galaaz 0.4.0

data/examples/islr/all.rb

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+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+require 'ggplot'
+
+# load ISLR and MASS Libraries
+R.install_and_loads('ISLR', 'MASS')
+
+require_relative 'ch2.spec'
+require_relative 'ch3.spec'
+require_relative 'ch6.spec'

data/examples/islr/ch2.spec.rb

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+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+require 'ggplot'
+
+context "ISLR" do
+
+  context "Chapter 2 - Basic Commands" do
+
+    it "Creates a vector" do
+      x = R.c(1, 3, 2, 5)
+      expect(x[1] == 1).to eq true
+      expect(x[3] == 2).to eq true
+      expect(x.length == 4).to eq true
+    end
+
+    it "should add vectors" do
+      x = R.c(1, 6, 2)
+      y = R.c(1, 4, 3)
+      expect(x.length == 3).to eq true
+      z = x + y
+      expect(z[1] == 2).to eq true
+      expect(z[3] == 5).to eq true
+    end
+
+    it "should create matrix by column" do
+      x = R.matrix(data: R.c(1, 2, 3, 4), nrow: 2, ncol: 2)
+      expect(x.rclass == "matrix").to eq true
+      expect(x[1, 1] == 1).to eq true
+      expect(x[1, 2] == 3).to eq true
+    end
+    
+    it "should create matrix by row" do
+      x = R.matrix(data: R.c(1, 2, 3, 4), nrow: 2, ncol: 2, byrow: true)
+      expect(x.rclass == "matrix").to eq true
+      expect(x[1, 1] == 1).to eq true
+      expect(x[1, 2] == 2).to eq true
+    end
+
+    it "should apply a function to all elements of the matrix: ex: sqrt" do
+      x = R.matrix(data: R.c(1, 2, 3, 4), nrow: 2, ncol: 2, byrow: true)
+      z = x.sqrt
+      expect(z[1, 2] == 1.73).to eq true
+      expect(z[2, 1] == 1.41).to eq true
+    end      
+
+    it "should generate a vector of random normal variables using rnorm" do
+      x = R.rnorm(50)
+      y = x + R.rnorm(50, mean: 40, sd: 0.1)
+      expect(R.cor(x, y) == 0.995).to eq true
+    end
+
+    it "should allow to setting the seed" do
+      R.set__seed(1303)
+      x = R.rnorm(50)
+      expect(x[1] == -1.1440).to eq true
+      expect(x[2] == 1.3421).to eq true
+      expect(x[4] == 0.5364).to eq true
+    end
+
+    it "should calculate the mean" do
+      R.set__seed(3)
+      y = R.rnorm(100)
+      expect(y.mean == 0.0110).to eq true
+    end
+
+    it "should calculate the variance" do
+      R.set__seed(3)
+      y = R.rnorm(100)
+      expect(y.var == 0.7329).to eq true
+      expect(y.var.sqrt == 0.8561).to eq true
+      expect(y.sd == 0.8561).to eq true
+    end
+
+  end
+
+  context "Chapter 2 - Graphics" do
+
+    it "should plot graphics" do
+      # To see the graphic we need to set the device to awt
+      R.awt
+      x = R.rnorm(100)
+      y = R.rnorm(100)
+      # plot commands do not work.  Need to work with ggplot or grid
+      # qplot uses a similar interface as plot
+      # Need to call print at the end of the plot
+      R.qplot(x, y,
+              xlab: "this is the x-axis",
+              ylab: "this is the y-axis",
+              main: "Plot of X vs Y")
+        .print
+      # the graphics dies when the script ends... waiting 3 secs
+      # so that the graphic can be seen
+      sleep(3)
+    end
+
+    # does not print anything... open issue!
+    it "should create a jpeg file" do
+      R.jpeg("/home/rbotafogo/desenv/galaaz/examples/islr/Figure.jpg")
+      x = R.rnorm(100)
+      y = R.rnorm(100)
+      plot = R.qplot(x, y, col: "green")
+      R.dev__off
+    end
+
+    it "creates sequences with 'seq'" do
+      x = R.seq(1, 10)
+      expect(x[5] == 5).to eq true
+      y = R.seq(-~:pi, ~:pi, length: 50)
+      expect(y[1] == -3.14159265).to eq true
+      expect(y[7] == -2.37222302).to eq true
+      expect(y[26] == 0.06411414).to eq true
+    end
+=begin
+    it "creates contour plots with ggplot" do
+      x = y = R.seq(-R.pi, R.pi, length: 50)
+      df = R.data__frame(x: x, y: y)
+      f = E.outer(:x, :y, lambda { |x, y| R.cos(y) / (1 + x**2) })
+      
+      R.awt
+      print R.ggplot(df, E.aes(:x, :y, z: f))      
+    end
+=end    
+  end
+
+
+end

