galaaz 0.4.6 → 0.4.7

data/blogs/nse_dplyr/nse_dplyr.md

@@ -0,0 +1,136 @@
+---
+title: "Non Standard Evaluation in dplyr with Galaaz"
+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
+---
+
+
+
+# Introduction
+
+
+```r
+df <- data.frame(x = 1:3, y = 3:1)
+print(df)
+```
+
+```
+##   x y
+## 1 1 3
+## 2 2 2
+## 3 3 1
+```
+
+```r
+print(filter(df, x == 1))
+```
+
+```
+##   x y
+## 1 1 3
+```
+
+```r
+#> # A tibble: 1 x 2
+#>       x     y
+#>   <int> <int>
+#> 1     1     3
+```
+
+
+```r
+my_var <- x
+#> Error in eval(expr, envir, enclos): object 'x' not found
+filter(df, my_var == 1)
+#> Error: object 'my_var' not found
+```
+
+
+```ruby
+@df = R.data__frame(x: (1..3), y: (3..1))
+puts @df
+
+puts @df.filter(:x.eq 1)
+```
+
+```
+##   x y
+## 1 1 3
+## 2 2 2
+## 3 3 1
+##   x y
+## 1 1 3
+```
+
+
+```ruby
+my_var = :x
+puts @df.filter(my_var.eq 1)
+```
+
+```
+##   x y
+## 1 1 3
+```
+
+>> dplyr code is ambiguous. Depending on what variables are defined where, 
+>> filter(df, x == y) could be equivalent to any of:
+
+```
+df[df$x == df$y, ]
+df[df$x == y, ]
+df[x == df$y, ]
+df[x == y, ]
+```
+
+In galaaz this ambiguity does not exist
+
+
+```ruby
+y = 2
+x = 2
+
+@df[:x.eq :y, :all]
+@df[:x.eq y, :all]
+# @df[x.eq :y, :all]
+# @df[x == y, :all]
+```
+
+```
+## Message:
+##  wrong number of arguments (given 2, expected 1)
+```
+
+```
+## Message:
+##  /home/rbotafogo/desenv/galaaz/lib/R_interface/rbinary_operators.rb:134:in `eq'
+## (eval):4:in `exec_ruby'
+## /home/rbotafogo/desenv/galaaz/lib/util/exec_ruby.rb:138:in `instance_eval'
+## /home/rbotafogo/desenv/galaaz/lib/util/exec_ruby.rb:138:in `exec_ruby'
+## /home/rbotafogo/desenv/galaaz/lib/gknit/knitr_engine.rb:650:in `block in initialize'
+## /home/rbotafogo/desenv/galaaz/lib/R_interface/ruby_callback.rb:77:in `call'
+## /home/rbotafogo/desenv/galaaz/lib/R_interface/ruby_callback.rb:77:in `callback'
+## (eval):3:in `function(...) {\n          rb_method(...)'
+## unknown.r:1:in `in_dir'
+## unknown.r:1:in `block_exec'
+## /home/rbotafogo/lib/graalvm-ce-1.0.0-rc12/jre/languages/R/library/knitr/R/block.R:91:in `call_block'
+## /home/rbotafogo/lib/graalvm-ce-1.0.0-rc12/jre/languages/R/library/knitr/R/block.R:6:in `process_group.block'
+## /home/rbotafogo/lib/graalvm-ce-1.0.0-rc12/jre/languages/R/library/knitr/R/block.R:3:in `<no source>'
+## unknown.r:1:in `withCallingHandlers'
+## unknown.r:1:in `process_file'
+## unknown.r:1:in `<no source>'
+## unknown.r:1:in `<no source>'
+## <REPL>:5:in `<repl wrapper>'
+## <REPL>:1
+```

data/lib/R_interface/r_libs.R

@@ -3,7 +3,12 @@ list.of.packages <- c('rlang', 'purrr', 'formula.tools', 'lobstr')
 new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
 if(length(new.packages)) install.packages(new.packages)
 
