scicom 0.3.0-java → 0.4.0-java

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data/README.md

@@ -1,74 +1,258 @@
-Announcement
-============
+## SciCom with Standard R Interface
 
-SciCom (Scientific Computing) for Ruby brings the power of R to the Ruby community. SciCom 
-is based on Renjin, a JVM-based interpreter for the R language for statistical computing.
+SciCom allows R programmers to use R commands inside a Ruby script in
+a way similar to RinRuby by calling method eval and passing to it an R
+script:
 
-R on the JVM
-------------
+    # Basic integration with R can always be done by calling eval and passing it a valid
+    # R expression.
+    > R.eval("r.i = 10L")
+    > R.eval("print(r.i)")
 
-Over the past two decades, the R language for statistical computing has emerged as the de 
-facto standard for analysts, statisticians, and scientists. Today, a wide range of 
-enterprises – from pharmaceuticals to insurance – depend on R for key business uses. Renjin 
-is a new implementation of the R language and environment for the Java Virtual Machine (JVM),
-whose goal is to enable transparent analysis of big data sets and seamless integration with 
-other enterprise systems such as databases and application servers.
+    [1] 10
 
-Renjin is still under development, but it is already being used in production for a number 
-of client projects, and supports most CRAN packages, including some with C/Fortran 
-dependencies.
+    > R.eval("vec = c(10, 20, 30, 40, 50)")
+    > R.eval("print(vec)")
 
-SciCom and Renjin
------------------
+    [1] 10 20 30 40 50
 
-SciCom integrates with Renjin and allows the use of R inside a Ruby script. In a sense, 
-SciCom is similar to other solutions such as RinRuby, Rpy2, PipeR, etc. However, since 
-SciCom and Renjin both target the JVM there is no need to integrate both solutions and 
-there is no need to send data between Ruby and R, as it all resides in the same JVM. 
-Further, installation of SciCom does not require the installation of GNU R; Renjin is the 
-interpreter and comes with SciCom. Finally, although SciCom provides a basic interface to 
-Renjin similar to RinRuby, a much tighter integration is also possible.
+    > R.eval("print(vec[1])")
 
-SciCom and Renjin Limitations
-------------------------------
+    [1] 10
 
-Renjin is in development and still has some limitations
+Programmers can also use here docs to integrate an R script inside a
+Ruby script.  The next example show a model for predicting baseball
+wins based on runs allowed and runs scored.  The data comes from
+Baseball-Reference.com.
 
-  + Renjin does not allow dynamic loading of libaries.  My understanding is that Renjin 
-  developers are actually working on a new version on which loading of libraries will be
-  possible.
-  + Renjin does not implement any of the graphical libaries such as plot or ggplot. We
-  hope that this limitation will be solved not by implementing those libraries but by the
-  use of Ruby libraries from SciRuby such as NyaPlot (https://github.com/domitry/nyaplot) 
-  or daru (https://github.com/v0dro/daru).
+      R.eval <<EOF
 
-What´s new:
-===========
+        # This dataset comes from Baseball-Reference.com.
+        baseball = read.csv("baseball.csv")
+        # str has a bug in Renjin
+        # str(data)
 
-This version includes integration of MDArray and SciCom. 
+        # Lets look at the data available for Momeyball.
+        moneyball = subset(baseball, Year < 2002)
 
+        # Let's see if we can predict the number of wins, by lookin at
+        # runs allowed (RA) and runs scored (RS).  RD is the runs difference.
+        # We are making a linear model from predicting wins (W) based on RD
+        moneyball$RD = moneyball$RS - moneyball$RA
+        WinsReg = lm(W ~ RD, data=moneyball)
+        print(summary(WinsReg))
 
-SciCom installation and download:
-==================================
+    EOF
 
-  + Install Jruby
-  + jruby –S gem install scicom
+The output of the program above is:
 
-SciCom Homepages:
-==================
+    Call:
+    lm(data = moneyball, formula = W ~ RD)
 
-  + http://rubygems.org/gems/scicom
-  + https://github.com/rbotafogo/scicom/wiki
+    Residuals:
+        Min      1Q  Median      3Q     Max
+    -14,266  -2,651   0,123   2,936  11,657
 
