galaaz 0.4.6 → 0.5.0

data/specs/r_list.spec.rb

@@ -59,7 +59,7 @@ describe R::List do
   end
 
   #----------------------------------------------------------------------------------------
-  context "When subsetting a list with '<<' (starts at 0)" do
+  context "When subsetting a list with '>>' (starts at 0)" do
     
     before(:each) do
       @l = R.list(1, a: 2, b: 3, c: R.list(4, 5, 6))
@@ -170,12 +170,12 @@ describe R::List do
       expect(@l[[4]][[1]]).to eq 4
     end
     
-    it "should subset with [[]] with multiple indexes" do
+    it "should subset with [[]] with a vector" do
       # Note that for a list or other recursive object, the index can be a vector
       # and each element of the vector is applied in turn to the list, the
       # selected component, the selected component of that component, and so on.
       # The result is still a single element.
-      expect(@l[[4, 1]]).to eq 4
+      expect(@l[[R.c(4, 1)]]).to eq 4
     end
 
   end
@@ -230,7 +230,7 @@ describe R::List do
   end
 
   #----------------------------------------------------------------------------------------
-  context "When modifying a list" do
+  context "When assigning to a list subset" do
 
     before(:each) do
       @l = R.list(a: 1, b: 2, c: 3, d: R.list(i: 4, j: 5, k: 6))

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/ruby_expression.spec.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+require 'ggplot'
 
 #========================================================================================
 # class Expression in the R module extends Ruby's symbols, so that they can be used in
@@ -288,18 +289,9 @@ describe Symbol do
 
       # df is a Ruby symbol and ToothGrowth is an R dataframe.  But at this point
       # there is no relationship between the two
-      df = :ToothGrowth
-      
-      # we now call a method on a Ruby symbol.  This will try to identify if this
-      # method exists in the R dataframe.  This is one of the columns of the R
-      # dataframe, so 'dose' is now an R expression
+      df = ~:ToothGrowth
       dose = df.dose
-      expect(dose.to_s).to eq "ToothGrowth[[\"dose\"]]"
-
-      # dose.assign is an R expression, equivalent to 'ToothGrowth[["dose"]] <-'
-      # an the whole expression becomes:
-      # 'ToothGrowth[["dose"]] <- as.factor(ToothGrowth[["dose"]])'
-      dose.assign dose.as__factor
+      dose = dose.as__factor
       
       df2 = R.data__frame(
         R.aggregate(df.len, by: R.list(dose), FUN: :mean),

data/specs/tmp.rb

@@ -22,51 +22,123 @@
 ##########################################################################################
 
 require 'galaaz'
-require 'ggplot'
+# require 'gknit'
 
-# Need to fix function 'str'... not printing anything
-# anymore
-# puts R.str(mtcars)
-# shouls allow mtcars[['car name']] = mtcars.rownames
+describe "error" do
+# describe R::DataFrame do
 
-# Data Prep
-mtcars = ~:mtcars
+  context "Bootsraping" do
 
-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)
+    it "should error with R" do
+      vec = R.c(2)
+      puts vec
+      # expect(vec[1]).to eq 2
+    end
 
-puts mtcars.car_name
+=begin
+    it "should error with Ruby" do
+      expect(1).to eq 2
+    end
+    
+    before(:each) do
+      R.len = 10
+      R.sd = 20
+      R.vec = R.c(1, 2, 3, 4)
+    end
+
+    it "should inline r objects in 'expressions'" do
+      e1 = :len + :sd + 5 + R.c(1, 2, 3, 4)
+      expect(e1.rclass).to eq "integer"
+      expect(e1.eval).to eq R.c(36, 37, 38, 39)
+      # expect(e1.eval).not_to eq R.c(35, 37, 38, 39)
+    end
+=end
+    
+  end
+  
+end
+
+
+=begin
+Polyglot.eval("R", <<-R)
+library(plotly)
+m <- highlight_key(mpg)
+p <- ggplot(m, aes(displ, hwy)) + geom_point()
+gg <- highlight(ggplotly(p), "plotly_selected")
+crosstalk::bscols(gg, DT::datatable(m))
+R
+=end
+
+# GKnit.draft(file: "rmd_test.Rmd", template: 'acm_article'))
+# GKnit.draft(file: "rmd_test.Rmd", template: 'acm_article2', package: 'rticles')
+# GKnit.draft(file: "rmd_test", template: 'acm_article', package: 'rticles')
 