+if (!('data.table' %in% installed.packages()[, "Package"])) {
+  install.fastr.packages('data.table')
+}
+
 library('formula.tools')
 library('lobstr')
 library('rlang')
 library('purrr')
+

data/lib/R_interface/robject.rb

@@ -331,6 +331,14 @@ module R
     #
     #--------------------------------------------------------------------------------------
 
+    def pretty_print(obj)
+      puts self
+    end
+    
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
     def to_s
 
       begin

data/lib/R_interface/rsupport.rb

@@ -244,18 +244,16 @@ module R
         # of the output is greater than 0
         if (@@exec_counter == 0)
           R::Support.stop_capture.call(@@con)
-=begin          
           if (R::Support.eval("length(r_capture) > 0")[0])
             cap = R::Object.build(R::Support.eval("r_capture"))
             (0...cap.size).each do |i|
-              puts cap << i
+              puts cap >> i
             end
           end
-=end          
         end
         
       rescue StandardError => e
-        R::Support.stop_capture.call(@@con)
+        R::Support.stop_capture.call(@@con) if (@@exec_counter == 0)
         raise e
       end
       

data/lib/R_interface/ruby_extensions.rb

@@ -21,6 +21,15 @@
 # OR MODIFICATIONS.
 ##########################################################################################
 
+module Kernel
+
+  def puts(*args)
+    print(*args)
+    print "\n"
+  end
+
+end
+
 #==========================================================================================
 #
 #==========================================================================================

data/lib/util/exec_ruby.rb

@@ -31,6 +31,10 @@ class StringIO
   
   def puts(*args)
 
+    print "========================\n"
+    print "Inside puts\n"
+    print "========================\n"
+    
     if args.empty?
       write(DEFAULT_RECORD_SEPARATOR)
     else
@@ -68,7 +72,6 @@ class StringIO
 
 end
 
-
 #----------------------------------------------------------------------------------------
 # Class RubyChunk is used only as a context for all ruby chunks in the rmarkdown file.
 # This allows for chunks to access instance_variables (@)

data/specs/figures/bg.svg

@@ -3,7 +3,7 @@
 <svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' version='1.1' viewBox='0 0 506 506' style='fill:transparent'>
 <g style='stroke-width:1.4226377952755906;stroke-linejoin:round;stroke-linecap:round'>
 <rect x='0' y='0' width='506' height='506' style='stroke:#FFFFFF;fill:#FFFFFF'/>
-<rect x='31' y='6' width='469' height='473' style='stroke:rgb(0,0,0);stroke-opacity:0.000;fill:#EBEBEB'/>
+<rect x='31' y='6' width='469' height='473' style='stroke:rgb(0,0,0);stroke-opacity:0,000;fill:#EBEBEB'/>
 </g><g style='stroke-width:0.7113188976377953;stroke-linejoin:round;stroke-linecap:butt'>
 <polyline points='31,446 500,446' style='stroke:#FFFFFF'/>
 <polyline points='31,301 500,301' style='stroke:#FFFFFF'/>
@@ -54,4 +54,4 @@
 <text x='410' y='490' lengthAdjust='spacingAndGlyphs' textLength='5px' style='font-size:8.8px;fill:#4D4D4D'>2</text>
 <text x='253' y='500' lengthAdjust='spacingAndGlyphs' textLength='26px' style='font-size:11.0px;fill:#000000'>dose</text>
 <text x='13' y='252' lengthAdjust='spacingAndGlyphs' textLength='20px' style='font-size:11.0px;fill:#000000' transform='rotate(-90,13,252)'>len</text>
-</svg>
+</svg>

