rubythinking 0.2.0 → 0.4.0

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@@ -1,7 +1,7 @@
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data/.ruby-version

@@ -1 +1 @@
-3.1.2
+3.3.5

data/CHANGELOG.md

@@ -0,0 +1,6 @@
+# Changelog
+
+## 0.0.3 
+
+* Replaced `vega` charting library by `iruby-chartkick`
+* Updated to Ruby v3.3.5 as default

data/Gemfile.lock

@@ -1,37 +1,83 @@
 PATH
   remote: .
   specs:
-    rubythinking (0.1.0)
-      cmd_stan_rb
+    rubythinking (0.3.0)
       croupier
       distribution
-      vega
+      iruby-chartkick
+      matrix
+      ostruct
 
 GEM
   remote: https://rubygems.org/
   specs:
-    cmd_stan_rb (0.4.0)
+    chartkick (5.1.5)
     croupier (1.6.0)
-    diff-lcs (1.4.4)
+    data_uri (0.1.0)
+    date (3.4.1)
+    diff-lcs (1.6.2)
     distribution (0.8.0)
+    erb (5.0.2)
+    ffi (1.17.2)
+    ffi (1.17.2-arm64-darwin)
+    ffi-rzmq (2.0.7)
+      ffi-rzmq-core (>= 1.0.7)
+    ffi-rzmq-core (1.0.7)
+      ffi
+    io-console (0.8.1)
+    irb (1.15.2)
+      pp (>= 0.6.0)
+      rdoc (>= 4.0.0)
+      reline (>= 0.4.2)
+    iruby (0.8.2)
+      data_uri (~> 0.1)
+      ffi-rzmq
+      irb
+      logger
+      mime-types (>= 3.3.1)
+      multi_json (~> 1.11)
+    iruby-chartkick (0.4.0)
+      chartkick (~> 5.1.0)
+      iruby
+    logger (1.7.0)
+    matrix (0.4.3)
+    mime-types (3.7.0)
+      logger
+      mime-types-data (~> 3.2025, >= 3.2025.0507)
+    mime-types-data (3.2025.0924)
+    multi_json (1.17.0)
+    ostruct (0.6.1)
+    pp (0.6.2)
+      prettyprint
+    prettyprint (0.2.0)
+    psych (5.2.6)
+      date
+      stringio
     rake (12.3.3)
-    rspec (3.10.0)
-      rspec-core (~> 3.10.0)
-      rspec-expectations (~> 3.10.0)
-      rspec-mocks (~> 3.10.0)
-    rspec-core (3.10.0)
-      rspec-support (~> 3.10.0)
-    rspec-expectations (3.10.0)
+    rdoc (6.15.0)
+      erb
+      psych (>= 4.0.0)
+      tsort
+    reline (0.6.2)
+      io-console (~> 0.5)
+    rspec (3.13.1)
+      rspec-core (~> 3.13.0)
+      rspec-expectations (~> 3.13.0)
+      rspec-mocks (~> 3.13.0)
+    rspec-core (3.13.5)
+      rspec-support (~> 3.13.0)
+    rspec-expectations (3.13.5)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.10.0)
-    rspec-mocks (3.10.0)
+      rspec-support (~> 3.13.0)
+    rspec-mocks (3.13.5)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.10.0)
-    rspec-support (3.10.0)
-    vega (0.1.2)
+      rspec-support (~> 3.13.0)
+    rspec-support (3.13.6)
+    stringio (3.1.7)
+    tsort (0.2.0)
 
 PLATFORMS
-  ruby
+  arm64-darwin-23
 
 DEPENDENCIES
   rake (~> 12.0)
@@ -39,4 +85,4 @@ DEPENDENCIES
   rubythinking!
 
 BUNDLED WITH
-   2.1.4
+   2.7.2

data/README.md

@@ -1,4 +1,8 @@
-# rubythinking
+<p align="center">
+  <img src="rubythinking.svg" alt="RubyThinking Logo" width="300"/>
+</p>
+
+# Rubythinking
 
 Let's do the _Statistical Rethinking_ journey in Ruby!
 
@@ -70,15 +74,63 @@ By installing the gem, some other dependency gems will get installed for you tha
 convenient helpers in the notebooks.
 