-R.awt
+## Renaming columns
 
-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
+#The rename function is used to rename columns
 
-sleep(3)
+#```{ruby rename}
+#puts @flights.rename(dep_time: 'deptime').head.as__data__frame
+#```
 
+# puts File.directory?(".")
 
+#===========================================================
 =begin
+# Add NULL to an element of the list
+# Not implemented yet.  Need to assing the
+# list(NULL) element.
+R::Support.eval(<<-R)
+y <- list(a = 1, b = 2)
+y["b"] <- list(NULL)
+str(y)
+
+print(list(NULL))
+R
+=end
+
 
-mtcars$`car name` <- factor(mtcars$`car name`, levels = mtcars$`car name`)  # convert to factor to retain sorted order in plot.
+=begin
+Polyglot.eval("R", <<-R)
+  fidx = function(idx) {
+      print(typeof(idx))
+      print(class(idx))
+      print(idx)
+      print(is_missing(idx))
+  }
 
-# Diverging Barcharts
-R.theme_set(R.theme_bw)  
+  ma = missing_arg()
+  f = fidx
+  params = list()
+  params = `[[<-`(params, 1, ma)
+  invoke(f, params)
 
-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()
+  print("======")
+  fidx(ma)
+
+R
 =end
+
+=begin
+ma = Polyglot.eval("R", "missing_arg()")
+
+puts "======"
+
+f = Polyglot.eval("R", "fidx")
+params = Polyglot.eval("R", "list()")
+params = Polyglot.eval("R", "`[[<-`").call(params, 1, ma)
+Polyglot.eval("R", "invoke").call(f, params)
+
+puts "======"
+
+Polyglot.eval("R", "fidx").call(ma)
+=end
+
+# Polyglot.eval("R", "print").call(pl)
+# ma2 = Polyglot.eval("R", "`[[`").call(pl, 1)
+# Polyglot.eval("R", "fidx").call(ma2)
+
+#R.fidx(ma)
+
+# R.fidx(Polyglot.eval("R", "missing_arg()"))
+# R.fidx(R.empty_symbol)

