galaaz 0.4.2 → 0.4.5

data/sty/galaaz.sty

@@ -0,0 +1,71 @@
+% usar portugues do Brasil
+% \usepackage[brazilian]{babel}
+\usepackage[utf8]{inputenc}
+
+\usepackage{geometry}
+\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
+% style 'fancy' adds the section name on the header
+% and the page number on the footer
+\pagestyle{fancy}
+
+% style 'fancyhf' leaves header and footer empty
+%\fancyhf{}
+
+% sets the left head element to \rightmark, which contains the
+% current section (\leftmark is the current chapter)
+%\fancyhead[L]{\rightmark} .
+
+% sets the right head element to the page number.
+% \fancyhead[R]{\thepage}
+
+% lets the head rule disappear.
+% \renewcommand{\headrulewidth}{0pt}
+% Possible selectors for the optional argument of \fancyhead/\fancyfoot
+% are L (left), C (center) or R (right) for the position of the element
+% and E (even) or O (odd) to distinguish even and odd pages. If you omit
+% E/O the element is set for all pages.
+
+% \usepackage{lipsum}
+
+% 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}}

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "galaaz"
-$version="0.4.2"
+$version="0.4.5"

metadata

@@ -1,29 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: galaaz
 version: !ruby/object:Gem::Version
-  version: 0.4.2
+  version: 0.4.5
 platform: ruby
 authors:
 - Rodrigo Botafogo
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-21 00:00:00.000000000 Z
+date: 2019-01-30 00:00:00.000000000 Z
 dependencies:
-- !ruby/object:Gem::Dependency
-  name: pry
-  prerelease: false
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.10'
-  type: :runtime
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.10'
 - !ruby/object:Gem::Dependency
   name: rspec
   prerelease: false
@@ -88,27 +74,25 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- LICENSE
 - README.md
 - Rakefile
 - bin/galaaz
 - bin/gknit
 - bin/gknit2
-- bin/gknit2~
 - bin/gstudio
 - bin/gstudio.rb
-- bin/ogk~
 - bin/prepareR.rb
-- bin/prepareR.rb~
 - bin/tmp.py
 - blogs/dev/dev.Rmd
-- blogs/dev/dev.Rmd~
 - blogs/dev/dev.html
 - blogs/dev/dev.md
 - blogs/dev/dev_files/figure-html/bubble-1.png
+- blogs/dev/dev_files/figure-html/diverging_bar.png
 - blogs/dev/model.rb
+- blogs/dplyr/dplyr.rb
 - blogs/galaaz_ggplot/galaaz_ggplot.Rmd
 - blogs/galaaz_ggplot/galaaz_ggplot.aux
-- blogs/galaaz_ggplot/galaaz_ggplot.dvi
 - blogs/galaaz_ggplot/galaaz_ggplot.html
 - blogs/galaaz_ggplot/galaaz_ggplot.md
 - blogs/galaaz_ggplot/galaaz_ggplot.out
@@ -118,11 +102,8 @@ files:
 - blogs/galaaz_ggplot/midwest.html
 - blogs/galaaz_ggplot/midwest.png
 - blogs/galaaz_ggplot/midwest_external_png
-- blogs/galaaz_ggplot/midwest_external_png~
 - blogs/galaaz_ggplot/scatter_plot.png
 - blogs/gknit/gknit.Rmd
-- blogs/gknit/gknit.Rmd~
-- blogs/gknit/gknit.Rnd~
 - blogs/gknit/gknit.html
 - blogs/gknit/gknit.md
 - blogs/gknit/gknit.pdf
@@ -130,7 +111,11 @@ files:
 - blogs/gknit/gknit_files/figure-html/bubble-1.png
 - blogs/gknit/gknit_files/figure-html/diverging_bar.png
 - blogs/gknit/model.rb
-- blogs/gknit/model.rb~
+- blogs/oh_my/not_so.rb
+- blogs/oh_my/oh_my.Rmd
+- blogs/oh_my/oh_my.html
+- blogs/oh_my/oh_my.md
+- blogs/oh_my/old.Rmd
 - blogs/ruby_plot/figures/dose_len.png
