galaaz 0.4.2 → 0.4.5

data/specs/all.rb

@@ -23,6 +23,15 @@
 
 require_relative 'r_eval.spec'
 
+# Specification for Functions
+require_relative 'r_function.spec'
+
+# Specification for Ruby expressions
+require_relative 'ruby_expression.spec'
+
+# Specification for R::Environment
+require_relative 'r_environment.spec'
+
 # Specification for R::Vector
 require_relative 'r_vector_creation.spec'
 require_relative 'r_vector_object.spec'
@@ -40,6 +49,7 @@ require_relative 'r_matrix.spec'
 # Specification for R::Dataframes
 require_relative 'r_dataframe.spec'
 
-# Specification for language features
-require_relative 'r_function.spec'
-require_relative 'r_language.spec'
+require_relative 'r_formula.spec'
+
+# Testes for NSE
+# require_relative 'r_nse.spec'

data/specs/r_dataframe.spec.rb

@@ -33,11 +33,13 @@ describe R::DataFrame do
       vec.dim = R.c(2, 3)
       
       # create a DataFrame from a vector
-      df = R.as__data__frame(vec)
+      df = vec.as__data__frame
       expect(df[1, "V1"]).to eq 1
-      expect df[1, 'V2'] == 3
-      expect df[1, :all] == R.c(V1: 1, V2: 3, V3: 5)
-      
+      expect(df[1, 'V2']).to eq 3
+      # When you extract a single row from a data frame you get a one-row data frame.
+      # Convert it to a numeric vector with 'as__numeric'
+      expect(df[1, :all].as__numeric).to eq R.c(V1: 1, V2: 3, V3: 5)
+     
     end
 
   end
@@ -69,26 +71,39 @@ describe R::DataFrame do
       expect(table2.fail[4]).to eq true
       
     end
+
+  end
+  #----------------------------------------------------------------------------------------
+  context "Ruby 'each'" do
     
     it "should do 'each_column'" do
       
       mtcars = ~:mtcars
       
       mtcars.each_column do |col, col_name|
-        # col_name is an R::Vector with one string element.
-        # Extract the 'native' value by indexing with '<< 0'
-        case col_name << 0
+        # col_name a Ruby string with the column name
+        case col_name
         when "mpg"
-          expect col[1] == 21
-          expect col[9] == 22.8
-          expect col[32] == 21.4
+          expect(col[1]).to eq 21
+          expect(col[9]).to eq 22.8
+          expect(col[32]).to eq 21.4
+          expect(col[1] == 21).to eq true
+          expect(col[9] == 22.8).to eq true
+          expect(col[9] == 30).to eq false
+          expect(col[32] == 21.4).to eq true
         when "cyl"
-          expect col[1] == 6
-          expect col[10] == 6
-          expect col[32] == 4
+          expect(col[1] == 6).to eq true
+          expect(col[10] == 6).to eq true
+          expect(col[32] == 4).to eq true
+          expect(col[1]).to eq 6
+          expect(col[10]).to eq 6
+          expect(col[32]).to eq 4
         when "disp"
-          expect col[1] == 160
-          expect col[32] == 121
+          expect(col[1]).to eq 160
+          expect(col[32]).to eq 121
+          expect(col[1] == 160).to eq true
+          expect(col[1] == 200).to eq false
+          expect(col[32] == 121).to eq true
         end
         
       end
@@ -100,20 +115,28 @@ describe R::DataFrame do
       mtcars = ~:mtcars
       
       mtcars.each_row do |row, row_name|
-        case row_name << 0
+        # row_name a Ruby string with the column name
+        case row_name
         when "Mazda RX4"
-          expect row['mpg'] == 21
-          expect row.qsec == 16.46
+          expect(row[['mpg']]).to eq 21
+          expect(row.mpg). to eq 21
+          expect(row.qsec).to eq 16.46
+          expect(row['mpg'] == 21).to eq true
+          expect(row.qsec == 16.46).to eq true
         when "Hornet Sportabout"
-          expect row['cyl'] == 8
-          expect row['wt'] == 3.44
+          expect(row[['cyl']]).to eq 8
+          expect(row.cyl).to eq 8
+          expect(row[['wt']]).to eq 3.44
+          expect(row['cyl'] == 8).to eq true
+          expect(row['wt'] == 3.44).to eq true
         when "Merc 240D"
-          expect row['hp'] == 62
-          expect row.drat == 3.69
+          expect(row[['hp']]).to eq 62
+          expect(row['hp'] == 62).to eq true
+          expect(row.drat).to eq 3.69
         when "Volvo 142E"
-          expect row.hp == 109
-          expect row.am == 1
-          expect row.carb == 2
+          expect(row.hp).to eq 109
+          expect(row.am).to eq 1
+          expect(row.carb).to eq 2
         end
         
