From 1f789133d961c29d3babfaf69cdde3d675288537 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Sat, 24 Aug 2019 14:44:52 +0200
Subject: initial refactored version for mutagenicity paper

---
 lib/array.rb | 87 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 87 insertions(+)
 create mode 100644 lib/array.rb

(limited to 'lib/array.rb')

diff --git a/lib/array.rb b/lib/array.rb
new file mode 100644
index 0000000..55186bd
--- /dev/null
+++ b/lib/array.rb
@@ -0,0 +1,87 @@
+class Array
+
+  # Sum the size of single arrays in an array of arrays
+  # @param [Array] Array of arrays
+  # @return [Integer] Sum of size of array elements
+  def sum_size
+    self.inject(0) { |s,a|
+      if a.respond_to?('size')
+        s+=a.size
+      else
+        internal_server_error "No size available: #{a.inspect}"
+      end
+    }
+  end
+
+  # Check if the array has just one unique value.
+  # @param [Array] Array to test.
+  # @return [TrueClass,FalseClass] 
+  def zero_variance?
+    return self.uniq.size == 1
+  end
+
+  # Get the median of an array
+  # @return [Numeric]
+  def median
+    sorted = self.sort
+    len = sorted.length
+    (sorted[(len - 1) / 2] + sorted[len / 2]) / 2.0
+  end
+
+  # Get the mean of an array
+  # @return [Numeric]
+  def mean
+    self.compact.inject{ |sum, el| sum + el }.to_f / self.compact.size
+  end
+
+  # Get the variance of an array
+  # @return [Numeric]
+  def sample_variance
+    m = self.mean
+    sum = self.compact.inject(0){|accum, i| accum +(i-m)**2 }
+    sum/(self.compact.length - 1).to_f
+  end
+
+  # Get the standard deviation of an array
+  # @return [Numeric]
+  def standard_deviation
+    Math.sqrt(self.sample_variance)
+  end
+  
+  # Calculate dot product 
+  # @param [Array]
+  # @return [Numeric]
+  def dot_product(a)
+    products = self.zip(a).map{|a, b| a * b}
+    products.inject(0) {|s,p| s + p}
+  end
+
+  # Calculate magnitude
+  # @return [Numeric]
+  def magnitude
+    squares = self.map{|x| x ** 2}
+    Math.sqrt(squares.inject(0) {|s, c| s + c})
+  end
+
+  # Convert array values for R
+  # @return [Array]
+  def for_R
+    if self.first.is_a?(String) 
+      #"\"#{self.collect{|v| v.sub('[','').sub(']','')}.join(" ")}\"" # quote and remove square brackets
+      "NA"
+    else
+      self.median
+    end
+  end
+
+  # Collect array with index
+  #   in analogy to each_with_index
+  def collect_with_index
+    result = []
+    self.each_with_index do |elt, idx|
+      result << yield(elt, idx)
+    end
+    result
+  end
+end
+
-- 
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