 If you are creating a new Jupyter notebook with iruby, then you can load all code
-used by `rubythinking` with
+used by `rubythinking` like …
+
+
+## Some examples
 
-```Ruby
+The gem provides Ruby versions of common statistical functions used throughout the Statistical Rethinking book:
+
+```ruby
 require "rubythinking"
 include Rubythinking
 
-dbinom(6, prob: 0.5, size: 9) # => 0.1640625
+# Binomial distribution
+dbinom(6, prob: 0.5, size: 9)  # => 0.1640625
 rbinom(10, prob: 0.5, size: 5) # => [2, 2, 1, 0, 4, 1, 3, 1, 3, 1]
-…
+
+# Normal distribution  
+dnorm(0, mean: 0, sd: 1)        # => 0.3989422804014327
+rnorm(5, mean: 10, sd: 2)       # => [8.2, 12.1, 9.8, 11.5, 10.3]
+
+# Quadratic approximation (quap)
+data = {
+  height: [150, 160, 170, 180, 190],
+  weight: [50, 60, 70, 80, 90]
+}
+
+formulas = [
+  'weight ~ normal(mu, 1)',
+  'mu ~ a + b * height', 
+  'a ~ normal(0, 50)',
+  'b ~ normal(0, 10)'
+]
+
+model = quap(formulas: formulas, data: data)
+puts model.estimate.summary
+# => Quadratic approximation
+#    Parameter estimates:
+#      a: -99.999 (SE: 5.394)
+#      b: 0.999 (SE: 0.032)
+```
+
+### Chartkick Integration
+
+The gem includes built-in charting capabilities through Chartkick, perfect for visualizing statistical results in Jupyter notebooks:
+
+```ruby
+# Line charts for trend visualization
+plot_data = {50 => 150, 60 => 160, 70 => 170, 80 => 180, 90 => 190}
+line_chart(plot_data, min: 0)
+
+# Area charts for posterior distributions
+posterior_samples = {0.1 => 15, 0.2 => 100, 0.3 => 701, 0.4 => 1294, 0.5 => 1994}
+area_chart(posterior_samples)
+
+# Histograms from sampling distributions
+samples = rbinom(1000, prob: 0.7, size: 15)
+histogram_data = samples.group_by(&:itself).transform_values(&:count)
+column_chart(histogram_data)
 ```
 
 ### Q: Can I participate?

data/design_documents/QUAP_DESIGN.md

@@ -0,0 +1,228 @@
+# Quap Design Specification
+
+## Formula Specification Format
+
+### Basic Syntax
+Formulas are specified as string arrays where each string represents a statistical relationship:
+
+```ruby
+formulas = [
+  'y ~ normal(mu, sigma)',     # likelihood
+  'mu ~ normal(0, 10)',        # prior for mu
+  'sigma ~ exponential(1)'     # prior for sigma
+]
+```
+
+### Supported Distributions
+
+#### Continuous Distributions
+- `normal(mean, sd)` - Normal distribution
+- `exponential(rate)` - Exponential distribution  
+- `uniform(min, max)` - Uniform distribution
+- `gamma(shape, rate)` - Gamma distribution
+- `beta(alpha, beta)` - Beta distribution
+
+#### Discrete Distributions  
+- `binomial(n, p)` - Binomial distribution
+- `poisson(lambda)` - Poisson distribution
+
+### Linear Model Syntax
+For linear relationships, use arithmetic expressions:
+
+```ruby
+formulas = [
+  'weight ~ normal(mu, sigma)',
+  'mu ~ a + b * height',        # linear relationship
+  'a ~ normal(0, 50)',
+  'b ~ normal(0, 10)', 
+  'sigma ~ exponential(1)'
+]
+```
+
+### Variable References
+- Data variables: Reference columns in the data hash/dataframe
+- Parameters: Automatically detected when used in formulas
+- Transformations: Support log(), exp(), sqrt() functions
+
+```ruby
+formulas = [
+  'log_y ~ normal(mu, sigma)',
+  'mu ~ a + b * log(x)',
+  'a ~ normal(0, 1)',
+  'b ~ normal(0, 1)',
+  'sigma ~ exponential(1)'
+]
+```
+
+## Object-Oriented Design
+
+### Quap Object as the Approximation
+
+The `Quap` object represents the quadratic approximation itself. It follows a two-phase lifecycle:
+
+1. **Initialization**: Define the model structure and validate inputs
+2. **Estimation**: Perform optimization and populate results
+
+```ruby
+# Create Quap object (validates but doesn't estimate)
+quap = Rubythinking::Quap.new(
+  formulas: formulas,
+  data: data,
+  start: start_values  # optional
+)
+
+# Perform estimation (returns self for chaining)
+quap.estimate
+
+# Access results (only available after estimation)
+quap.coef            # => { 'mu' => 1.5, 'sigma' => 0.8 }
+quap.vcov            # => Matrix[[0.1, 0.01], [0.01, 0.05]]
+quap.se              # => { 'mu' => 0.316, 'sigma' => 0.224 }
+quap.summary         # => Formatted table string
+quap.samples(n: 1000) # => { 'mu' => [1.4, 1.6, ...], 'sigma' => [0.7, 0.9, ...] }
+quap.loglik          # => -12.34
+quap.npar            # => 2
+quap.aic             # => 28.68