       end
@@ -121,7 +144,7 @@ describe R::DataFrame do
     end
     
   end
-  
+
   #----------------------------------------------------------------------------------------
   context "Boostraping" do
     

data/specs/r_environment.spec.rb

@@ -0,0 +1,140 @@
+# -*- 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'
+
+describe R::Environment do
+  
+  #----------------------------------------------------------------------------------------
+  context "Using environment" do
+
+    before(:each) do
+      # create two environments
+      @a_env = R.env
+      @b_env = R.env
+    end
+    
+    it "should allow the creation of new environments" do
+      expect(@a_env.typeof).to eq R.c("environment")
+      expect(@a_env.rclass).to eq R.c("environment")
+      expect(@a_env.env_names.length).to eq 0
+      expect(@b_env.env_names.length).to eq 0
+    end
+
+    it "should allow accessing key, value pairs to environments, with 'set' and 'get'" do
+      @a_env.set(:a, 25)
+      expect(@a_env.env_names.length).to eq 1
+      expect(@a_env.env_names).to eq R.c("a")
+      
+      expect(@b_env.env_names.length).to eq 0
+      expect(@a_env.get(:a)).to eq 25
+      @a_env.set(:b, 33)
+      expect(@a_env.env_names.length).to eq 2
+      expect(@a_env.env_names).to eq R.c("a", "b")
+      
+      expect(@a_env.get(:b)).to eq 33
+      expect(@a_env.get(:b)).not_to eq 25
+    end
+
+    it "should allow accessing key, value pairs to environments, with '.x' and 'x ='" do
+      expect(@a_env.env_names.length).to eq 0
+      @a_env.a = 30
+      expect(@a_env.env_names.length).to eq 1
+      expect(@a_env.a).to eq 30
+
+      @b_env.vec = R.c(1, 2, 3, 4)
+      expect(@b_env.env_names).to eq "vec"
+      expect(@b_env.env_names.length).to eq 1
+      expect(@b_env.vec).to eq R.c(1, 2, 3, 4)
+    end
+
+    it "should allow accessing key, value pairs to environments, with '[[" do
+      expect(@a_env.env_names.length).to eq 0
+      @a_env.a = "This is a string"
+      expect(@a_env[["a"]]).to eq R.c("This is a string")
+    end
+
+    it "should call methods on the environment as every other R::Object" do
+      # we have already seen that we can apply 'ls' to an environment
+      expect(@a_env.env_names.length).to eq 0
+      expect(R.env_names(@a_env).length).to eq 0
+    end
+
+    it "allows multiple names to point to the same object" do
+      @a_env.a = false
+      @a_env.b = "a"
+      @a_env.c = (2..3)
+      @a_env.d = (1..3)
+      
+      expect(@a_env.b).to eq "a"
+      expect(@a_env.d).to eq R.c(1, 2, 3)
+
+      @a_env.a = @a_env.d
+      expect(@a_env.a).to eq R.c(1, 2, 3)
+    end
+
+    it "should allow removing elements from an environment" do
+      @a_env.a = false
+      @a_env.b = "a"
+      @a_env.c = (2..3)
+      @a_env.d = (1..3)
+
+      expect(@a_env.a).to eq false
+      expect(@a_env.b).to eq "a"
+      R.rm("a", envir: @a_env)
+      expect { @a_env.a }.to raise_error(NoMethodError)
+    end
+
+    it "should not be able to subset the environment with '['" do
+      @a_env.a = false
+      expect { @a_env['a'] }.to raise_error(RuntimeError)
+    end
+    
+  end
+
+  #----------------------------------------------------------------------------------------
+  context "Evaluating expressions" do
+
+    before(:each) do
+      R.len = 10
+      R.sd = 20
+      vec = R.c(1, 2, 3, 4)
+      R.x = R.c(1, 2, 3, 4)
+    end
+
+    it "should evaluate an expression in the context of a data maks" do
+      myenv = R.env
+      myenv.e1 = R.expr(:len)
+      myenv.e2 = R.expr(:sd)
+      myenv.e3 = R.expr(R.c(1, 2, 3, 4))
+      
+      e4 = R.expr(:e1 + :e2 + :e3)
+      expect(e4.to_s).to eq "e1 + e2 + e3"
+      expect(e4.eval(myenv.new_data_mask)).to eq R.c(31, 32, 33, 34)
+
+    end
+    
+  end
+    
+end
+