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "galaaz"
-$version="0.4.6"
+$version="0.5.0"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: galaaz
 version: !ruby/object:Gem::Version
-  version: 0.4.6
+  version: 0.5.0
 platform: ruby
 authors:
 - Rodrigo Botafogo
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-02-21 00:00:00.000000000 Z
+date: 2020-06-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
@@ -72,6 +72,7 @@ executables:
 - gstudio
 - gknit
 - grun
+- gknit-draft
 extensions: []
 extra_rdoc_files: []
 files:
@@ -80,62 +81,68 @@ files:
 - Rakefile
 - bin/galaaz
 - bin/gknit
-- bin/gknit_old_r
+- bin/gknit-draft
+- bin/gknit-draft.rb
+- bin/gknit_Rscript
 - bin/grun
 - bin/gstudio
-- bin/gstudio.rb
-- 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.
-- blogs/dev/dev_files/figure-html/diverging_bar.png
-- blogs/dev/model.rb
-- blogs/dplyr/dplyr.rb
+- bin/gstudio_irb.rb
+- bin/gstudio_pry.rb
 - blogs/galaaz_ggplot/galaaz_ggplot.Rmd
-- blogs/galaaz_ggplot/galaaz_ggplot.aux
 - blogs/galaaz_ggplot/galaaz_ggplot.html
-- blogs/galaaz_ggplot/galaaz_ggplot.log
 - blogs/galaaz_ggplot/galaaz_ggplot.md
-- blogs/galaaz_ggplot/galaaz_ggplot.out
 - blogs/galaaz_ggplot/galaaz_ggplot.pdf
-- blogs/galaaz_ggplot/galaaz_ggplot.tex
+- blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/midwest_rb.png
+- blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/scatter_plot_rb.png
 - blogs/galaaz_ggplot/midwest.Rmd
 - blogs/galaaz_ggplot/midwest.html
-- blogs/galaaz_ggplot/midwest.png
 - blogs/galaaz_ggplot/midwest_external_png
-- blogs/galaaz_ggplot/scatter_plot.png
 - blogs/gknit/gknit.Rmd
+- blogs/gknit/gknit.html
+- blogs/gknit/gknit.pdf
+- blogs/gknit/lst.rds
 - blogs/gknit/model.rb
+- blogs/gknit/stats.bib
+- blogs/manual/lst.rds
 - blogs/manual/manual.Rmd
 - blogs/manual/manual.html
 - blogs/manual/manual.md
+- blogs/manual/manual.pdf
+- blogs/manual/manual.tex
+- blogs/manual/manual_files/figure-html/bubble-1.png
 - blogs/manual/manual_files/figure-html/diverging_bar.png
+- blogs/manual/manual_files/figure-latex/bubble-1.png
+- blogs/manual/manual_files/figure-latex/diverging_bar.pdf
+- blogs/manual/model.rb
+- blogs/nse_dplyr/nse_dplyr.Rmd
+- blogs/nse_dplyr/nse_dplyr.html
+- blogs/nse_dplyr/nse_dplyr.md
+- blogs/nse_dplyr/nse_dplyr.pdf
 - 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/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/dose_len.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color2.png
 - 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
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.png
+- blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.png
 - examples/50Plots_MasterList/Images/midwest-scatterplot.PNG
 - examples/50Plots_MasterList/ScatterPlot.rb
 - examples/50Plots_MasterList/scatter_plot.rb
+- examples/Bibliography/master.bib
+- examples/Bibliography/stats.bib
 - examples/R/calc.R
 - examples/R/java_interop.R
 - examples/islr/all.rb
@@ -145,11 +152,67 @@ files:
 - examples/islr/ch3_multiple_regression.rb
 - examples/islr/ch6.spec.rb
 - examples/islr/x_y_rnorm.jpg
+- examples/latex_templates/Test-acm_article/Makefile
+- examples/latex_templates/Test-acm_article/Test-acm_article.Rmd
+- examples/latex_templates/Test-acm_article/acm_proc_article-sp.cls
+- examples/latex_templates/Test-acm_article/sensys-abstract.cls
+- examples/latex_templates/Test-acm_article/sigproc.bib
+- examples/latex_templates/Test-acs_article/Test-acs_article.Rmd
+- examples/latex_templates/Test-acs_article/Test-acs_article.pdf
+- examples/latex_templates/Test-acs_article/acs-Test-acs_article.bib
+- examples/latex_templates/Test-acs_article/acs-my_output.bib
+- examples/latex_templates/Test-acs_article/acstest.bib
