kaplan_meier 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 22b752531bfcfd551c6faa4484fff906aa938dd4
+  data.tar.gz: 74360ad770530dd57933d8ad5db8b685d3561f25
+SHA512:
+  metadata.gz: 41a6c1663a0467a96fc763e82ecd0bcd47f78a57112861acaff58b472a6f9ee50477e7b09cd9b9e10ef85976e10585d152b319e8a42933309663f3739b25805f
+  data.tar.gz: ed0202e12f3a97e6cf7f585025cd8ad20b9c10b7b34b861a009599ef7642b72ace5add4b4e2b650e7a4f89ea5c9ed0d4b3198f18dad641b009cc3b73d77b986c

data/.gitignore

@@ -0,0 +1,12 @@
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status
+.idea

data/.rspec

@@ -0,0 +1,3 @@
+--format documentation
+--color
+--require spec_helper

data/.travis.yml

@@ -0,0 +1,5 @@
+sudo: false
+language: ruby
+rvm:
+  - 2.4.2
+before_install: gem install bundler -v 1.16.0

data/Gemfile

@@ -0,0 +1,6 @@
+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in kaplan_meier.gemspec
+gemspec

data/Gemfile.lock

@@ -0,0 +1,35 @@
+PATH
+  remote: .
+  specs:
+    kaplan_meier (0.1.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    diff-lcs (1.3)
+    rake (10.5.0)
+    rspec (3.7.0)
+      rspec-core (~> 3.7.0)
+      rspec-expectations (~> 3.7.0)
+      rspec-mocks (~> 3.7.0)
+    rspec-core (3.7.1)
+      rspec-support (~> 3.7.0)
+    rspec-expectations (3.7.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.7.0)
+    rspec-mocks (3.7.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.7.0)
+    rspec-support (3.7.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.16)
+  kaplan_meier!
+  rake (~> 10.0)
+  rspec (~> 3.0)
+
+BUNDLED WITH
+   1.16.0

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2018 seigel
+
+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

@@ -0,0 +1,70 @@
+# KaplanMeier
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/kaplan_meier`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+This current intent of this library is to support doing a Kaplan-Meier Survival Analysis and generating survival plots for subjects that have a brain tumour diagnosis.  This is in support of research being conducted to help create better treatments and improve outcomes.
+
+This does not mean it is only useful for that, but it is the initial driver of the interface for better or for worse.
+
+Please dive in and suggest changes through issues and pull requests.  The latter getting more attention.
+
+I will be using a couple of sites to validate the approach.  The current two sources I am using as truth are:
+
+* [Example from graphpad](https://s3.amazonaws.com/cdn.graphpad.com/faq/1757/file/P4-Survival%20analysis.pdf) 
+* [Survival Analysis From Stats Direct](https://statsdirect.com/help/survival_analysis/kaplan.htm)
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'kaplan_meier'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install kaplan_meier
+
+## Usage
+
+TODO: Improve these but taking the example data and results from graphpad, here is the current way it would be used.
+
+```ruby
+ # At some point I will try and generate decent docs.  If you look at the code
+ # it is using named parameters.
+  
+
+km = KaplanMeier.new
+km.add(46, 1, 1)
+km.add(64, 0, 1)
+km.add(78)
+km.add(124)
+km.add(130, 0, 1)
+km.add(150, 0, 2)
+
+km.raw_probabilities
+km.raw_probabilities(as_percent: true)
+km.probabilities
+km.probabilities(as_percent: true)
+
+km.range 
+km.values_for_range
+```
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/seigel/kaplan_meier.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/Rakefile

@@ -0,0 +1,6 @@
+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "kaplan_meier"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/kaplan_meier.gemspec

@@ -0,0 +1,36 @@
+
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "kaplan_meier/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "kaplan_meier"
+  spec.version       = KaplanMeier::VERSION
+  spec.authors       = ["seigel"]
+  spec.email         = ["kaplan_meier@paddlethis.com"]
+
+  spec.summary       = %q{Library to perform the Kaplan-Meier Survival Analysis.}
+  spec.description   = %q{Evolving library to support analysing data for subjects with brain tumours, and driving graphical representations.}
+  spec.homepage      = "https://github.com/seigel/kaplan_meier."
+  spec.license       = "MIT"
+
+  # Prevent pushing this gem to RubyGems.org. To allow pushes either set the 'allowed_push_host'
+  # to allow pushing to a single host or delete this section to allow pushing to any host.
+  if spec.respond_to?(:metadata)
+    spec.metadata["allowed_push_host"] = "https://rubygems.org"
+  else
+    raise "RubyGems 2.0 or newer is required to protect against " \
+      "public gem pushes."
+  end
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.16"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+end