data/specs/r_eval.spec.rb

@@ -146,19 +146,4 @@ describe R do
     
   end
 
-  context "Call Non-standard Evaluation methods" do
-
-    it "should pass delayed evaluation parameters to methods" do
-      # call the subset method filtering by 'cyl == 8 & carb > 3'
-      # In order to convert a Ruby symbol to an R symbol we use the '.r' method on the
-      # Ruby symbol.  Ruby bitwise operators '&' and '|' are overloaded and used as 
-      # the equivalent R operators and not as bitwise operators.
-      mt_subset = (~:mtcars).subset((:cyl == 8) & (:carb > 3))
-      expect(mt_subset.mpg == R.c(14.3, 10.4, 10.4, 14.7, 13.3, 15.8, 15.0)).to eq true
-      expect((mt_subset.cyl == 8).all).to eq true
-      expect((mt_subset.carb > 3).all).to eq true
-    end
-    
-  end
-  
 end

data/specs/r_formula.spec.rb

@@ -0,0 +1,232 @@
+# -*- 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')
+
+describe R::Language do
+
+  #========================================================================================
+  context "When working with Formulas" do
+    
+    it "should create formulas with the 'formula' function" do
+      formula = R.formula("log(y) ~ a + log(x)")
+      # formulas also capture their environment.  When printing the
+      # formula, two lines are printed: the first one with the formula
+      # and the second one with the environmnet. We are keeping only the
+      # first line for comparing with the expected formula
+      expect(formula.to_s.lines.first.chomp).to eq "log(y) ~ a + log(x)"
+    end
+
+    it "should create formulas with the '.til' function" do
+      formula = R.formula("cyl ~ exp")
+      expect(formula.to_s.lines.first.chomp).to eq "cyl ~ exp"
+      
+      formula = (:cyl.til :exp)
+      expect(formula.to_s.lines.first.chomp).to eq "cyl ~ exp"
+      rform = R.identity(formula)
+      expect(rform.typeof).to eq 'language'
+      expect(rform.rclass).to eq 'formula'
+    end
+
+    it "should create a formula with '.' by using the ':all' keyword in the rhs" do
+      formula = R.formula("supp ~ .")
+      expect(formula.to_s.lines.first.chomp).to eq "supp ~ ."
+      
+      # this formula is interpreted as 'supp ~ .' In this statement formula
+      # is an R::Expression which has infix and prefix notation
+      formula = :supp.til :__
+      expect(formula.to_s.lines.first.chomp).to eq "supp ~ ."
+      expect(formula.rclass).to eq "formula"
+      expect(formula.typeof).to eq "language"
+    end
+    
+    it "should create a formula with '.' by using the ':__' keyword in the lhs" do
+      formula = R.formula(". ~ supp")
+      expect(formula.to_s.lines.first.chomp).to eq ". ~ supp"
+
+      # this formula is interpreted as '. ~ supp'
+      formula = :__.til :supp
+      expect(formula.to_s.lines.first.chomp).to eq ". ~ supp"
+      expect(formula.rclass).to eq "formula"
+      expect(formula.typeof).to eq "language"
+    end
+
+    it "should create a formula starting with '~' with the ':all' symbol in the lhs" do
+      formula = R.formula("~ supp")
+      expect(formula.to_s.lines.first.chomp).to eq "~supp"
+      
+      formula = :all.til :supp
+      expect(formula.to_s.lines.first.chomp).to eq " ~ supp"
+      expect(formula.rclass).to eq "formula"
+      expect(formula.typeof).to eq "language"
+    end
+
+    it "should allow formulas with conditional" do
+      formula = R.formula("Sepal.Width ~ Petal.Width | Species")
+      expect(formula.to_s.lines.first.chomp).to eq "Sepal.Width ~ Petal.Width | Species"
+      
+      formula = :Sepal__Width.til :Petal__Width | :Species
+      expect(formula.to_s.lines.first.chomp).to eq "Sepal.Width ~ Petal.Width | Species"
+    end
+
+    it "should allow creating formulas with functions in the lhs" do
+      formula = E.log(:y).til :a + E.log(:x)
+      expect(formula.to_s.lines.first.chomp).to eq "log(y) ~ a + log(x)"
+    end
+    
+  end
+
+  #========================================================================================
+  context "Formula operators" do
+
+    it "should add multiple independent variables to a formula with '+'" do
+      # Use multiple independent variables
+      formula = :y.til :x1 + :x2
+      expect(formula.to_s.lines.first.chomp).to eq "y ~ x1 + x2"
+    end
+
+    it "should ignore objects in an analysis with '-'" do
+      # Ignore objects in an analysis
+      formula = :y.til :x1 - :x2
+      expect(formula.to_s.lines.first.chomp).to eq "y ~ x1 - x2"
+    end
+    
+    it "should create interaction between objects with '*'" do
+      # Ignore objects in an analysis
