galaaz 0.4.10 → 2.0.0

data/examples/islr/ch3_boston.rb

@@ -25,12 +25,23 @@ require 'ggplot'
 
 R.install_and_loads('ISLR', 'MASS')
 
+# Minimal breadcrumb logging to understand where the script gets stuck
+# when running `rake islr:all` (chapters are executed as scripts).
+def galaaz_islr_debug(msg)
+  STDERR.puts "[DEBUG islr][ch3_boston] #{Time.now.strftime('%H:%M:%S')} #{msg}"
+  STDERR.flush
+end
+
 # Simple linear regression from ISLR book.  Chapter 3 Lab
 # We are using qplot for plotting.  It would be better to use
 # ggplot2, but this is just to show simple ploting.
 
 # load boston data frame on variable boston
+bala = nil
+bala2 = nil
+galaaz_islr_debug('start; loading Boston')
 boston = ~:Boston
+galaaz_islr_debug('Boston loaded; printing names/lm')
 
 puts boston.names
 
@@ -49,7 +60,9 @@ puts pred
 puts boston.lstat
 puts boston.medv
 
+galaaz_islr_debug('before R.awt')
 R.awt
+galaaz_islr_debug('after R.awt; before first plot')
 
 puts R.qplot(:lstat, :medv, data: :Boston, col: "red") +
      R.geom_abline(intercept: boston_lm.coef[1],
@@ -62,25 +75,39 @@ puts R.qplot(:lstat, :medv, data: :Boston, col: "red") +
 # a = gets.chomp
 
 # sleep two seconds so that the graph shows up
+galaaz_islr_debug('sleep(2) after first plot')
 sleep(2)
+galaaz_islr_debug('grid__newpage #1')
 R.grid__newpage
 
+galaaz_islr_debug('building my_data #2 and plotting #2')
 R.my_data = R.data__frame(pred: R.predict(boston_lm), res: R.residuals(boston_lm))
 puts R.qplot(:pred, :res, data: :my_data)
 
+galaaz_islr_debug('sleep(2) after plot #2')
 sleep(2)
+galaaz_islr_debug('grid__newpage #2')
 R.grid__newpage
 
+galaaz_islr_debug('building my_data #3 and plotting #3')
 R.my_data = R.data__frame(pred: R.predict(boston_lm), res: R.rstudent(boston_lm))
 puts R.qplot(:pred, :res, data: :my_data)
 
+galaaz_islr_debug('sleep(2) after plot #3')
 sleep(2)
+galaaz_islr_debug('grid__newpage #3')
 R.grid__newpage
 
+galaaz_islr_debug('hatvalues + plotting #4')
 vals = R.hatvalues(boston_lm)
 R.my_data = R.data__frame(size: (1..vals.size), values: vals)
 # method size returns a Numeric... size is equivalent to 'length << 0'
 puts R.qplot(:size, :values, data: :my_data)
 
+galaaz_islr_debug('sleep(2) after plot #4')
 sleep(2)
+galaaz_islr_debug('grid__newpage #4')
 R.grid__newpage
+
+# Close the graphics device so later chapters don't keep an open AWT window.
+R.dev__off

data/examples/islr/ch6.spec.rb

@@ -29,34 +29,57 @@ context "ISLR" do
 
   context "Chapter 6 - Subset Selection Methods - page 244" do
 
+    def galaaz_islr_debug(msg)
+      STDERR.puts "[DEBUG islr][ch6.spec][#{Time.now.strftime('%H:%M:%S')}] #{msg}"
+      STDERR.flush
+    end
+
     before(:each) do
       @hitters = ~:Hitters
     end
     
     it "Should access the names of the dataset" do
+      galaaz_islr_debug 'test1 start (names/dim)'
       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
+      galaaz_islr_debug 'test1 end'
     end
 
     it "Should count na's using 'R.sum'" do
+      galaaz_islr_debug 'test2 start (R.sum)'
       expect(R.sum(@hitters.Salary.is__na) == 59).to eq true
       expect(R.sum(@hitters.Salary.is__na)).to eq 59
+      galaaz_islr_debug 'test2 end'
     end
 
     it "Should count na's using Ruby Enumerable 'sum'" do
+      galaaz_islr_debug "test3 start (Ruby Enumerable sum over Salary)"
+      yielded = 0
+      salary = @hitters.Salary
+      galaaz_islr_debug "test3 salary fetched; about to salary.size"
+      sz = salary.size
+      galaaz_islr_debug "test3 salary.size=#{sz}; about to Salary.sum"
       # 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)? 1 : 0 }).to eq 59
+      got = @hitters.Salary.sum do |e|
+        yielded += 1
+        galaaz_islr_debug("test3 yield #{yielded}") if yielded % 100 == 0
+        (e.is__na == true) ? 1 : 0
+      end
+      galaaz_islr_debug "test3 end (yielded=#{yielded}, got=#{got})"
+      expect(got).to eq 59
     end
 
     it "should remove missing values with na__omit" do
+      galaaz_islr_debug 'test4 start (na__omit)'
       @hitters = @hitters.na__omit
       expect(@hitters.dim == R.c(263, 20)).to eq true
       expect(R.sum(@hitters.is__na)).to eq 0
+      galaaz_islr_debug 'test4 end'
     end
     
