galaaz 0.4.10 → 0.5.0

data/lib/R_interface/r.rb

@@ -64,7 +64,7 @@ module R
 
   def self.install_rlibs(*libs)
 
-    packages = R.c(libs)
+    packages = R.c(*libs)
 
     new_packages = packages[!(packages._ :in, R.installed__packages[:all, "Package"])]
     

data/lib/R_interface/r_libs.R

@@ -1,4 +1,4 @@
-list.of.packages <- c('rlang', 'purrr', 'formula.tools', 'lobstr')
+list.of.packages <- c('rlang', 'purrr', 'formula.tools', 'lobstr', 'rticles')
 
 new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
 if(length(new.packages)) install.packages(new.packages)

data/lib/R_interface/r_methods.rb

@@ -171,6 +171,16 @@ module R
         R
     end
 
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    Polyglot.eval("R", <<-R)
+      plot = function(...) {
+        print("Function 'plot' is not implemented in fastR.  Please, use ggplot instead")
+      }
+    R
+
   end
   
 end

data/lib/R_interface/rpkg.rb

@@ -42,6 +42,7 @@ module R
     end
     
     def method_missing(symbol, *args)
+      symbol = R::Support.convert_symbol2r(symbol)
       R::Support.exec_function_name("#{@package_name}::#{symbol}", *args)
     end
 

data/lib/R_interface/rsupport.rb

@@ -209,8 +209,6 @@ module R
     
     #----------------------------------------------------------------------------------------
     # @param function [R function (Interop)] R function to execute
-    # @param internal [Boolean] true if returning to an internal object, i.e., does not
-    # wrap the return object in a Ruby object
     # @args [Array] Array of arguments for the function
     #----------------------------------------------------------------------------------------
     
@@ -235,7 +233,7 @@ module R
           res = @@exec_from_ruby.call(R::Object.method(:build), function, pl)
           # R::Object.build(R::Support.eval("do.call").call(function, pl))
         end
-        
+
         @@exec_counter = @@exec_counter - 1
         
         # When execution counter back to 0, print the captured output if the length
@@ -249,12 +247,12 @@ module R
             end
           end
         end
-        
+
       rescue StandardError => e
         R::Support.stop_capture.call(@@con) if (@@exec_counter == 0)
         raise e
       end
-      
+
       res
       
     end
@@ -266,7 +264,7 @@ module R
     
     def self.exec_function_name(function_name, *args)
       # @TODO: should check all that can go wrong when calling eval(function_name) to
-      # raise the proper exception
+      # raise the proper exception      
       f = R::Support.eval(function_name)
       R::Support.exec_function(f, *args)
     end

data/lib/gknit.rb

@@ -27,3 +27,5 @@ require_relative 'gknit/knitr_engine'
 require_relative 'gknit/ruby_engine'
 require_relative 'gknit/rb_engine'
 require_relative 'gknit/include_engine'
+require_relative 'gknit/draft'
+

data/lib/gknit/draft.rb

@@ -0,0 +1,105 @@
+# -*- 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.
+##########################################################################################
+
+module GKnit
+
+  #--------------------------------------------------------------------------------------
+  #
+  #--------------------------------------------------------------------------------------
+  
+  Polyglot.eval("R", <<-R)
+    ruby_template = function(gem, family, template, type, ...) {
+    print(gem)
+    print(family)
+    print(template)
+    print(type)
+    data_dir = eval.polyglot("ruby", "GKnit")$template_path(gem, family, template)
+    print(data_dir)
+    invoke(type, list(template = "template.tex", pandoc_args = paste0("--data-dir=", data_dir), ...))
+  }
+  R
+
+  #--------------------------------------------------------------------------------------
+  #
+  #--------------------------------------------------------------------------------------
+
+  def self.template_path(gem, family, template)
+    full_filename = Dir.glob("gknit-templates*", base: "#{Gem.default_dir}/gems")
+    template_path = "#{Gem.default_dir}/gems/#{full_filename[0]}/#{family}/#{template}"
+  end
+  
+  #--------------------------------------------------------------------------------------
+  #
+  #--------------------------------------------------------------------------------------
+
+  def self.draft(file:, template:, package: nil,
+                 create_dir: 'default', is_package: true, edit: true)
+    
+    # ignore the file extension if given. It should always be an .Rmd file
+    file_basename = File.basename(file, File.extname(file))
+    file = "#{file_basename}.Rmd"
+    
+    # resolve package file
+    # TODO: if package is a rubygem, then look there somehow
+    if (is_package)
+      template_path =
+        R.system__file("rmarkdown", "templates", template, package: package) >> 0
+      raise "The template '#{template}' was not found in the package '#{package}'" if
+        !(R.nzchar(template_path) >> 0)
+    else
+      full_filename = Dir.glob("gknit-templates*", base: "#{Gem.default_dir}/gems")
+      template_path = "#{Gem.default_dir}/gems/#{full_filename[0]}/#{template}"
+      puts template_path
+      # raise "this is not an R package"
+    end
+
+    # read the template.yaml and confirm it has the right fields
+    template_yaml = File.expand_path("template.yaml", template_path)
+    raise "No 'template.yaml' file found for template '#{template}" if
+      !File.file?(template_yaml)
+
+    template_meta = R::Yaml::yaml__load(R.read_utf8(template_yaml))
+    raise "template.yaml must contain 'name' and 'description' fields" if
+      (template_meta.name.is__null || template_meta.description.is__null) >> 0
+    puts "Creating template:"
+    puts "Template name: #{template_meta.name >> 0}"
+    puts "Description: #{template_meta.description >> 0}"
+
+    if (create_dir == 'default')
+      # check if template asks for new directory
+      create_dir = template_meta.create_dir.isTRUE >> 0
+
+      if (create_dir)
+        raise "The directory '#{file_basename}' already exists" if Dir.exist?(file_basename)
+      end
+      
+    end
+
+    raise "File #{file} already exists" if File.file?("#{file_basename}/#{file}")
+    FileUtils.cp_r("#{template_path}/skeleton", "#{file_basename}")
+    # FileUtils.cp("#{template_path}/resources/template.tex", "#{file_basename}")
+    File.rename("#{file_basename}/skeleton.Rmd", "#{file_basename}/#{file}")
+  end
+  
+end
+

