survival 0.0.1
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- data/.gitignore +17 -0
- data/Gemfile +6 -0
- data/LICENSE.txt +22 -0
- data/README.md +34 -0
- data/Rakefile +24 -0
- data/lib/survival.rb +3 -0
- data/lib/survival/KaplanMeier.rb +56 -0
- data/lib/survival/SurvivalSample.rb +59 -0
- data/lib/survival/version.rb +3 -0
- data/survival.gemspec +19 -0
- data/test/survival_test.rb +21 -0
- data/test/test_helper.rb +5 -0
- metadata +59 -0
data/.gitignore
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2012 TODO: Write your name
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# Survival
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Functions related to survival analysis, such as Kaplan-Meier estimator of survival curves.
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## Installation
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Add this line to your application's Gemfile:
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gem 'survival'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install survival
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## Usage
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To generate a Kaplan-Meier survival plot:
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#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)
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points = KaplanMeier.generate_plot_points(SurvivalSample.create_survival_objects(survivals))
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#points is an array of [x,y] pairs for plotting. Use your favorite plotting library to plot the line graph.
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## Contributing
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1. Fork it
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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data/Rakefile
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require "bundler/gem_tasks"
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require 'rake/testtask'
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require 'rdoc/task'
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desc 'Default: run tests.'
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task :default => :test
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desc 'Run unit tests.'
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Rake::TestTask.new(:test) do |t|
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t.libs << 'lib'
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t.libs << 'test'
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t.pattern = 'test/**/*_test.rb'
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t.verbose = true
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end
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desc 'Generate documentation'
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Rake::RDocTask.new(:rdoc) do |rdoc|
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = 'Survival'
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rdoc.options << '--line-numbers' << '--inline-source'
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rdoc.rdoc_files.include('README.md')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/lib/survival.rb
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#########################################
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#
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# Creates a survival plot using the
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# Kaplan-Meier method.
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#
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#########################################
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class KaplanMeier
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#Creates the x,y pairs for plotting a survival curve,
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#using the Kaplan-Meier method.
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def self.generate_plot_points(survivals)
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bins = SurvivalSample.bin_survivals(survivals)
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points = [[0,100]]
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terms = Array.new
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n = survivals.length #Number we are considering at this time point (total surviving minus censored)
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prev = 100
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bins.keys.sort.each do |t|
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survs = bins[t]
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#Update counts for this time point
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d = 0 #Number that have died at this time point
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survs.each do |s|
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n = n-1
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if not s.censored
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d = d + 1
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end
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end
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#Calculate the probability of survival for this time point
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s_t = 1
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terms.each do |term|
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s_t = s_t * term
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end
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curr_term = (n - d).to_f / n
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terms << curr_term
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s_t = s_t * 100.0
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#Add to plot points
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points << [t, prev] #Horizontal line from previous point
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points << [t, s_t] #Current point
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prev = s_t
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end
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return points
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end
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end
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#########################################
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#
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# Object for holding survival data.
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#
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# Roman Eisner
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#
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#########################################
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class SurvivalSample
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attr_accessor :censored, :event
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def initialize(censored, event)
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@censored = censored
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@event = event
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end
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def to_s
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"Survival: {Event: #{@event}, Censored: #{@censored}}"
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end
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#Sort method:
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def <=>(o)
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if self.event != o.event
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return self.event <=> o.event
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else
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if (self.censored == o.censored)
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return 0
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elsif self.censored
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return 1
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else
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return -1
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end
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end
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end
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#Takes an array of Survival objects, and returns a binned hash.
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def SurvivalSample.bin_survivals(survs)
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bins = Hash.new
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survs.each do |s|
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bins[s.event] ||= Array.new
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bins[s.event] << s
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end
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return bins
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end
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#Takes an array of hashes, each has must have two keys:
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# :event => The event time
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# :censored => A boolean, true if this patient has been right-censored.
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def SurvivalSample.create_survival_objects(surv_array)
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return surv_array.map { |s| SurvivalSample.new(s[:censored], s[:event]) }
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end
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end
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data/survival.gemspec
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# -*- encoding: utf-8 -*-
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'survival/version'
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Gem::Specification.new do |gem|
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gem.name = "survival"
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gem.version = Survival::VERSION
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gem.authors = ["Roman Eisner"]
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gem.email = ["ithmatic@gmail.com"]
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gem.description = %q{A gem that provides survival analysis functionality}
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gem.summary = %q{Kaplan-Meier Estimation}
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gem.homepage = "https://github.com/reisner/survival"
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gem.files = `git ls-files`.split($/)
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gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
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gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
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gem.require_paths = ["lib"]
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end
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require 'test_helper'
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class SurvivalTest < ActiveSupport::TestCase
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@@survivals = [{:event => 3, :censored => false}, {:event => 4, :censored => true}]
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test 'km plot' do
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p = KaplanMeier.generate_plot_points(SurvivalSample.create_survival_objects(@@survivals))
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assert_equal [[0, 100], [3, 100], [3, 100.0], [4, 100.0], [4, 0.0]], p
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end
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test 'survival_sample array' do
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assert_equal 2, SurvivalSample.create_survival_objects(@@survivals).length
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end
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test 'survival_sample new' do
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assert_equal false, SurvivalSample.new(false, 34).censored
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assert_equal 34, SurvivalSample.new(false, 34).event
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end
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end
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data/test/test_helper.rb
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metadata
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--- !ruby/object:Gem::Specification
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name: survival
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version: !ruby/object:Gem::Version
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version: 0.0.1
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prerelease:
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platform: ruby
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authors:
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- Roman Eisner
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-11-23 00:00:00.000000000 Z
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dependencies: []
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description: A gem that provides survival analysis functionality
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email:
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- ithmatic@gmail.com
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executables: []
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extensions: []
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extra_rdoc_files: []
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files:
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- .gitignore
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- Gemfile
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- LICENSE.txt
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- README.md
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- Rakefile
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- lib/survival.rb
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- lib/survival/KaplanMeier.rb
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- lib/survival/SurvivalSample.rb
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- lib/survival/version.rb
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- survival.gemspec
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- test/survival_test.rb
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- test/test_helper.rb
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homepage: https://github.com/reisner/survival
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licenses: []
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 1.8.23
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signing_key:
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specification_version: 3
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summary: Kaplan-Meier Estimation
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test_files:
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- test/survival_test.rb
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- test/test_helper.rb
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