data/examples/islr/ch3.spec.rb

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+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+require 'ggplot'
+
+require_relative 'ch3_boston'
+require_relative 'ch3_multiple_regression'

data/examples/islr/ch3_boston.rb

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+# coding: utf-8
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+require 'ggplot'
+
+R.install_and_loads('ISLR', 'MASS')
+
+# Simple linear regression from ISLR book.  Chapter 3 Lab
+
+# load boston data frame on variable boston
+boston = ~:Boston
+
+puts boston.names
+
+boston_lm = R.lm(+:medv =~ +:lstat, data: :Boston)
+# puts boston_lm.str
+# puts boston_lm.summary
+puts boston_lm.names
+puts boston_lm.coef
+puts boston_lm.confint
+conf = R.predict(boston_lm, R.data__frame(lstat: (R.c(5, 10, 15))), interval: "confidence")
+puts conf
+pred = R.predict(boston_lm, R.data__frame(lstat: (R.c(5, 10, 15))), interval: "prediction")
+puts pred
+
+R.awt
+
+puts R.qplot(boston.lstat, boston.medv, col: "red") +
+     R.geom_abline(intercept: boston_lm.coef[1],
+                   slope: boston_lm.coef[2],
+                   color: "blue",
+                   linetype: "dashed",
+                   size: 1.5)
+
+# uncomment if needed to pause while analysing graph. reads input from user 
+# a = gets.chomp
+
+# sleep two seconds so that the graph shows up
+sleep(2)
+R.grid__newpage
+
+puts R.qplot(R.predict(boston_lm), R.residuals(boston_lm))
+
+sleep(2)
+R.grid__newpage
+
+puts R.qplot(R.predict(boston_lm), R.rstudent(boston_lm))
+
+sleep(2)
+R.grid__newpage
+
+vals = R.hatvalues(boston_lm)
+# method size returns a Numeric... size is equivalent to 'length << 0'
+puts R.qplot((1..vals.size), vals)
+
+sleep(2)
+R.grid__newpage

data/examples/islr/ch3_multiple_regression.rb

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+# coding: utf-8
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+require 'ggplot'
+
+R.install_and_loads('ISLR', 'MASS')
+
+# Multiple linear regression from ISLR book.  Chapter 3 Lab, pg 113
+lm_fit = R.lm(+:medv =~ +:lstat + +:age, data: :Boston)
+puts lm_fit.summary
+
+#   Non-linear Transformations of the Predictors
+# Creating a more complex formula requires the use of R.formula
+lm_fit5 = R.lm(R.formula("medv ~ poly(lstat, 5)"), data: :Boston)
+puts lm_fit5.summary