data/lib/gknit/knitr_engine.rb

@@ -687,36 +687,3 @@ class KnitrEngine
   end
   
 end
-
-=begin
-module R
-
-  class Object
-
-    #--------------------------------------------------------------------------------------
-    # Redefine to_s in order to capture plots when in knitr
-    #--------------------------------------------------------------------------------------
-    
-    def to_s
-
-      STDERR.puts "+++++++++++++++++++++++++++"
-      STDERR.puts "in to_s"
-      STDERR.puts "+++++++++++++++++++++++++++"
-      
-      cap = nil
-      cap = R::Support.capture.call(r_interop)
-      str = String.new
-      (0...(cap.size - 1)).each do |i|
-        str << cap[i] << "\n"
-      end
-      str << cap[cap.size - 1] if cap.size >= 1
-      re = RubyEngine.instance
-      re.capture_plot
-      str
-    end
-
-  end
-  
-end
-
-=end

data/lib/util/exec_ruby.rb

@@ -98,7 +98,7 @@ module GalaazUtil
       # Execute the Ruby code in the scope of class RubyChunk. This is done
       # so that instance variables created in one chunk can be used again on
       # another chunk
-      # RubyChunk.instance_eval(code) if (options[["eval"]] >> 0)
+      # RChunk.instance_eval(code) if (options[["eval"]] >> 0)
       eval(code, RCbinding, __FILE__, __LINE__ + 1) if (options[["eval"]] >> 0)
       
       # add the returned value to the list
@@ -137,30 +137,4 @@ module GalaazUtil
     
   end
   
-  #----------------------------------------------------------------------------------------
-  # Used by old gknit.  Will eventually be replaced by exe_ruby
-  #----------------------------------------------------------------------------------------
-
-  def self.exec_ruby_tor(code)
-
-    # the output should be a list with the proper structure to pass to
-    # function engine_output.
-    out_list = R.list(R.structure(R.list(src: code), class: 'source'))
-    
-    # Set up standard output as a StringIO object.
-    $stdout = StringIO.new
-    RubyChunk.instance_eval(code)
-
-    # this should have captured everything in the evaluation code
-    # it is not working since at least RC10.
-    out = $stdout.string
-
-    out_list = R.c(out_list, out)
-    
-    # return $stdout to standard output
-    $stdout = STDOUT
-    R::Support.parse_arg(out_list)
-
-  end
-  
 end

data/specs/r_dataframe.spec.rb

@@ -321,7 +321,7 @@ describe R::DataFrame do
   end
 
   #----------------------------------------------------------------------------------------
-  context "Boostraping" do
+  context "Bootsraping" do
     
     before(:each) do
       @df = R.data__frame(x: R.rep((1..3), each: 2), y: (6..1), z: (~:letters)[(1..6)])
@@ -331,8 +331,8 @@ describe R::DataFrame do
     it "should do reordering with integer subsetting" do
       
       table = @df[R.sample(@df.nrow), :all]
-      expect(table.x[3]).to eq 3
-      expect(table.y[2]).to eq 5
+      expect(table.x[3]).to eq 1
+      expect(table.y[2]).to eq 6
       expect(table.z.levels[6]).to eq "f"
       
     end
@@ -340,17 +340,17 @@ describe R::DataFrame do
     it "should select random rows with integer subsetting" do
       table = @df[R.sample(@df.nrow, 3), :all]
       