data/specs/figures/no_args.svg

@@ -3,7 +3,7 @@
 <svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' version='1.1' viewBox='0 0 506 506' style='fill:transparent'>
 <g style='stroke-width:1.4226377952755906;stroke-linejoin:round;stroke-linecap:round'>
 <rect x='0' y='0' width='506' height='506' style='stroke:#FFFFFF;fill:#FFFFFF'/>
-<rect x='31' y='6' width='469' height='473' style='stroke:rgb(0,0,0);stroke-opacity:0.000;fill:#EBEBEB'/>
+<rect x='31' y='6' width='469' height='473' style='stroke:rgb(0,0,0);stroke-opacity:0,000;fill:#EBEBEB'/>
 </g><g style='stroke-width:0.7113188976377953;stroke-linejoin:round;stroke-linecap:butt'>
 <polyline points='31,446 500,446' style='stroke:#FFFFFF'/>
 <polyline points='31,301 500,301' style='stroke:#FFFFFF'/>
@@ -54,4 +54,4 @@
 <text x='410' y='490' lengthAdjust='spacingAndGlyphs' textLength='5px' style='font-size:8.8px;fill:#4D4D4D'>2</text>
 <text x='253' y='500' lengthAdjust='spacingAndGlyphs' textLength='26px' style='font-size:11.0px;fill:#000000'>dose</text>
 <text x='13' y='252' lengthAdjust='spacingAndGlyphs' textLength='20px' style='font-size:11.0px;fill:#000000' transform='rotate(-90,13,252)'>len</text>
-</svg>
+</svg>

data/specs/r_list_apply.spec.rb

@@ -62,20 +62,20 @@ describe R::List do
       expect(quant.a[1]).to eq R.c('0%': 1.0)
       expect(quant.a[[1]]).to eq 1.0
              
-      expect(quant.a[["50%"]]).to eq 5.50
-      expect(quant.a['50%']).to eq R.c('50%': 5.50)
-      expect(R.all__equal(quant.beta["100%"],
-                          R.c('100%': 20.08553692),
+      expect(quant.a[['50,00000%']]).to eq 5.50
+      expect(quant.a['50,00000%']).to eq R.c('50,00000%': 5.50)
+      expect(R.all__equal(quant.beta['100,0000%'],
+                          R.c('100,0000%': 20.08553692),
                           tolerance: (~:".Machine").double__eps ** 0.5)).to eq true
       expect(quant.logic[[2]]).to eq 0.0
     end
-    
+
     it "should allow using method lapply with quantile" do
       x = R.lapply(@x, @q, R.c(0.25, 0.50, 0.75))
       expect(x.a[[1]]).to eq 3.25
-      expect(x.a[["50%"]]).to eq 5.50
-      expect(R.all__equal(x.beta['75%'],
-                          R.c('75%': 5.0536690),
+      expect(x.a[['50,00000%']]).to eq 5.50
+      expect(R.all__equal(x.beta['75,00000%'],
+                          R.c('75,00000%': 5.0536690),
                           tolerance: (~:".Machine").double__eps ** 0.5)).to eq true
       expect(x.logic[[2]]).to eq 0.5
     end
@@ -84,8 +84,9 @@ describe R::List do
       # sapply will return a matrix
       quant = R.sapply(@x, @q)
       expect(quant.rclass).to eq 'matrix'
-      
-      expect(quant[:all, 'a']).to eq R.c('0%': 1, '25%': 3.25, '50%': 5.50, '75%': 7.75, '100%': 10)
+      expect(quant[:all, 'a']).to eq R.c('0%': 1, '25,00000%': 3.25,
+                                         '50,00000%': 5.50, '75,00000%': 7.75,
+                                         '100,0000%': 10)
       
       expect(quant[3, 'beta']).to eq 1.0
     end

data/specs/tmp.rb

@@ -22,51 +22,55 @@
 ##########################################################################################
 
 require 'galaaz'
-require 'ggplot'
+R.require 'stats'
+
+# require 'ggplot'
 
 # Need to fix function 'str'... not printing anything
 # anymore
 # puts R.str(mtcars)
 # shouls allow mtcars[['car name']] = mtcars.rownames
 
