survival 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in survival.gemspec
+gemspec
+
+gem "rails", "~> 3.2.6"

data/LICENSE.txt

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+Copyright (c) 2012 TODO: Write your name
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Survival
+
+Functions related to survival analysis, such as Kaplan-Meier estimator of survival curves.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'survival'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install survival
+
+## Usage
+
+To generate a Kaplan-Meier survival plot:
+
+    #survivals is an array of hashes. Each represents a sample, and must define :event (the event time) and :censored (boolean describing whether this sample is censored)
+    points = KaplanMeier.generate_plot_points(SurvivalSample.create_survival_objects(survivals))
+
+    #points is an array of [x,y] pairs for plotting. Use your favorite plotting library to plot the line graph.
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+
+require 'rake/testtask'
+require 'rdoc/task'
+
+desc 'Default: run tests.'
+task :default => :test
+
+desc 'Run unit tests.'
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'lib'
+  t.libs << 'test'
+  t.pattern = 'test/**/*_test.rb'
+  t.verbose = true
+end
+
+desc 'Generate documentation'
+Rake::RDocTask.new(:rdoc) do |rdoc|
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title    = 'Survival'
+  rdoc.options << '--line-numbers' << '--inline-source'
+  rdoc.rdoc_files.include('README.md')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/lib/survival.rb

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+require 'survival/version'
+require 'survival/KaplanMeier'
+require 'survival/SurvivalSample'

data/lib/survival/KaplanMeier.rb

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+#########################################
+#
+# Creates a survival plot using the
+# Kaplan-Meier method.
+#
+#########################################
+
+class KaplanMeier
+
+  #Creates the x,y pairs for plotting a survival curve, 
+  #using the Kaplan-Meier method.
+  def self.generate_plot_points(survivals)
+
+    bins = SurvivalSample.bin_survivals(survivals)
+
+    points = [[0,100]]
+
+    terms = Array.new
+    n = survivals.length #Number we are considering at this time point (total surviving minus censored)
+    prev = 100
+    bins.keys.sort.each do |t|
+
+      survs = bins[t]
+
+      #Update counts for this time point
+      d = 0 #Number that have died at this time point
+      survs.each do |s|
+        n = n-1 
+
+        if not s.censored
+          d = d + 1
+        end
+      end
+
+      #Calculate the probability of survival for this time point
+      s_t = 1
+      terms.each do |term|
+        s_t = s_t * term
+      end
+
+      curr_term = (n - d).to_f / n
+      terms << curr_term
+
+      s_t = s_t * 100.0
+
+      #Add to plot points
+      points << [t, prev] #Horizontal line from previous point
+      points << [t, s_t] #Current point
+      prev = s_t
+
+    end
+
+    return points
+  end
+
+end

data/lib/survival/SurvivalSample.rb

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+#########################################
+#
+# Object for holding survival data.
+#
+# Roman Eisner
+#
+#########################################
+
+class SurvivalSample
+
+  attr_accessor :censored, :event
+
+  def initialize(censored, event)
+    @censored = censored
+    @event = event
+  end
+
+    def to_s
+    "Survival: {Event: #{@event}, Censored: #{@censored}}"
+  end
+
+  #Sort method:
+  def <=>(o)
+
+    if self.event != o.event
+      return self.event <=> o.event
+    else
+      if (self.censored == o.censored)
+        return 0
+      elsif self.censored
+        return 1
+      else
+        return -1
+      end
+    end
+
+  end
+
+  #Takes an array of Survival objects, and returns a binned hash.
+  def SurvivalSample.bin_survivals(survs)
+    bins = Hash.new
+
+    survs.each do |s|
+      bins[s.event] ||= Array.new
+
+      bins[s.event] << s
+    end
+
+    return bins
+  end
+
+  #Takes an array of hashes, each has must have two keys:
+  # :event => The event time
+  # :censored => A boolean, true if this patient has been right-censored.
+  def SurvivalSample.create_survival_objects(surv_array)
+    return surv_array.map { |s| SurvivalSample.new(s[:censored], s[:event]) }
+  end
+
+end

data/lib/survival/version.rb

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+module Survival
+  VERSION = "0.0.1"
+end

data/survival.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'survival/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "survival"
+  gem.version       = Survival::VERSION
+  gem.authors       = ["Roman Eisner"]
+  gem.email         = ["ithmatic@gmail.com"]
+  gem.description   = %q{A gem that provides survival analysis functionality}
+  gem.summary       = %q{Kaplan-Meier Estimation}
+  gem.homepage      = "https://github.com/reisner/survival"
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+end

data/test/survival_test.rb

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+require 'test_helper'
+
+class SurvivalTest < ActiveSupport::TestCase
+
+  @@survivals = [{:event => 3, :censored => false}, {:event => 4, :censored => true}]
+
+  test 'km plot' do
+    p = KaplanMeier.generate_plot_points(SurvivalSample.create_survival_objects(@@survivals))
+    assert_equal [[0, 100], [3, 100], [3, 100.0], [4, 100.0], [4, 0.0]], p
+  end
+
+  test 'survival_sample array' do
+    assert_equal 2, SurvivalSample.create_survival_objects(@@survivals).length
+  end
+
+  test 'survival_sample new' do
+    assert_equal false, SurvivalSample.new(false, 34).censored
+    assert_equal 34, SurvivalSample.new(false, 34).event
+  end
+
+end

data/test/test_helper.rb

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+require 'active_support'
+require 'test/unit'
+require 'survival'
+
+ENV["RAILS_ENV"] = "test"

metadata

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+--- !ruby/object:Gem::Specification
+name: survival
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Roman Eisner
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-11-23 00:00:00.000000000 Z
+dependencies: []
+description: A gem that provides survival analysis functionality
+email:
+- ithmatic@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/survival.rb
+- lib/survival/KaplanMeier.rb
+- lib/survival/SurvivalSample.rb
+- lib/survival/version.rb
+- survival.gemspec
+- test/survival_test.rb
+- test/test_helper.rb
+homepage: https://github.com/reisner/survival
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Kaplan-Meier Estimation
+test_files:
+- test/survival_test.rb
+- test/test_helper.rb