-      expect(table.x[3]).to eq 3
-      expect(table.y[1]).to eq 3
-      expect(table.z.levels[table.z[2]]).to eq "b"
+      expect(table.x[3]).to eq 1
+      expect(table.y[1]).to eq 4
+      expect(table.z.levels[table.z[2]]).to eq "a"
     end
     
     it "should randomly reorder a dataframe" do
       df2 = @df[R.sample(@df.nrow), (3..1)]
       
-      expect(df2.z.levels[df2.z[4]]).to eq "c"
-      expect(df2.y[2]).to eq 5
-      expect(df2.x[5]).to eq 1
+      expect(df2.z.levels[df2.z[4]]).to eq "f"
+      expect(df2.y[2]).to eq 6
+      expect(df2.x[5]).to eq 2
     end
     
     it "should reorder by a given variable" do
@@ -358,8 +358,8 @@ describe R::DataFrame do
       df2 = df2[df2.x.order, :all]
       
       expect(df2.x[1]).to eq 1
-      expect(df2.y[1]).to eq 5
-      expect(df2.z.levels[df2.z[1]]).to eq "b"
+      expect(df2.y[1]).to eq 6
+      expect(df2.z.levels[df2.z[1]]).to eq "a"
     end
     
     it "should reorder variables" do

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

data/specs/tmp.rb

@@ -22,35 +22,56 @@
 ##########################################################################################
 
 require 'galaaz'
+# require 'gknit'
 
-puts RChunk
-puts RCbinding
-
-eval("a = 10", RCbinding)
-eval("puts a", RCbinding)
-
-code = <<-EOC
-     def test
-       puts "hello from test"
-     end
-EOC
-
-eval(code, RCbinding)
-eval("test", RCbinding)
+describe "error" do
+# describe R::DataFrame do
 
+  context "Bootsraping" do
 
+    it "should error with R" do
+      vec = R.c(2)
+      puts vec
+      # expect(vec[1]).to eq 2
+    end
 
 =begin
-code6 = <<-EOC
-  test
-EOC
+    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
 
-puts code2
 
-eval(code2, RubyChunk.binding)
+=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')
 
 ## Renaming columns
 

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "galaaz"
-$version="0.4.10"
+$version="0.5.0"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: galaaz
 version: !ruby/object:Gem::Version
-  version: 0.4.10
+  version: 0.5.0
 platform: ruby
 authors:
 - Rodrigo Botafogo
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-05-07 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:
@@ -80,88 +81,68 @@ files:
 - Rakefile
 - bin/galaaz
 - bin/gknit
+- bin/gknit-draft
+- bin/gknit-draft.rb
+- bin/gknit_Rscript
 - bin/grun
 - bin/gstudio
-- bin/gstudio.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.out
+- blogs/galaaz_ggplot/galaaz_ggplot.md
 - blogs/galaaz_ggplot/galaaz_ggplot.pdf
 - 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/galaaz_ggplot_files/figure-latex/midwest_rb.pdf
-- blogs/galaaz_ggplot/galaaz_ggplot_files/figure-latex/scatter_plot_rb.pdf
 - blogs/galaaz_ggplot/midwest.Rmd
 - blogs/galaaz_ggplot/midwest.html
 - blogs/galaaz_ggplot/midwest_external_png
 - blogs/gknit/gknit.Rmd
 - blogs/gknit/gknit.html
-- blogs/gknit/gknit.md
 - blogs/gknit/gknit.pdf
-- blogs/gknit/gknit.tex
 - blogs/gknit/lst.rds
-- blogs/gknit/marshal.dump
 - blogs/gknit/model.rb
 - blogs/gknit/stats.bib
-- blogs/manual/graph.rb
+- 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/nse_dplyr/nse_dplyr.tex
 - 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_files/figure-html/dose_len.png
-- blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.png
-- blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.png
-- blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.png
-- 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.png
-- 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.png
-- blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.png
-- blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.png
-- blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.png
-- blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.png
-- blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.svg
-- blogs/ruby_plot/ruby_plot_files/figure-latex/dose_len.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_delivery.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_dose.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color2.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_decorations.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_jitter.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_points.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/final_box_plot.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/final_violin_plot.png
-- blogs/ruby_plot/ruby_plot_files/figure-latex/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
@@ -171,11 +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
@@ -232,6 +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