+- examples/latex_templates/Test-aea_article/AEA.cls
+- examples/latex_templates/Test-aea_article/BibFile.bib
+- examples/latex_templates/Test-aea_article/Test-aea_article.Rmd
+- examples/latex_templates/Test-aea_article/Test-aea_article.pdf
+- examples/latex_templates/Test-aea_article/aea.bst
+- examples/latex_templates/Test-aea_article/multicol.sty
+- examples/latex_templates/Test-aea_article/references.bib
+- examples/latex_templates/Test-aea_article/setspace.sty
+- examples/latex_templates/Test-amq_article/Test-amq_article.Rmd
+- examples/latex_templates/Test-amq_article/Test-amq_article.pdf
+- examples/latex_templates/Test-amq_article/Test-amq_article.pdfsync
+- examples/latex_templates/Test-amq_article/pics/Figure2.pdf
+- examples/latex_templates/Test-ams_article/Test-ams_article.Rmd
+- examples/latex_templates/Test-ams_article/amstest.bib
+- examples/latex_templates/Test-asa_article/Test-asa_article.Rmd
+- examples/latex_templates/Test-asa_article/Test-asa_article.pdf
+- examples/latex_templates/Test-asa_article/agsm.bst
+- examples/latex_templates/Test-asa_article/bibliography.bib
+- examples/latex_templates/Test-ieee_article/IEEEtran.bst
+- examples/latex_templates/Test-ieee_article/IEEEtran.cls
+- examples/latex_templates/Test-ieee_article/Test-ieee_article.Rmd
+- examples/latex_templates/Test-ieee_article/Test-ieee_article.pdf
+- examples/latex_templates/Test-ieee_article/mybibfile.bib
+- examples/latex_templates/Test-rjournal_article/RJournal.sty
+- examples/latex_templates/Test-rjournal_article/RJreferences.bib
+- examples/latex_templates/Test-rjournal_article/RJwrapper.pdf
+- examples/latex_templates/Test-rjournal_article/Test-rjournal_article.Rmd
+- examples/latex_templates/Test-springer_article/Test-springer_article.Rmd
+- examples/latex_templates/Test-springer_article/Test-springer_article.pdf
+- examples/latex_templates/Test-springer_article/bibliography.bib
+- examples/latex_templates/Test-springer_article/spbasic.bst
+- examples/latex_templates/Test-springer_article/spmpsci.bst
+- examples/latex_templates/Test-springer_article/spphys.bst
+- examples/latex_templates/Test-springer_article/svglov3.clo
+- examples/latex_templates/Test-springer_article/svjour3.cls
 - examples/misc/baseball.csv
 - examples/misc/ggplot.rb
 - examples/misc/moneyball.rb
 - examples/misc/subsetting.rb
-- examples/paper/paper.rb
+- examples/rmarkdown/svm-rmarkdown-anon-ms-example/svm-rmarkdown-anon-ms-example.Rmd
+- examples/rmarkdown/svm-rmarkdown-anon-ms-example/svm-rmarkdown-anon-ms-example.pdf
+- examples/rmarkdown/svm-rmarkdown-article-example/svm-rmarkdown-article-example.Rmd
+- examples/rmarkdown/svm-rmarkdown-article-example/svm-rmarkdown-article-example.pdf
+- examples/rmarkdown/svm-rmarkdown-beamer-example/svm-rmarkdown-beamer-example.Rmd
+- examples/rmarkdown/svm-rmarkdown-beamer-example/svm-rmarkdown-beamer-example.pdf
+- examples/rmarkdown/svm-rmarkdown-cv/svm-rmarkdown-cv.Rmd
+- examples/rmarkdown/svm-rmarkdown-cv/svm-rmarkdown-cv.pdf
+- examples/rmarkdown/svm-rmarkdown-syllabus-example/attend-grade-relationships.csv
+- examples/rmarkdown/svm-rmarkdown-syllabus-example/svm-rmarkdown-syllabus-example.Rmd
+- examples/rmarkdown/svm-rmarkdown-syllabus-example/svm-rmarkdown-syllabus-example.pdf
+- examples/rmarkdown/svm-xaringan-example/svm-xaringan-example.Rmd
 - examples/sthda_ggplot/README.md
 - examples/sthda_ggplot/all.rb
 - examples/sthda_ggplot/one_variable_continuous/density_gg.rb
@@ -206,6 +269,7 @@ files:
 - lib/R_interface/rvector.rb
 - lib/galaaz.rb
 - lib/gknit.rb
+- lib/gknit/draft.rb
 - lib/gknit/include_engine.rb
 - lib/gknit/knitr_engine.rb
 - lib/gknit/rb_engine.rb
@@ -269,8 +333,7 @@ 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