data/examples/islr/ch6.spec.rb

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+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+
+R.install_and_loads('ISLR', 'MASS')
+
+context "ISLR" do
+
+  context "Chapter 6 - Subset Selection Methods - page 244" do
+
+    before(:each) do
+      @hitters = ~:Hitters
+    end
+    
+    it "Should access the names of the dataset" do
+      expect(@hitters.names[1] == "AtBat").to eq true
+      expect(@hitters.names[5] == "RBI").to eq true
+      expect(@hitters.names[11] == "CRuns").to eq true
+      expect(@hitters.dim == R.c(322, 20)).to eq true
+    end
+
+    it "Should count na's using 'R.sum'" do
+      expect(R.sum(@hitters.Salary.is__na) == 59).to eq true
+      expect(R.sum(@hitters.Salary.is__na)).to eq 59
+    end
+
+    it "Should count na's using Ruby Enumerable 'sum'" do
+      # method 'sum' is a Ruby Enumerable method.  To count na's we can loop through
+      # every element and check if they are na or not.  Note that the return os
+      # is__na is an R::Vector, so we need to 'pop' the value to a Ruby value in
+      # ordet to apply the '?' method
+      expect(@hitters.Salary.sum { |e| ((e.is__na == true).pop) ? 1 : 0 }).to eq 59
+    end
+
+    it "should remove missing values with na__omit" do
+      @hitters = @hitters.na__omit
+      expect(@hitters.dim == R.c(263, 20)).to eq true
+      expect(R.sum(@hitters.is__na)).to eq 0
+    end
+    
+  end
+
+end

data/examples/paper/paper.rb

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+# coding: utf-8
+
+require 'galaaz'
+require 'ggplot'
+
+faithful = ~:faithful
+
+# sp is the basic plot having in the x axis the eruption data and in y the waiting
+
+# Note that function 'aes' is called with E.aes. This prevents the execution of the aes function and
+
+# passes it “as-is” to function ggplot.  Note that :eruption and :waiting are column names for the
+
+# faithful data frame and do not exist in the scope of the aes method.  Calling aes with R.aes will fail.
+
+sp = faithful.ggplot(E.aes(x: :eruptions, y: :waiting)) 
+
+# create the output device for plotting
+
+R.awt
+
+# Use stat_density_2d with geom = "polygon"
+
+# Note that in order to call a method without any arguments we pass an empty argument list.
+
+# in Ruby, parenthesis are unnecessary, however in R, writing the function name without
+
+# parenthesis returns the actual function and not a call to it.
+
+print sp + R.geom_point + 
+      R.stat_density_2d(E.aes_string(fill: '..level..'),
+                        geom: "polygon")
+
+
+a = gets.chomp
+

data/examples/sthda_ggplot/README.md

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+The examples presented in this directory are extracted from:
+
+http://www.sthda.com/english/wiki/be-awesome-in-ggplot2-a-practical-guide-to-be-highly-effective-r-software-and-data-visualization
+
+# Basics
+
+ggplot2 is a powerful and a flexible R package, implemented by Hadley Wickham, for
+producing elegant graphics. The gg in ggplot2 means Grammar of Graphics, a graphic concept
+which describes plots by using a “grammar”.
+
+According to ggplot2 concept, a plot can be divided into different fundamental parts:
+Plot = data + Aesthetics + Geometry.
+
+The principal components of every plot can be defined as follow:
+
+ * data is a data frame
+ * Aesthetics is used to indicate x and y variables. It can also be used to control the
+   color, the size or the shape of points, the height of bars, etc…..
+ * Geometry corresponds to the type of graphics (histogram, box plot, line plot,
+   density plot, dot plot, ….)
+
+Two main functions, for creating plots, are available in ggplot2 package : a qplot() and
+ggplot() functions.
+
+  * qplot() is a quick plot function which is easy to use for simple plots.
+  * The ggplot() function is more flexible and robust than qplot for building a plot piece by piece.
+
+The generated plot can be kept as a variable and then printed at any time using the function
+print().
+
+After creating plots, two other important functions are:
+
+  * last_plot(), which returns the last plot to be modified
+  * ggsave(“plot.png”, width = 5, height = 5), which saves the last plot in the current
+    working directory.
+
+This document describes how to create and customize different types of graphs using ggplot2.
+Many examples of code and graphics are provided.