anthro 0.1.0

data/lib/anthro/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module Anthro
+  VERSION = "0.1.0"
+end

data/lib/anthro.rb

@@ -0,0 +1,146 @@
+# frozen_string_literal: true
+
+require "distribution"
+require_relative "anthro/version"
+require_relative "anthro/data"
+
+module Anthro
+  class Calculator
+    VALID_MEASUREMENTS = DATA.keys.freeze
+    VALID_SEXES = %w[male female m f].freeze
+    AGE_RANGE_MONTHS = (0..240)
+    DAYS_PER_MONTH = 30.4375
+
+    def self.load_reference_data
+      @reference_data ||= begin
+        data = {}
+
+        Anthro::DATA.keys.each do |measurement|
+          data[measurement] = { m: {}, f: {} }
+          Anthro::DATA[measurement].keys.each do |source|
+            Anthro::DATA[measurement][source].each do |sex, month, l, m, s|
+              sex = sex == 1 ? :m : :f
+              data[measurement][sex][month.to_f] = {
+                l: l,
+                m: m,
+                s: s
+              }
+            end
+          end
+        end
+
+        data
+      end
+    end
+
+    attr_reader :z_score, :percentile
+
+    def initialize(measurement_type:, sex:, value:, age_months: nil, age_days: nil)
+      @measurement_type = measurement_type.to_sym
+      @sex = sex[0].downcase
+      @value = value.to_f
+      @reference_data = self.class.load_reference_data
+
+      raise ArgumentError, "Specify either age_months or age_days, not both" if age_months && age_days
+      raise ArgumentError, "Either age_months or age_days must be provided" unless age_months || age_days
+
+      @key_value = if age_months
+                     age_months.to_f
+                   else
+                     age_days.to_f / DAYS_PER_MONTH
+                   end
+
+      validate_inputs
+      @z_score = calculate_z_score
+      @percentile = calculate_percentile
+    end
+
+    private
+
+    def validate_inputs
+      unless VALID_MEASUREMENTS.include?(@measurement_type)
+        raise ArgumentError, "Invalid measurement type. Must be one of: #{VALID_MEASUREMENTS.join(", ")}"
+      end
+      raise ArgumentError, "Invalid sex. Must be 'male', 'female', 'm', or 'f'" unless VALID_SEXES.include?(@sex)
+
+      unless AGE_RANGE_MONTHS.cover?(@key_value)
+        raise ArgumentError, "Age must be between 0 and 240 months (0 to 7305 days)"
+      end
+      if @measurement_type == :bmi_for_age && @key_value < 24
+        raise ArgumentError, "BMI is only valid for ages 24 months (730.5 days) and up"
+      end
+      if @measurement_type == :head_circumference_for_age && @key_value > 24
+        raise ArgumentError, "Head circumference is only valid for ages 0 to 24 months"
+      end
+
+      return unless @value <= 0
+
+      raise ArgumentError, "Value must be positive"
+    end
+
+    def calculate_z_score
+      lms = get_lms_params
+      raise "No LMS data available for #{@measurement_type}, #{@sex}, #{@key_value}" unless lms
+
+      l = lms[:l]
+      m = lms[:m]
+      s = lms[:s]
+      if l.zero?
+        Math.log(@value / m) / s
+      else
+        (((@value / m)**l) - 1) / (l * s)
+      end
+    end
+
+    def calculate_percentile
+      z = @z_score
+      return nil unless z
+
+      Distribution::Normal.cdf(z) * 100
+    end
+
+    def get_lms_params
+      data = @reference_data[@measurement_type]
+      return nil unless data && data[@sex.to_sym]
+
+      data_set = data[@sex.to_sym]
+      return data_set[@key_value] if data_set[@key_value]
+
+      keys = data_set.keys.sort
+      lower_key = keys.select { |k| k <= @key_value }.last
+      upper_key = keys.select { |k| k > @key_value }.first
+
+      raise "No LMS data available for #{@measurement_type}, #{@sex}, #{@key_value}" unless lower_key && upper_key
+
+      interpolate_lms(data_set[lower_key], data_set[upper_key], lower_key, upper_key)
+    end
+
+    def interpolate_lms(lower, upper, lower_key, upper_key)
+      fraction = (@key_value - lower_key) / (upper_key - lower_key)
+      {
+        l: lower[:l] + (upper[:l] - lower[:l]) * fraction,
+        m: lower[:m] + (upper[:m] - lower[:m]) * fraction,
+        s: lower[:s] + (upper[:s] - lower[:s]) * fraction
+      }
+    end
+  end
+
+  def self.weight_for_age(sex:, value:, age_months: nil, age_days: nil)
+    Calculator.new(measurement_type: :weight_for_age, sex: sex, age_months: age_months, age_days: age_days,
+                   value: value)
+  end
+
+  def self.height_for_age(sex:, value:, age_months: nil, age_days: nil)
+    Calculator.new(measurement_type: :height_for_age, sex: sex, age_months: age_months, age_days: age_days,
+                   value: value)
+  end
+
+  def self.bmi_for_age(sex:, value:, age_months: nil, age_days: nil)
+    Calculator.new(measurement_type: :bmi_for_age, sex: sex, age_months: age_months, age_days: age_days, value: value)
+  end
+
+  def self.head_circumference_for_age(sex:, value:, age_months: nil, age_days: nil)
+    Calculator.new(measurement_type: :head_circumference_for_age, sex: sex, age_months: age_months, age_days: age_days,
+                   value: value)
+  end
+end

data/sig/anthro.rbs

@@ -0,0 +1,4 @@
+module Anthro
+  VERSION: String
+  # See the writing guide of rbs: https://github.com/ruby/rbs#guides
+end

metadata

@@ -0,0 +1,183 @@
+--- !ruby/object:Gem::Specification
+name: anthro
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Joon Lee
+bindir: exe
+cert_chain: []
+date: 2025-03-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bigdecimal
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.1'
+- !ruby/object:Gem::Dependency
+  name: distribution
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: prime
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.1.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.1.3
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+- !ruby/object:Gem::Dependency
+  name: irb
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.15.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.15.1
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.25'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.25'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.2'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.74'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.74'
+description: A Ruby gem for calculating anthropometric z-scores and percentiles based
+  on the WHO and CDC 2000 growth chart data.
+email:
+- seouri@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".devcontainer/devcontainer.json"
+- ".rubocop.yml"
+- CHANGELOG.md
+- LICENSE.md
+- README.md
+- Rakefile
+- data/.DS_Store
+- data/WHO-Boys-Head-Circumference-for-age-Percentiles.csv
+- data/WHO-Boys-Length-for-age-Percentiles.csv
+- data/WHO-Boys-Weight-for-age-Percentiles.csv
+- data/WHO-Girls-Head-Circumference-for-age-Percentiles.csv
+- data/WHO-Girls-Length-for-age-Percentiles.csv
+- data/WHO-Girls-Weight-for-age%20Percentiles.csv
+- data/bmiagerev.csv
+- data/statage.csv
+- data/wtage.csv
+- lib/anthro.rb
+- lib/anthro/data.rb
+- lib/anthro/version.rb
+- sig/anthro.rbs
+homepage: https://github.com/hms-dbmi/anthro
+licenses:
+- MIT
+metadata:
+  homepage_uri: https://github.com/hms-dbmi/anthro
+  source_code_uri: https://github.com/hms-dbmi/anthro
+  changelog_uri: https://github.com/hms-dbmi/anthro/CHANGELOG.md
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 3.1.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.6.2
+specification_version: 4
+summary: Calculate anthropometric z-scores and percentiles using WHO and CDC 2000
+  growth charts.
+test_files: []