-Contributors:
-=============
-Contributors are welcome.
+    Coefficients:
+                Estimate   Std. Error t value    Pr(>|t|)             
+    (Intercept) 80,881     0,131      616,675    <0         ***       
+             RD 0,106      0,001       81,554    <0         ***       
+    ---
+    Signif. codes:  0 '***' 0,001 '**' 0,01 '*' 0,05 '.' 0,1 ' ' 1 
 
-SciCom History:
-================
+    Residual standard error: 3,939 on 900 degrees of freedom
+    Multiple R-squared: 0,8808,	Adjusted R-squared: 0,8807 
+    F-statistic: 6.650,9926 on 1 and 900 DF,  p-value: < 0
+
+## The SciCom “language”
+
+SciCom also allows for implementing R scripts in a “language” that is
+just like Ruby, so that the developer does not need to know that she
+is actually writing an R script.  All R methods are accessible through
+an R namespace.
+
+The next script is the same baseball model done in R above using
+SciCom ‘language’:
+
+    require ‘scicom’
+    # This dataset comes from Baseball-Reference.com.
+    baseball = R.read__csv("baseball.csv")
+    # Lets look at the data available for Momeyball.
+    moneyball = baseball.subset(baseball.Year < 2002)
+
+    # Let's see if we can predict the number of wins, by looking at
+    # runs allowed (RA) and runs scored (RS).  RD is the runs difference.
+    # We are making a linear model for predicting wins (W) based on RD
+    moneyball.RD = moneyball.RS - moneyball.RA
+    wins_reg = R.lm("W ~ RD", data: moneyball)
+    wins_reg.summary.pp
+
+We show bellow an example of calculating the correlation matrix
+without using the build-in functions.  First this is done in an R
+script and then using SciCom:
+
+    # Create a matrix and give it rownames and colnames
+    set.seed(42)
+    Xij <- matrix(sample(seq(0, 9), 40, replace = TRUE), ncol = 4)
+    rownames(Xij) <- paste("S", seq(1, dim(Xij)[1]), sep = "")
+    colnames(Xij) <- paste("V", seq(1, dim(Xij)[2]), sep = "")
+ 
+    # find the means of the columns
+    n <- dim(Xij)[1]
+    one <- rep(1, n)
+    X.means <- t(one) %*% Xij/n
+ 
+    # find the covariance of the matrix
+    X.diff <- Xij - one %*% X.means
+    X.cov <- t(X.diff) %*% X.diff/(n - 1)
+    round(X.cov, 2)
+ 
+    # find the correlation 
+    sdi <- diag(1/sqrt(diag(X.cov)))
+    rownames(sdi) <- colnames(sdi) <- colnames(X.cov)
+    round(sdi, 2)
+    X.cor <- sdi %*% X.cov %*% sdi
+    rownames(X.cor) <- colnames(X.cor) <- colnames(X.cov)
+    round(X.cor, 2)
+
+Now the same code using SciCom
+
+    require ‘scicom’
+    # Create a matrix and give it rownames and colnames
+    R.set__seed(42)
+	R.seq(0,9).sample(40, replace: TRUE).matrix(ncol: 4)
+	  .fassign(:rownames, R.paste("S", R.seq(1, xij.attr.dim[1]), sep: ""))
+      .fassign(:colnames, R.paste("V", R.seq(1, xij.attr.dim[2]), sep: ""))
+ 
+    # find the means of the columns
+    n = xij.dim[1]
+    one = R.rep(1, n)
+    x_means = one.t._ :*, xij/n
+ 
+    # find the covariance of the matrix
+    x_diff = xij - (one._ :*, x_means)
+    x_cov = (x_diff.t._ :*, x_diff/(n - 1)).round(2)
+ 
+    # find the correlation 
+    sdi = (1 / x_cov.diag.sqrt).diag.round(2)
+    sdi.fassign(:rownames, x_cov.rownames)
+    sdi.fassign(:colnames, x_cov.colnames)
+    x_cor = ((sdi._ :*, x_cov)._ :*, sdi)
+      .round(2)
+      .fassign(:rownames, x_cov.rownames)
+      .fassign(:colnames, x_cov.colnames)
+
+As another example, here is a SciCom script to print the number of