data/lib/kaplan_meier/survival.rb

@@ -0,0 +1,110 @@
+require "kaplan_meier/version"
+
+module KaplanMeier
+  class Survival
+
+    def initialize
+      @data = {}
+    end
+
+    def add(time, event_count = 1, censored_count = 0)
+      leaf = @data[time]
+      if leaf.nil?
+        @data[time] = KaplanMeierCoord.new(time, event_count, censored_count)
+      else
+        leaf.add_count(event_count: event_count, censored_count: censored_count)
+      end
+    end
+
+    def initial_at_risk_count
+      self.to_a.length
+    end
+
+    def time_periods
+      @data.keys.sort
+    end
+
+    def to_a
+      @data.keys.sort.map do |k|
+        @data[k].to_a
+      end.flatten
+    end
+
+    def raw_probabilities(as_percent: false)
+      return [] if @data.keys.length < 1
+      self.probabilities.map {|i| as_percent ? (i[:probability] * 100.0).round(2) : i[:probability]}
+    end
+
+    def probabilities(as_percent: false)
+      return [] if @data.keys.length < 1
+      result = [{time: 0, probability: 1}]
+      time_points = self.to_a
+      n = time_points.length
+      percent = 1
+      (0...n).each do |i|
+        percent = (1.0 - (time_points[i][:event].to_f / (n - i))) * percent
+        result << {time: time_points[i][:time_point], probability: as_percent ? (percent * 100.0).round(2) : percent}
+      end
+      result
+    end
+
+    def range(start_time: 0, end_time: nil)
+      (start_time..(end_time || time_periods[-1])).to_a
+    end
+
+    def values_for_range(start_time: 0, end_time: nil, as_percent: false)
+      return [] if @data.keys.length < 1
+      result = []
+      range_array = range(start_time: start_time, end_time: end_time)
+      periods = probabilities(as_percent: as_percent)
+      current_period = periods.shift
+      range_value = range_array.shift
+      until range_value.nil?
+        if periods[0] && range_value >= periods[0][:time]
+          current_period = periods.shift
+          next
+        end
+        result << current_period[:probability]
+        range_value = range_array.shift
+      end
+      result
+    end
+
+  end
+end
+
+class KaplanMeierCoord
+  def initialize(time_point, event_count = 1, censored_count = 0)
+    @time_point = time_point
+    @event_count = event_count
+    @censored_count = censored_count
+  end
+
+  def add_event_count(event_count)
+    @event_count += event_count
+  end
+
+  def add_censored_count(censored_count)
+    @censored_count += censored_count
+  end
+
+  def add_count(event_count: 0, censored_count: 0)
+    add_event_count(event_count)
+    add_censored_count(censored_count)
+  end
+
+  def to_s
+    "@#{@time_point}: #{@event_count} event(s). #{@censored_count} censored."
+  end
+
+  def to_a
+    result = []
+    @event_count.times do
+      result << {time_point: @time_point, event: 1}
+    end
+    @censored_count.times do
+      result << {time_point: @time_point, event: 0}
+    end
+    result
+  end
+end

data/lib/kaplan_meier/version.rb

@@ -0,0 +1,3 @@
+module KaplanMeier
+  VERSION = "0.1.0"
+end

data/lib/kaplan_meier.rb

@@ -0,0 +1,6 @@
+require "kaplan_meier/version"
+require "kaplan_meier/survival"
+
+# module KaplanMeier
+#   # Your code goes here...
+# end

metadata

@@ -0,0 +1,102 @@
+--- !ruby/object:Gem::Specification
+name: kaplan_meier
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- seigel
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2018-02-16 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+description: Evolving library to support analysing data for subjects with brain tumours,
+  and driving graphical representations.
+email:
+- kaplan_meier@paddlethis.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- kaplan_meier.gemspec
+- lib/kaplan_meier.rb
+- lib/kaplan_meier/survival.rb
+- lib/kaplan_meier/version.rb
+homepage: https://github.com/seigel/kaplan_meier.
+licenses:
+- MIT
+metadata:
+  allowed_push_host: https://rubygems.org
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.13
+signing_key: 
+specification_version: 4
+summary: Library to perform the Kaplan-Meier Survival Analysis.
+test_files: []