+      formula = :y.til :x * :x2
+      expect(formula.to_s.lines.first.chomp).to eq "y ~ x * x2"
+
+      # Set seed
+      R.set__seed(123)
+      
+      # Data
+      R.x = R.rnorm(5)
+      R.x2 = R.rnorm(5)
+      R.y = R.rnorm(5)
+      
+      # Model frame
+      model = R.model__frame(formula, data: R.data__frame(x: :x, y: :y, x2: :x2))
+      expect(model[1, 1].all__equal(1.22408179743946)).to eq true
+      expect(model[1, 3].all__equal(1.71506498688328)).to eq true
+      expect(model[3, 2].all__equal(1.55870831414912)).to eq true
+      expect(model[5, 1].all__equal(-0.555841134754075)).to eq true
+    end
+
+    it "should allow creating formulas with interaction between variables with 'inter'" do
+      formula = :y.til :x + :x2 + (:x.inter :x2)
+      expect(formula.to_s.lines.first.chomp).to eq "y ~ x + x2 + x:x2"
+
+      # Set seed
+      R.set__seed(123)
+      
+      # Data
+      R.x = R.rnorm(5)
+      R.x2 = R.rnorm(5)
+      R.y = R.rnorm(5)
+      
+      # Model frame
+      model = R.model__frame(formula, data: R.data__frame(x: :x, y: :y, x2: :x2))
+      expect(model[1, 1].all__equal(1.22408179743946)).to eq true
+      expect(model[1, 3].all__equal(1.71506498688328)).to eq true
+      expect(model[3, 2].all__equal(1.55870831414912)).to eq true
+      expect(model[5, 1].all__equal(-0.555841134754075)).to eq true
+    end
+
+    it "should allow creating formulas with interaction with ':in'" do
+      # note that '_' is a method with two arguments ':in' and ':a' and
+      # that it is necessary to put the whole expression in parenthesis or
+      # add parenthesis on the arguments
+      formula = :y.til :a + (:b._ :in, :a)
+      expect(formula.to_s.lines.first.chomp).to eq "y ~ a + b %in% a"
+    end
+
+  end
+
+  #========================================================================================
+  context "When modeling with formulas - Simple linear regression" do
+
+    before(:each) do
+      @boston_lm = R.lm((:medv.til :lstat), data: :Boston)
+    end
+
+    it "should obtain data from the model" do
+      expect(@boston_lm.coefficients[[1]].all__equal(34.5538408)).to eq true
+      expect(@boston_lm.coefficients[[2]].all__equal(-0.950049353)).to eq true
+
+      expect(@boston_lm.names[[1]]).to eq "coefficients"
+      expect(@boston_lm.names[[2]]).to eq "residuals"
+      expect(@boston_lm.names[[12]]).to eq "model"
+    end
+
+    it "should do predictions (confidence) based on the model" do
+      # predict the confidence interval
+      conf = R.predict(@boston_lm, R.data__frame(lstat: (R.c(5, 10, 15))),
+                       interval: "confidence")
+      expect(conf[1, :all][['fit']].all__equal(29.8035941)).to eq true
+      expect(conf[2, :all][['lwr']].all__equal(24.4741320)).to eq true
+      expect(conf[3, :all][['upr']].all__equal(20.8746129)).to eq true
+    end
+
+    it "should do prediction (prediction) based on the model" do
+      pred = R.predict(@boston_lm, R.data__frame(lstat: (R.c(5, 10, 15))),
+                       interval: "prediction")
+      expect(pred[1, :all][['fit']].all__equal(29.8035941)).to eq true
+      expect(pred[2, :all][['lwr']].all__equal(12.82762634)).to eq true
+      expect(pred[3, :all][['upr']].all__equal(32.5284590)).to eq true
+    end
+
+  end
+
+  #========================================================================================
+  context "Multiple linear regression" do
+
+    it "should do multiple linear regression" do
+      # Multiple linear regression from ISLR book.  Chapter 3 Lab, pg 113
+      lm_fit = R.lm((:medv.til :lstat + :age), data: :Boston)
+      
+      # Intercept
+      expect(lm_fit.coefficients[[1]].all__equal(33.2227605317)).to eq true
+      # lstat
+      expect(lm_fit.coefficients[[2]].all__equal(-1.0320685641)).to eq true
+      expect(lm_fit.coefficients[['lstat']].all__equal(-1.0320685641)).to eq true
+      # age
+      expect(lm_fit.coefficients[[3]].all__equal(0.0345443385)).to eq true
+    end
+
+    it "should do multiple linear regression with polynomials" do
+      lm_fit5 = R.lm((:medv.til E.poly(:lstat, 5)), data: :Boston)
+
+      # Intercept
+      expect(lm_fit5.coefficients[[1]].all__equal(22.53280632411)).to eq true
+      # Poly 1
+      expect(lm_fit5.coefficients[[2]].all__equal(-152.4595487225)).to eq true
+      # Poly 3
+      expect(lm_fit5.coefficients[[4]].all__equal(-27.0510978864097)).to eq true
+      # Poly 5
+      expect(lm_fit5.coefficients[[6]].all__equal(-19.2524177100554)).to eq true
+    end
+    
+  end
+  
+end