 - blogs/ruby_plot/figures/facet_by_delivery.png
 - blogs/ruby_plot/figures/facet_by_dose.png
@@ -143,29 +128,38 @@ files:
 - blogs/ruby_plot/figures/final_violin_plot.png
 - blogs/ruby_plot/figures/violin_with_jitter.png
 - blogs/ruby_plot/ruby_plot.Rmd
-- blogs/ruby_plot/ruby_plot.Rmd~
+- blogs/ruby_plot/ruby_plot.Rmd_external_figs
 - blogs/ruby_plot/ruby_plot.html
 - blogs/ruby_plot/ruby_plot.md
 - blogs/ruby_plot/ruby_plot.pdf
 - blogs/ruby_plot/ruby_plot.tex
+- blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color2.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_decorations.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.svg
+- blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.svg
 - examples/50Plots_MasterList/Images/midwest-scatterplot.PNG
 - examples/50Plots_MasterList/ScatterPlot.rb
 - examples/50Plots_MasterList/scatter_plot.rb
 - examples/R/calc.R
 - examples/R/java_interop.R
-- examples/islr/Figure.jpg
 - examples/islr/all.rb
 - examples/islr/ch2.spec.rb
 - examples/islr/ch3.spec.rb
 - examples/islr/ch3_boston.rb
 - examples/islr/ch3_multiple_regression.rb
 - examples/islr/ch6.spec.rb
+- examples/islr/x_y_rnorm.jpg
 - examples/misc/baseball.csv
 - examples/misc/ggplot.rb
 - examples/misc/moneyball.rb
-- examples/misc/moneyball.rb~
 - examples/misc/subsetting.rb
-- examples/misc/subsetting.rb~
 - examples/paper/paper.rb
 - examples/sthda_ggplot/README.md
 - examples/sthda_ggplot/all.rb
@@ -197,18 +191,15 @@ files:
 - examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb
 - examples/sthda_ggplot/two_variables_error/geom_crossbar.rb
 - lib/R/eng_ruby.R
-- lib/R/eng_ruby.R~
-- lib/R_interface/capture_plot.rb~
-- lib/R_interface/expression.rb
 - lib/R_interface/r.rb
-- lib/R_interface/r.rb~
+- lib/R_interface/r_libs.R
 - lib/R_interface/r_methods.rb
+- lib/R_interface/r_module_s.rb
 - lib/R_interface/rbinary_operators.rb
 - lib/R_interface/rclosure.rb
 - lib/R_interface/rdata_frame.rb
 - lib/R_interface/rdevices.R
 - lib/R_interface/rdevices.rb
-- lib/R_interface/rdevices.rb~
 - lib/R_interface/renvironment.rb
 - lib/R_interface/rexpression.rb
 - lib/R_interface/rindexed_object.rb
@@ -227,33 +218,32 @@ files:
 - lib/R_interface/rvector.rb
 - lib/galaaz.rb
 - lib/gknit.rb
-- lib/gknit.rb~
 - lib/gknit/knitr_engine.rb
-- lib/gknit/knitr_engine.rb~
 - lib/gknit/ruby_engine.rb
-- lib/gknit/ruby_engine.rb~
 - lib/util/exec_ruby.rb
 - lib/util/inline_file.rb
-- lib/util/inline_file.rb~
 - r_requires/ggplot.rb
 - r_requires/knitr.rb
-- r_requires/knitr.rb~
 - specs/all.rb
+- specs/figures/dose_len.png
 - specs/r_dataframe.spec.rb
+- specs/r_environment.spec.rb
 - specs/r_eval.spec.rb
+- specs/r_formula.spec.rb
 - specs/r_function.spec.rb
-- specs/r_language.spec.rb
 - specs/r_list.spec.rb
 - specs/r_list_apply.spec.rb
 - specs/r_matrix.spec.rb
+- specs/r_nse.spec.rb
 - specs/r_plots.spec.rb
-- specs/r_plots.spec.rb~
 - specs/r_vector_creation.spec.rb
 - specs/r_vector_functions.spec.rb
 - specs/r_vector_object.spec.rb
 - specs/r_vector_operators.spec.rb
 - specs/r_vector_subsetting.spec.rb
+- specs/ruby_expression.spec.rb
 - specs/tmp.rb
+- sty/galaaz.sty
 - version.rb
 homepage: http://github.com/rbotafogo/galaaz/wiki
 licenses:

data/bin/gknit2~

@@ -1,6 +0,0 @@
-#!/usr/bin/env ruby
-# coding: utf-8
-
-dir = Dir.pwd
-puts "Knitting #{dir}/#{ARGV[0]}"
-

data/bin/ogk~

@@ -1,4 +0,0 @@
-#!/bin/bash
-
-echo $PWD/$1
-Rscript --jvm --polyglot -e "library('knitr'); library('rmarkdown'); rmarkdown::render('$PWD/$1')"

data/bin/prepareR.rb~

@@ -1 +0,0 @@
-R.install_and_loads('knitr')

data/blogs/dev/dev.Rmd~

@@ -1,104 +0,0 @@
----
-title: "gKnit - Ruby and R Knitting with Galaaz in GraalVM"
-author: "Rodrigo Botafogo"
-tags: [Galaaz, Ruby, R, TruffleRuby, FastR, GraalVM, knitr]
-date: "19 October 2018"
-output:
-  html_document:
-    self_contained: true
-    keep_md: true
-  pdf_document:
-    includes:
-      in_header: ["../../sty/galaaz.sty"]
-    number_sections: yes
----
-
-```{r setup, echo=FALSE}
-
-```
-
-# Introduction
-
-
-```{r bubble}
-# load package and data
-library(ggplot2)
-data(mpg, package="ggplot2")
-# mpg <- read.csv("http://goo.gl/uEeRGu")
-
-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)
-```
-
-### Plotting
-
-```{ruby diverging_bar}
-require 'ggplot'
-
-R.theme_set R.theme_bw
-
-# Data Prep
-mtcars = ~:mtcars
-mtcars.car_name = R.rownames(:mtcars)
-# compute normalized mpg 
-mtcars.mpg_z = ((mtcars.mpg - mtcars.mpg.mean)/mtcars.mpg.sd).round 2
-mtcars.mpg_type = mtcars.mpg_z < 0 ? "below" : "above"
-mtcars = mtcars[mtcars.mpg_z.order, :all]
-# convert to factor to retain sorted order in plot
-mtcars.car_name = mtcars.car_name.factor levels: mtcars.car_name
-
-# Diverging Barcharts
-gg = 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()
-
-print gg
-```
-
-### Plotting with keep value
-
-```{ruby diverging_bar2, fig.keep = 1, fig.showtext = TRUE}
-require 'ggplot'
-
-R.theme_set R.theme_bw
-
-# Data Prep
-mtcars = ~:mtcars
-mtcars.car_name = R.rownames(:mtcars)
-# compute normalized mpg 
-mtcars.mpg_z = ((mtcars.mpg - mtcars.mpg.mean)/mtcars.mpg.sd).round 2
-mtcars.mpg_type = mtcars.mpg_z < 0 ? "below" : "above"
-mtcars = mtcars[mtcars.mpg_z.order, :all]
-# convert to factor to retain sorted order in plot
-mtcars.car_name = mtcars.car_name.factor levels: mtcars.car_name
-
-# Diverging Barcharts
-# R.png
-gg = 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()
-
-# print gg
-
-
-# R.dev__off
-# R.include_graphics("Rplot001.png")
-```

data/blogs/galaaz_ggplot/midwest_external_png~

@@ -1 +0,0 @@
-![Midwest Plot with 'glm' function and modified theme](https://user-images.githubusercontent.com/3999729/47120345-a903ae80-d244-11e8-9be3-a0db13cf51ab.PNG)