   end

data/examples/latex_templates/Test-acm_article/Makefile

@@ -0,0 +1,16 @@
+# Produce sensys-abstract compliant PDFs from all Markdown files in a directory
+# Manuel Moraga | mmoraga@kth.se
+
+# List files to be made
+PDFS := $(patsubst %.md,%.pdf,$(wildcard *.md))
+
+all : $(PDFS)
+
+# Accepts PDF target with markdown syntax, makes them using pandoc
+%.pdf : %.md
+		pandoc $< -o $@ --template=shortpaper.latex --filter pandoc-citeproc --csl=acm-sig-proceedings.csl
+
+clean :
+		rm $(PDFS)
+
+rebuild: clean all

data/examples/latex_templates/Test-acm_article/Test-acm_article.Rmd

@@ -0,0 +1,65 @@
+---
+title: Short Paper
+author:
+  - name: Alice Anonymous
+    email: alice@example.com
+    affiliation: Some Institute of Technology
+  - name: Bob Security
+    email: bob@example.com
+    affiliation: Another University
+abstract: |
+  This is the abstract.
+
+  It consists of two paragraphs.
+bibliography: sigproc.bib
+output: rticles::acm_article
+    keep_md: true
+---
+
+
+
+# Introduction 
+Lorem ipsum dolor sit[@meier2012] amet, consectetur adipiscing[@fenner2012a] elit. Pellentesque rhoncus ut tellus eu tristique. Duis pharetra velit vitae viverra elementum. Nulla metus dui, pulvinar id enim at, pellentesque semper ipsum. Phasellus cursus dignissim ipsum, sed congue orci pretium quis. Maecenas rhoncus leo a cursus euismod. Fusce a erat eu ipsum tristique tempus at sed tortor. Aliquam erat volutpat. Donec at pretium lorem. Donec pretium nunc id nunc bibendum convallis. Phasellus quis enim id massa feugiat egestas hendrerit sollicitudin nibh. Sed blandit eros id tellus porta, eget ullamcorper urna posuere. Pellentesque laoreet lacus nibh, a mattis libero viverra sit amet. Sed vitae diam interdum, pharetra neque sit amet, dictum lectus.
+
+Donec massa justo, ultricies quis facilisis sed, tristique nec metus. Vestibulum id condimentum diam. Integer semper augue id porttitor ultrices. Cras vulputate felis eu diam porttitor, ac pulvinar nisi imperdiet. Donec eros felis, imperdiet vel malesuada at, varius et quam. Phasellus facilisis non risus eu placerat. Sed ac mollis lorem.
+
+# Evaluation
+Nullam semper imperdiet orci, at lacinia est aliquet et. Sed justo nibh, aliquet et velit at, pharetra consequat velit. Nullam nec ligula sagittis, adipiscing nisl sed, varius massa. Mauris quam ante, aliquet a nunc et, faucibus imperdiet libero. Suspendisse odio tortor, bibendum vel semper sit amet, euismod ac ante. Nunc nec dignissim turpis, ac blandit massa. Donec auctor massa ac vestibulum aliquam. Fusce auctor dictum lobortis. Vivamus tortor augue, convallis quis augue sit amet, laoreet tristique quam. Donec id volutpat orci. Suspendisse at mi vel elit accumsan porta ac ut diam. Nulla ut dapibus quam.
+
+Sed est odio, ornare in rutrum et, dapibus in urna. Suspendisse varius massa in ipsum placerat, quis tristique magna consequat. Suspendisse non convallis augue. Quisque fermentum justo et lorem volutpat euismod. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Morbi sagittis interdum justo, eu consequat nisi convallis in. Sed tincidunt risus id lacinia ultrices. Phasellus ac ligula sed mi mattis lacinia ac non felis. Etiam at dui tellus.
+
+# Conclusion
+Duis nec purus sed neque porttitor tincidunt vitae quis augue. Donec porttitor aliquam ante, nec convallis nisl ornare eu. Morbi ut purus et justo commodo dignissim et nec nisl. Donec imperdiet tellus dolor, vel dignissim risus venenatis eu. Aliquam tempor imperdiet massa, nec fermentum tellus sollicitudin vulputate. Integer posuere porttitor pharetra. Praesent vehicula elementum diam a suscipit. Morbi viverra velit eget placerat pellentesque. Nunc congue augue non nisi ultrices tempor.
+
+# References
+
+---
+references:
+- id: meier2012
+  title: Professinal Android 4 Application Development
+  author: 
+  - family: Meier
+    given: Reto
+  type: book
+  publisher: John Wiley & Sons, Inc.
+  issued:
+    year: 2012
+    month: 5
+- id: fenner2012a
+  title: One-click science marketing
+  author:
+  - family: Fenner
+    given: Martin
+  container-title: Nature Materials
+  volume: 11
+  URL: 'https://doi.org/10.1038/nmat3283'
+  DOI: 10.1038/nmat3283
+  issue: 4
+  publisher: Nature Publishing Group
+  page: 261-263
+  type: article-journal
+  issued:
+    year: 2012
+    month: 3
+...
+