-# Data Prep
-mtcars = ~:mtcars
+# (~:mtcars).str
 
-mtcars.car_name = mtcars.rownames  # create new column for car names
-mtcars.mpg_z = ((mtcars.mpg - mtcars.mpg.mean) / mtcars.mpg.sd).round 2
-mtcars.mpg_type = (mtcars.mpg_z < 0).ifelse('below', 'above')
-mtcars = mtcars[mtcars.mpg_z.order, :all]
-mtcars.car_name = R.factor(mtcars.car_name, levels: mtcars.car_name)
+describe R::List do
+  
+  context "The apply family of functions with lists" do
 
-puts mtcars.car_name
 
-R.awt
+    x = R.list(a: (1..10), beta: R.exp(-3..3), logic: R.c(true, false, false, true))
+#puts x
 
-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
+    quant = R.lapply(x, ~:quantile)
+#puts quant
+#puts quant.a[['50,00000%']]
 
-sleep(3)
+# puts quant.beta['100%']
 
+    it "ss" do
+      
+      ret = R.all__equal(quant.beta["100%"],
+                         R.c('100%': 20.08553692),
+                         tolerance: (~:".Machine").double__eps ** 0.5)
+      expect(R.c(1, 2, 3)).to eq false
+      # expect(5 == 10).to eq true
+    end
+  end
+end
 
 =begin
+# Make @q the function R quantile
+
+#puts quant.a
 
-mtcars$`car name` <- factor(mtcars$`car name`, levels = mtcars$`car name`)  # convert to factor to retain sorted order in plot.
+# puts quant.a[["50%"]]
+=end
 
-# Diverging Barcharts
-R.theme_set(R.theme_bw)  
 
-ggplot(mtcars, aes(x=`car name`, y=mpg_z, label=mpg_z)) + 
-  geom_bar(stat='identity', aes(fill=mpg_type), width=.5)  +
-  scale_fill_manual(name="Mileage", 
-                    labels = c("Above Average", "Below Average"), 
-                    values = c("above"="#00ba38", "below"="#f8766d")) + 
-  labs(subtitle="Normalised mileage from 'mtcars'", 
-       title= "Diverging Bars") + 
-  coord_flip()
+=begin
+R::Support.eval(<<R)
+  x = list(a = (1:10), beta = exp(-3:3), logic = c(TRUE, FALSE, FALSE, TRUE))
+  quant = lapply(x, quantile)
+  print(quant)
+R
 =end

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "galaaz"
-$version="0.4.6"
+$version="0.4.7"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: galaaz
 version: !ruby/object:Gem::Version
-  version: 0.4.6
+  version: 0.4.7
 platform: ruby
 authors:
 - Rodrigo Botafogo
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-02-21 00:00:00.000000000 Z
+date: 2019-03-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
@@ -106,11 +106,18 @@ files:
 - blogs/galaaz_ggplot/midwest_external_png
 - blogs/galaaz_ggplot/scatter_plot.png
 - blogs/gknit/gknit.Rmd
+- blogs/gknit/gknit.html
+- blogs/gknit/gknit.md
+- blogs/gknit/gknit_files/figure-html/bubble-1.png
+- blogs/gknit/gknit_files/figure-html/diverging_bar.png
 - blogs/gknit/model.rb
 - blogs/manual/manual.Rmd
 - blogs/manual/manual.html
 - blogs/manual/manual.md
 - blogs/manual/manual_files/figure-html/diverging_bar.png
+- blogs/nse_dplyr/nse_dplyr.Rmd
+- blogs/nse_dplyr/nse_dplyr.html
+- blogs/nse_dplyr/nse_dplyr.md
 - blogs/oh_my/not_so.rb
 - blogs/oh_my/oh_my.Rmd
 - blogs/oh_my/oh_my.html
@@ -269,8 +276,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.14.1
+rubygems_version: 3.0.3
 signing_key: 
 specification_version: 4
 summary: Tightly coupling Ruby and R