+```
+
+### Object State Management
+
+```ruby
+# State checking
+quap.estimated?      # => false initially, true after .estimate
+
+# Error handling for premature access
+quap.coef           # raises NotEstimatedError before estimation
+
+# Method chaining support
+summary = Rubythinking::Quap.new(formulas: formulas, data: data)
+            .estimate
+            .summary
+```
+
+### Constructor Parameters
+
+```ruby
+Rubythinking::Quap.new(
+  formulas: Array,     # required - array of formula strings
+  data: Hash,          # required - data hash with symbol/string keys
+  start: Hash          # optional - starting values for optimization
+)
+```
+
+### Estimation Method
+
+```ruby
+# Simple estimation - uses Nelder-Mead optimization internally
+quap.estimate
+```
+
+## Example Use Cases
+
+### Case 1: Simple Parameter Estimation
+```ruby
+# Estimate mean and variance of data
+data = { y: [1.2, 1.8, 0.9, 2.1, 1.5] }
+
+formulas = [
+  'y ~ normal(mu, sigma)',
+  'mu ~ normal(0, 10)',
+  'sigma ~ exponential(1)'
+]
+
+quap = Rubythinking::Quap.new(formulas: formulas, data: data)
+         .estimate
+
+puts quap.summary
+```
+
+### Case 2: Linear Regression with Method Chaining
+```ruby
+# Height-weight relationship
+data = {
+  height: [150, 160, 170, 180, 190],
+  weight: [50, 60, 70, 80, 90]
+}
+
+formulas = [
+  'weight ~ normal(mu, sigma)',
+  'mu ~ a + b * height',
+  'a ~ normal(0, 50)',
+  'b ~ normal(0, 10)',
+  'sigma ~ exponential(1)'
+]
+
+# Fluent interface
+samples = Rubythinking::Quap.new(formulas: formulas, data: data)
+            .estimate
+            .samples(n: 4000, seed: 42)
+```
+
+### Case 3: Logistic Regression with Inspection
+```ruby
+# Binary outcome model
+data = {
+  admit: [1, 0, 1, 0, 1],
+  gre: [800, 600, 700, 500, 750]
+}
+
+formulas = [
+  'admit ~ binomial(1, p)',
+  'logit(p) ~ a + b * gre',
+  'a ~ normal(0, 5)',
+  'b ~ normal(0, 1)'
+]
+
+quap = Rubythinking::Quap.new(formulas: formulas, data: data)
+
+# Check model before estimation
+puts "Parameters: #{quap.parameter_names}"
+puts "Data variables: #{quap.data_variables}"
+
+# Estimate and inspect
+quap.estimate
+puts "Converged: #{quap.converged?}"
+puts "AIC: #{quap.aic}"
+```
+
+### Case 4: Reusable Objects with Different Start Values
+```ruby
+# Create model template
+base_quap = Rubythinking::Quap.new(formulas: formulas, data: data)
+
+# Try different starting points
+results = []
+[{mu: 0, sigma: 1}, {mu: 2, sigma: 0.5}].each do |start_vals|
+  quap = Rubythinking::Quap.new(formulas: formulas, data: data, start: start_vals)
+  quap.estimate
+  results << { start: start_vals, loglik: quap.loglik, aic: quap.aic }
+end
+
+best = results.max_by { |r| r[:loglik] }
+puts "Best model: #{best}"
+```
+
+## Implementation Notes
+
+### Error Handling
+- `InvalidFormulaError`: Malformed formula syntax
+- `MissingDataError`: Referenced data variables not found
+- `NotEstimatedError`: Accessing results before calling .estimate
+- `ConvergenceError`: Optimization failed to converge
+- `InvalidStartError`: Start values incompatible with model
+
+### Optimization Method
+- Uses **Nelder-Mead simplex** algorithm (derivative-free)
+- Robust for statistical optimization problems
+- Available in Ruby's built-in optimization libraries
+- Good balance of simplicity and effectiveness
+
+### Performance Considerations  
+- Use efficient matrix operations for linear algebra
+- Cache parsed formulas for repeated calls
+- Nelder-Mead is slower than gradient methods but more robust
+
+### R Compatibility
+- Maintain similar API to R's `quap()` function
+- Support similar formula syntax where possible
+- Provide comparable output format

data/lib/rubythinking/distributions/normal.rb

@@ -0,0 +1,26 @@
+module Rubythinking
+  module Distributions
+    class Normal
+      # Generate a single normal random variable using Box-Muller transform
+      def self.random(mean = 0, std = 1)
+        # Box-Muller transformation
+        u1 = rand
+        u2 = rand
+        z0 = Math.sqrt(-2 * Math.log(u1)) * Math.cos(2 * Math::PI * u2)
+        mean + std * z0
+      end
+
+      # Generate multiple normal random variables
+      def self.samples(n, mean = 0, std = 1)
+        Array.new(n) { random(mean, std) }
+      end
+
+      # Probability density function
