoding = Encoding.find("filesystem")
-
-    paths.collect!{|d| raise Errno::ENOENT, d unless File.exist?(d); d.dup}.each do |path|
-      path = path.to_path if path.respond_to? :to_path
-      enc = path.encoding == Encoding::US_ASCII ? fs_encoding : path.encoding
-      ps = [path]
-      while file = ps.shift
-        catch(:prune) do
-          yield file.dup.taint
-          begin
-            s = File.lstat(file)
-          rescue Errno::ENOENT, Errno::EACCES, Errno::ENOTDIR, Errno::ELOOP, Errno::ENAMETOOLONG
-            raise unless ignore_error
-            next
-          end
-          if s.directory? then
-            begin
-              fs = Dir.children(file, encoding: enc)
-            rescue Errno::ENOENT, Errno::EACCES, Errno::ENOTDIR, Errno::ELOOP, Errno::ENAMETOOLONG
-              raise unless ignore_error
-              next
-            end
-            fs.sort!
-            fs.reverse_each {|f|
-              f = File.join(file, f)
-              ps.unshift f.untaint
-            }
-          end
-        end
-      end
-    end
-    nil
-  end
-
-  #
-  # Skips the current file or directory, restarting the loop with the next
-  # entry. If the current file is a directory, that directory will not be
-  # recursively entered. Meaningful only within the block associated with
-  # Find::find.
-  #
-  # See the +Find+ module documentation for an example.
-  #
-  def prune
-    throw :prune
-  end
-
-  module_function :find, :prune
-end
-```
-
-## Converting to PDF
-
-One of the beauties of knitr is that the same input can be converted to many different outputs.
-One very useful format, is, of course, PDF.  In order to converted an __R markdown__ file to PDF
-it is necessary to have LaTeX installed on the system.  We will not explain here how to
-install LaTeX as there are plenty of documents on the web showing how to proceed.
-
-gKnit comes with a simple LaTeX style file for gknitting this blog as a PDF document.  Here is
-the Yaml header to generate this blog in PDF format instead of HTML:
-
-```
----
-title: "gKnit - Ruby and R Knitting with Galaaz in GraalVM"
-author: "Rodrigo Botafogo"
-tags: [Galaaz, Ruby, R, TruffleRuby, FastR, GraalVM, knitr, gknit]
-date: "29 October 2018"
-output:
-  pdf\_document:
-    includes:
-      in\_header: ["../../sty/galaaz.sty"]
-    number\_sections: yes
----
-```
-
-
-# Conclusion
-
-In order to do reproducible research, one of the main basic tools needed is a systhem that
-allows "literate programming" where text, code and possibly a set of files can be compiled
-onto a report that can be easily distributed to peers. Peers should be able to use this
-same set of files to rerun the compilation by their own obtaining the exact same original
-report.  gKnit is such a system for Ruby and R.  It uses __R Markdown__ to integrate
-text and code chunks, where code chunks can either be part of the __R Markdwon__ file or
-be imported from files in the system.  Ideally, in reproducible research, all the files
-needed to rebuild a report should be easilly packed together (in the same zipped directory)
-and distributed to peers for reexecution.
-
-One of the promises of Oracle's GraalVM is that users/developers will be able to use the best tool
-for their task at hand, independently of the programming language the tool was written on.
-We developed and implemented Galaaz atop the GraalVM and Truffle interop messages and
-the time and effort to wrap Ruby over R - Galaaz - or to
-wrap Knitr with gKnit was a fraction of a fraction of a fraction (one man effort for a couple
-of hours a day, for approximately six months) of the time require to
-implement the original tools.  Trying to reimplement all R packages in Ruby would require the
-same effort it is taking Python to implement NumPy, Pandas and all supporting libraries and it
-is unlikely that this effort would ever be done.  GraalVM has allowed Ruby to profit "almost
-for free" from this huge set of libraries and tools that make R one of the most used
-languages for data analysis and machine learning.
-
-More interesting than wrapping the R libraries with Ruby, is that Ruby adds
-value to R, by allowing developers to use powerful and modern constructs for code reuse that
-are not the strong points of R.  As shown in this blog, R and Ruby can easily communicate
-and R can be structured in classes and modules in a way that greatly expands its power and
-readability.
-
-# Installing gKnit
-
-## Prerequisites
-
-* GraalVM (>= rc8)
-* TruffleRuby
-* FastR
-
-The following R packages will be automatically installed when necessary, but could be installed prior
-to using gKnit if desired:
-
-* ggplot2
-* gridExtra
-* knitr
-
-Installation of R packages requires a development environment and can be time consuming.  In Linux,
-the gnu compiler and tools should be enough.  I am not sure what is needed on the Mac.
-
-## Preparation
-
-* gem install galaaz
-
-## Usage
-
-* gknit \<filename\>
-
-# References
-