byar 0.1.1 → 1.0.0

checksums.yaml

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data/.gitignore

@@ -0,0 +1,7 @@
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/tmp/

data/CHANGELOG.md

@@ -0,0 +1,18 @@
+# Changelog
+
+## v1.0.0
+
+* MIT License added
+
+## v0.1.1
+
+* Support for passing custom `z_value`
+
+## v0.1.0
+
+* Internal refactor
+* Change version number to follow pre-1.0 semantic versioning
+
+## v.0.0.1
+
+* Initial release

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in byar.gemspec
+gemspec

data/Gemfile.lock

@@ -0,0 +1,22 @@
+PATH
+  remote: .
+  specs:
+    byar (1.0.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    minitest (5.11.3)
+    rake (10.5.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.17)
+  byar!
+  minitest (~> 5.11)
+  rake (~> 10.0)
+
+BUNDLED WITH
+   1.17.1

data/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2011-2033 Floris Huetink
+
+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 +1,48 @@
+# Byar
+
+Byar's approximation calculator in Ruby. Useful when working with (H)SMR mortality models used in hospitals worldwide.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'byar'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install byar
+
+## Usage
+
+Use `Byar.lower(observed, expected)` and `Byar.upper(observed, expected)` to get 95% Byar confidence intervals.
+
+Other features:
+
+* Call `Byar.new` to instantiate an object
+* Change the `z_value` used (defaults to 1.96, which corresponds to 95% confidence interval)
+
+Please note that 1 is used as reference point for cases where `observed` == `expected` (not 100).
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake test` 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/florish/byar. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## License
+
+Byar is released under the [MIT License](./LICENSE).
+
+## Code of Conduct
+
+Everyone interacting in the Byar project’s codebases, issue trackers, and related communication channels is expected to follow the [code of conduct](./CODE_OF_CONDUCT.md).

data/Rakefile

@@ -0,0 +1,9 @@
+require 'bundler/gem_tasks'
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+end
+
+desc "Run tests"
+task :default => :test

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "byar"
+
+# 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/byar.gemspec

@@ -0,0 +1,30 @@
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "byar/version"
+
+Gem::Specification.new do |spec|
+  spec.name = 'byar'
+  spec.version = Byar::VERSION
+  spec.authors = ['Floris Huetink']
+  spec.email = 'floris@avocado.nl'
+
+  spec.summary = "Byar's approximation"
+  spec.description = "Byar's approximation for use in (H)SMR calculations"
+  spec.license = 'MIT'
+
+  spec.homepage = 'https://github.com/florish/byar'
+  spec.required_ruby_version = '>= 1.9.2'
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files         = Dir.chdir(File.expand_path('..', __FILE__)) do
+    `git ls-files -z`.split("\x0").reject { |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', '~> 1.17'
+  spec.add_development_dependency 'rake', '~> 10.0'
+  spec.add_development_dependency 'minitest', '~> 5.11'
+end

data/lib/byar.rb

@@ -1,3 +1,5 @@
+require 'byar/version'
+
 ##
 # Byar is a Byar's approximation confidence interval tool with SMR calculation.
 #
@@ -18,23 +20,23 @@ class Byar
   # Z_VALUE defaults to 1.96 for 95% confidence interval
   #
   Z_VALUE = 1.96
-  
+
   ##
   # Create new Byar approximation calculator for +obs+ observed cases
   def initialize(obs)
     @obs = obs
   end
-  
+
   ##
   # Calculate SMR-like lower boundary (1 equals SMR of 100)
-  # 
+  #
   # Give +obs+ observed and +exp+ expected values to return a lower SMR-like
   # boundary value (0 - Infinite)
   def self.lower(obs, exp)
     return nil if exp == 0
     lower_bound(obs).quo(exp)
   end
-  
+
   ##
   # Calculate SMR-like upper boundary (1 equals SMR of 100)
   #
@@ -44,14 +46,14 @@ class Byar
     return nil if exp == 0
     upper_bound(obs).quo(exp)
   end
-  
+
   ##
   # Calculate lower boundary for observed cases
   def self.lower_bound(obs, z_value = Z_VALUE)
     return 0 if obs == 0
     obs * (1 - 1.quo(9 * obs) - z_value.quo(3 * Math.sqrt(obs))) ** 3
   end
-  
+
   ##
   # Calculate upper boundary for observed cases
   def self.upper_bound(obs, z_value = Z_VALUE)
@@ -62,45 +64,45 @@ class Byar
   def self.z_value=(value)
     @z_value = value
   end
-  
+
   def self.z_value
     @z_value ||= Z_VALUE
   end
-  
+
   ##
   # Give lower SMR-like boundary for +expected+ cases
   def lower(expected)
     self.class.lower(@obs, expected)
   end
-  
+
   ##
   # Give upper SMR-like boundary for +expected+ cases
   def upper(expected)
     self.class.upper(@obs, expected)
   end
-  
+
   ##
   # Give lower boundary for observed value
   def lower_bound
     self.class.lower_bound(@obs, z_value)
   end
-  
+
   ##
   # Give upper boundary for observed value
   def upper_bound
     self.class.upper_bound(@obs, z_value)
   end
-  
+
   ##
   # Give object's Z value, with fallback to Class variable or Z_VALUE
   def z_value
     @z_value ||= self.class.z_value
   end
-  
+
   ##
   # Set custom Z value for this Byar instance
   def z_value=(value)
     @z_value = value
   end
-  
-end
+
+end

data/lib/byar/version.rb

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+class Byar
+  VERSION = "1.0.0"
+end

metadata

@@ -1,45 +1,97 @@
 --- !ruby/object:Gem::Specification
 name: byar
 version: !ruby/object:Gem::Version
-  version: 0.1.1
-  prerelease: 
+  version: 1.0.0
 platform: ruby
 authors:
 - Floris Huetink
 autorequire: 
-bindir: bin
+bindir: exe
 cert_chain: []
-date: 2012-10-29 00:00:00.000000000 Z
-dependencies: []
+date: 2019-01-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.17'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.17'
+- !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: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.11'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.11'
 description: Byar's approximation for use in (H)SMR calculations
 email: floris@avocado.nl
 executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- ".gitignore"
+- CHANGELOG.md
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- byar.gemspec
 - lib/byar.rb
+- lib/byar/version.rb
 homepage: https://github.com/florish/byar
-licenses: []
+licenses:
+- MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: 1.9.2
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.7.7
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Byar's approximation
 test_files: []