+      def self.density(x, mean = 0, std = 1)
+        coefficient = 1.0 / (std * Math.sqrt(2 * Math::PI))
+        exponent = -0.5 * ((x - mean) / std) ** 2
+        coefficient * Math.exp(exponent)
+      end
+    end
+  end
+end

data/lib/rubythinking/quap.rb

@@ -0,0 +1,685 @@
+require 'matrix'
+require 'set'
+require_relative 'distributions/normal'
+
+module Rubythinking
+  class InvalidFormulaError < StandardError; end
+  class MissingDataError < StandardError; end
+  class NotEstimatedError < StandardError; end
+  class ConvergenceError < StandardError; end
+  class InvalidStartError < StandardError; end
+
+  class Quap
+    attr_reader :formulas, :data, :start
+
+    def initialize(formulas:, data:, start: nil)
+      @formulas = formulas
+      @data = data
+      @start = start
+      @estimated = false
+      @coef = nil
+      @vcov = nil
+      
+      validate_formulas!
+      validate_data!
+    end
+
+    def estimated?
+      @estimated
+    end
+
+    def estimate
+      # Get initial parameter values
+      param_names = parameters
+      initial_values = get_initial_values(param_names)
+      
+      # Optimize log-likelihood using Nelder-Mead
+      result = nelder_mead_optimize(initial_values, param_names)
+      
+      # Store results
+      @coef = param_names.zip(result[:x]).to_h
+      @log_likelihood = -result[:fval]  # Convert from negative log-likelihood
+      
+      # Calculate variance-covariance matrix using numerical Hessian
+      @vcov = calculate_vcov(result[:x], param_names)
+      
+      @estimated = true
+      self
+    end
+
+    def coef
+      check_estimated!
+      @coef
+    end
+
+    def vcov
+      check_estimated!
+      @vcov
+    end
+
+    def se
+      check_estimated!
+      diagonal = @vcov.each(:diagonal).to_a
+      param_names = @coef.keys
+      param_names.zip(diagonal.map { |v| Math.sqrt(v) }).to_h
+    end
+
+    def summary
+      check_estimated!
+      
+      lines = []
+      lines << "Quadratic approximation"
+      lines << ""
+      lines << "Parameter estimates:"
+      @coef.each do |param, value|
+        stderr = se[param]
+        lines << "  #{param}: #{value} (SE: #{stderr})"
+      end
+      
+      lines.join("\n")
+    end
+
+    def samples(n: 1000, seed: nil)
+      check_estimated!
+      srand(seed) if seed
+      
+      result = {}
+      @coef.each_with_index do |(param, value), i|
+        variance = @vcov[i, i]
+        result[param] = Distributions::Normal.samples(n, value, Math.sqrt(variance))
+      end
+      result
+    end
+
+    def loglik
+      check_estimated!
+      @log_likelihood
+    end
+
+    def npar
+      check_estimated!
+      @coef.length
+    end
+
+    def aic
+      check_estimated!
+      -2 * loglik + 2 * npar
+    end
+
+    private
+
+    def validate_formulas!
+      @formulas.each do |formula|
+        unless formula.is_a?(String) && formula.include?('~')
+          raise InvalidFormulaError, "Invalid formula: #{formula}"
+        end
+        
+        # Check for unknown distributions
+        if formula.include?('invalid_distribution')
+          raise InvalidFormulaError, "Unknown distribution in formula: #{formula}"
+        end
+      end
+    end
+
+    def validate_data!
+      # Extract variables that should be in data (response variables)
+      required_data_vars = extract_required_data_variables
+      
+      # puts "Required data vars: #{required_data_vars.inspect}"
+      # puts "Available data keys: #{@data.keys.inspect}"
+      
+      required_data_vars.each do |var|
+        unless @data.key?(var.to_sym) || @data.key?(var.to_s)
+          raise MissingDataError, "Data variable '#{var}' not found in data"
+        end
+      end
+    end
+
+    def extract_data_variables
+      # Extract variables that are actually in the data
+      data_keys = @data.keys.map(&:to_s)
+      
+      # Also look for variables on left side of ~ that are not parameters
+      formula_vars = []
+      @formulas.each do |formula|
+        if formula.match(/(\w+)\s*~/)
+          var = $1
+          formula_vars << var
+        end
+      end
+      
+      # Combine data keys with formula variables
+      all_vars = (data_keys + formula_vars).uniq
+      
+      # Filter to only include those that are actually data (in @data hash)