+days for every month is 2005:
+
+    require ‘scicom’
+    everyday = R.seq(from: R.as__Date('2005-1-1'), to: R.as__Date('2005-12-31'), by: 'day')
+    cmonth = everyday.format('%b')
+    cmonth
+      .factor(levels: cmonth.unique, ordered: TRUE)
+      .table
+      .pp
+
+As can be seen from these examples, R methods can be accessed through
+the R namespace in SciCom, so, R method ‘seq’ is called in SciCom as
+‘R.seq’.  R methods that are applied on objects can be called in two
+ways, either using the R namespace as in ‘R.factor’ or directly on the
+object, as in this case we did ‘cmonth.factor’.  This last example
+shows how SciCom allows method chaining, which is not possible in an R
+script.
+
+## R Functions
+
+SciCom allows programmers to access any R function in the R namespace.  For instance, as shown
+above, function _c_ in R can be access in SciCom by a call to R.c.  As another example,
+method _seq_ in R is accessed in SciCom by a call to R.seq.
+
+Parameters can be passed to R functions normaly.  For example, the code bellow creates a vector
+with with doubles:
+
+	> vec = R.c(2.4, 5.55, 10, 18.27, 34.45)
+	> vec.pp
+
+	[1]   2,4  5,55    10 18,27 34,45
+
+Ruby variable can also be passed as arguments to R methods:
+
+	> vec2 = R.c(vec, 3.5)
+	> vec2.pp
+
+	[1]   2,4  5,55    10 18,27 34,45   3,5
+
+	> dbl = 3.5
+	> vec3 = R.c(vec2, dbl)
+	> vec3.pp
+
+	[1]   2,4  5,55    10 18,27 34,45   3,5  5,75
+
+More complex Ruby classes, such ar Ruby hashes, of course, cannot be passed as argument to R
+methods.  SciCom, in principle, should support every Ruby method that is available in
+Renjin.  Note that Renjin is still under development and not all methods and libraries are
+available.
+
+Some methods and variables in R have a '.' in their names.  This is standard R notation;
+however, '.' in Ruby is interpreted as a method call and thus cannot be part of a
+variable name or function.  In order to access names in R that have a '.' on them
+in SciCom, the '.' is substituted by '__':
+
+	> # variable defined in R with a '.' in the name
+	> R.eval("r.d = 10.35")
+	> # access the variable 'r.d' in Ruby by using '__' notation
+	> R.r__d.pp
+
+	[1] 10,35
+
+Accessing method _as.complex_ in R is also done by using '__' notation:
+
+	# acess R method 'as.complex' using 'as__complex' notation
+	> comp = R.as__complex(-1)
+	> p R.Re(comp).gz
+
+	-1.0
+	
+	> p R.Im(comp).gz
+
+	0.0
+
+	> # now method 'is.complex'
+	> p R.is__complex(comp).gt
+
+	true
+
+### Method Chaining
+
+SciCom allows methods to be chained.  The code above can be written as:
+
+	# prints the real part of a complex number by using method chaining
+	> R.as__complex(-1)
+		.Re
+		.pp
+
+	[1] -1
+
+We will see more examples of method chaining later in this documentation.
+In principle, we will try to use method chaining whenever possible, but
+in some situations normal use of R methods through the 'R.' notation will
+be used to remind the reader that this notation is also possible.
+
+### Named Parameters
+
+R allows the use of named parameters in function calls.  SciCom also allows
+for named parameters.  Named parameters in SciCom require the use of
+Ruby hashes in the normal Ruby way.
+
+    > # R code to create a complex number
+	> R.eval("comp = complex(real = 0, imaginary = 1)")
+	> R.eval("print(comp)")
+
+	[0.0+1.0i]
+
+	> # Same code as above in SciCom notation, with chaining
+	> R.complex(real: 0, imaginary: 1)
+	>   .pp
+
+	[0.0+1.0i]
 