data/blogs/gknit/gknit.Rmd~

@@ -1,184 +0,0 @@
----
-title: "gKnit - Ruby and R Knitting with Galaaz"
-author: "Rodrigo Botafogo"
-tags: [Galaaz, Ruby, R, TruffleRuby, FastR, GraalVM, knitr]
-date: "19 October 2018"
-output:
-  html_document:
-    keep_md: true
----
-
-```{r setup, echo=FALSE}
-
-```
-
-# Introduction
-
-The idea of "literate programming" was first introduced by Donald Knuth in the 1980's.
-The main intention of this approach was to develop code and at the same time document it
-is as understandably as possible to humans.  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 envolved into the idea of reproducible research, in which
-all the data, information and documentation needed to reproduce a research is included in a
-single document that can be distributed to peers that can rerun the research obtaining
-the same results.
-
-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 hight quality PDF documents.  Those
-documents could include the code, the result of executing the code, graphics and text.  This
-contained the whole narrative to reproduce the research.  But Sweave had many problems and in
-2012, Knitr, developed by Yihui Xie from RStudio was released, solving many of the long lasting
-problems from Sweave and including in one single package many extensions and add-on packages that
-were necessary for Sweave.  With Knitr, R markdown was also developed, an extension the 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 in the same document.  However, other than R and Python (with
-the reticulate package), each chunk of code in any other language will execute in a new
-process, so memory and variables cannot be shared between chunks.
-
-In the Python community, the same effort to have code and text in an integrated environment
-started also on the first decade of 2000 and 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).  I am not sure if multiple languages can be used
-in a Jupyter notebook.
-
-# gKnitting a Document
-
-This document describes gKnit.  gKnit used Knitr and R markdown to knit a document in any of the
-available formats for R markdown.  The only difference between gKnit and normal Knitr documents
-is that gKnit runs atop of GraalVM, and Galaaz (an integration library between Ruby and R).
-Another blog post on Galaaz and its integration with ggplot2 can be found at: https://towardsdatascience.com/ruby-plotting-with-galaaz-an-example-of-tightly-coupling-ruby-and-r-in-graalvm-520b69e21021.  With
-Galaaz gKnit can knit documents in Ruby and R and both Ruby and R execute on the same process
-sharing variables and memory and variables, classes, etc. will be preserved between chunks of
-code.
-
-This is not a blog post on rmarkdown, and the intereste user is directed to https://bookdown.org/yihui/rmarkdown/ for detailed information on its capabilities and use.  Some of the features available for R code
-chunks are not yet available for Ruby code.  But we are working for removing any limitations.
-Here, we will describe quickly the main aspects of R markdown, so the user can start gKnit simple
-documents quickly.
-
-## The Yaml header
-
-An R markdown document should start with a Yaml header.  This document has the following header that
-when gKitted will generate and HTML document.
-
-```
----
-title: "gKnit - Ruby and R Knitting with Galaaz"
-author: "Rodrigo Botafogo"
-tags: [Galaaz, Ruby, R, TruffleRuby, FastR, GraalVM, knitr]
-date: "19 October 2018"
-output:
-  html_document:
-    keep_md: true
----
-```
-
-For more information on the options in the Yaml header, check https://bookdown.org/yihui/rmarkdown/html-document.html.
-
-## R Markdown formatting
-
-Document formating 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
-
-
-```
-
-Please, go to https://rmarkdown.rstudio.com/authoring_basics.html, for more R markdown formating.
-
-## Code Chunks
-
-### R chunks
-
-Running and executing Ruby and R code is actually what really interests us is this blog.  Doing so
-is very simple with code chunks.
-
-In order to add R code to a text, a code chunk is added with the following markup:
-
-So, for instance, here we create an R code chunk setting a variable to a vector:
-
-<code>```{r var_setting}
-
-r_vec <- c(1, 2, 3)
-
-</code>
-
-<code>```</code>
-
-```{r var_setting}
-r_vec <- c(1, 2, 3)
-```
-
-
-### Galaaz chunks
-
-```{galaaz split_data}
-
-$a = [1, 2, 3]
-```
-
-
-```{galaaz split2}
-
-puts $a
-
-```
-
-# Installing gKnit
-
-## Prerequisites
-
-* GraalVM (>= rc7)
-* 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]