-  + 30/Dec/2014: Version 0.2.3 - Integration with MDArray
-  + 19/Nov/2014: Version 0.2.2 - Printing in Jirb
-  + 17/Nov/2014: Version 0.2.1 - Added MDArray dependency
-  + 17/Nov/2014: Version 0.2.0 - Most R functionality available to SciCom	
-  + 21/Jul/2014: Version 0.0.1 - Initial release

data/Rakefile

@@ -1,14 +1,67 @@
+require 'rbconfig'
 require 'rake/testtask'
-require_relative 'version'
+require 'jars/installer'
+require 'jars/classpath'
+require 'rake/javaextensiontask'
+
+require './version'
+
+$env = `uname -o`.strip
+$mdarray = `bundle show mdarray`.strip
+# $mdarray_vendor = "#{$mdarray}/vendor/"
+
+##########################################################################################
+# Prepare environment to work inside Cygwin
+##########################################################################################
+
+if $env == 'Cygwin'
+
+  #---------------------------------------------------------------------------------------
+  # Return the cygpath (windows format) of a path in POSIX format, i.e., /home/...
+  #---------------------------------------------------------------------------------------
+  
+  def set_path(path)
+    `cygpath -a -w #{path}`.tr("\n", "")
+  end
+  
+else
+  
+  #---------------------------------------------------------------------------------------
+  # Return the given path.  When not in cygwin then just use the given path
+  #---------------------------------------------------------------------------------------
+  
+  def set_path(path)
+    path
+  end
+  
+end
+##########################################################################################
+
+# $mdarray_path = set_path($mdarray_vendor)
+
+# p "#{$mdarray_path}"
+# p Dir.entries("#{$mdarray_path}")
+# p FileList["#{$mdarray_path}/*.jar"]
 
 name = "#{$gem_name}-#{$version}.gem"
 
-rule '.class' => '.java' do |t|
-  sh "javac #{t.source}"
+task :install_jars do
+  Jars::JarInstaller.new.vendor_jars
+end
+
+Rake::JavaExtensionTask.new("scicom") do |ext|
+  jruby_home = RbConfig::CONFIG['prefix']
+  # ext.ext_dir = 'ext/java'
+  # ext.lib_dir = 'lib/nokogiri'
+  # jars = ["#{jruby_home}/lib/jruby.jar"] + FileList['lib/*.jar']
+  # jars = FileList["#{$mdarray_path}/*.jar"]
+  jars = FileList['vendor/*.jar']
+  ext.classpath = jars.map { |x| File.expand_path x }.join ':'
+  # ext.debug = true if ENV['JAVA_DEBUG']
 end
 
-desc 'default task'
-task :default => [:install_gem]
+desc 'compile java files'
+Rake::JavaExtensionTask.new("scicom")
 
 desc 'Makes a Gem'
 task :make_gem do

data/config.rb

@@ -1,5 +1,19 @@
 require 'rbconfig'
+require 'java'
+
+#
+# In principle should not be in this file.  The right way of doing this is by executing
+# bundler exec, but I don't know how to do this from inside emacs.  So, should comment
+# the next line before publishing the GEM.  If not commented, this should be harmless
+# anyway.
+#
+
+begin
+  require 'bundler/setup'
+rescue LoadError
+end
 
+=begin
 ##########################################################################################
 # Configuration. Remove setting before publishing Gem.
 ##########################################################################################
@@ -8,14 +22,15 @@ require 'rbconfig'
 $DVLP = true
 
 # Set to 'cygwin' when in cygwin
-# $ENV = 'cygwin'
+$ENV = 'cygwin'
 
 # Set development dependency: those are gems that are also in development and thus not
 # installed in the gem directory.  Need a way of accessing them if we are in development
 # otherwise gem install will install the dependency
 if $DVLP
-  $DEPEND=["MDArray"]
+  $DEPEND=["SciCom", "MDArray"]
 end
+=end
 
 ##########################################################################################
 
@@ -36,6 +51,7 @@ end
   else 'default'
   end
 
+=begin
 #---------------------------------------------------------------------------------------
 # Add path to load path
 #---------------------------------------------------------------------------------------
@@ -77,6 +93,7 @@ else
   end
   
 end
+=end
 
 #---------------------------------------------------------------------------------------
 # Set the project directories
@@ -124,6 +141,7 @@ class SciCom
 
 end
 
+=begin
 #---------------------------------------------------------------------------------------
 # Set dependencies
 #---------------------------------------------------------------------------------------
@@ -166,5 +184,19 @@ if ($DVLP == true)
 
 end
 
+
 # Add cran directory to the $LOAD_PATH search path
 mklib(SciCom.cran_dir, false)
+=end
+
+##########################################################################################
+# Load necessary jar files
+##########################################################################################
+
+Dir["#{SciCom.vendor_dir}/*.jar"].each do |jar|
+  require jar
+end
+
+Dir["#{SciCom.target_dir}/*.jar"].each do |jar|
+  require jar
+end