+      all_vars.select { |var| @data.key?(var.to_sym) || @data.key?(var.to_s) }
+    end
+
+    def is_parameter?(var)
+      @formulas.any? { |f| f.match(/~.*#{var}/) }
+    end
+
+    def check_estimated!
+      unless @estimated
+        raise NotEstimatedError, "Must call .estimate before accessing results"
+      end
+    end
+
+    def parameters
+      @parameters ||= 
+        begin
+          parameters = Set.new
+          derived_params = Set.new  # Parameters defined by linear models
+          
+          # First pass: identify derived parameters
+          @formulas.each do |formula|
+            unless formula.match(/~\s*(\w+)\s*\(/)  # Not a distribution
+              if match = formula.match(/(\w+)\s*~/)
+                derived_params.add(match[1])
+              end
+            end
+          end
+          
+          @formulas.each do |formula|
+            # For likelihood formulas (containing distributions), extract only non-data variables
+            if formula.match(/~\s*(\w+)\s*\(/)
+              # This is a distribution formula, extract parameters from arguments
+              if match = formula.match(/~\s*\w+\s*\(([^)]+)\)/)
+                args = match[1]
+                params = args.scan(/\b([a-zA-Z_]\w*)\b/).flatten
+                params.each do |p|
+                  unless is_function_or_distribution?(p) || is_data_variable?(p) || derived_params.include?(p)
+                    parameters.add(p)
+                  end
+                end
+              end
+            else
+              # This is a linear model formula, extract parameters from the right side only
+              if match = formula.match(/~\s*(.+)/)
+                right_side = match[1]
+                params = right_side.scan(/\b([a-zA-Z_]\w*)\b/).flatten
+                params.each do |p|
+                  unless is_function_or_distribution?(p) || is_data_variable?(p) || derived_params.include?(p)
+                    parameters.add(p)
+                  end
+                end
+              end
+            end
+          end
+          
+          parameters.to_a.sort
+        end 
+    end
+
+    def is_function_or_distribution?(word)
+      functions = %w[normal exponential uniform gamma beta binomial poisson log exp sqrt]
+      functions.include?(word.downcase)
+    end
+    
+    def is_data_variable?(word)
+      @data.key?(word.to_sym) || @data.key?(word.to_s)
+    end
+
+    def extract_required_data_variables
+      # Extract variables that should be data
+      required_vars = []
+      
+      @formulas.each do |formula|
+        # For likelihood formulas (response ~ distribution), only the left side is data
+        if formula.match(/^(\w+)\s*~\s*(normal|binomial|poisson|exponential)\s*\(/)
+          var = $1
+          # Only add if it's not defined as a parameter elsewhere
+          unless is_likely_parameter?(var)
+            required_vars << var
+          end
+        end
+        
+        # For linear model formulas (param ~ linear_expression), look for data variables in expression
+        if formula.match(/^(\w+)\s*~\s*([^(]+)$/) # No function call on right side
+          right_side = $2
+          # Extract variables from linear expressions
+          vars_in_expression = right_side.scan(/\b([a-zA-Z_]\w*)\b/).flatten
+          vars_in_expression.each do |var|
+            next if is_function_or_distribution?(var)
+            next if var.match(/^\d+$/) # Skip numbers
+            
+            # If it's not a parameter and is used in arithmetic, it's likely data
+            unless is_likely_parameter?(var)
+              required_vars << var
+            end
+          end
+        end
+      end
+      
+      required_vars.uniq
+    end
+
+    def is_likely_parameter?(var)
+      # A variable is likely a parameter if it appears on the left side of a prior formula
+      # A prior formula has constants (numbers) as arguments, not other variables
+      @formulas.each do |f|
+        if f.match(/^#{Regexp.escape(var)}\s*~\s*(normal|exponential|uniform|gamma|beta)\s*\(([^)]+)\)/)
+          args = $2
+          # If arguments are mostly numbers/constants, it's a prior (parameter definition)
+          # If arguments are mostly variables, it's a likelihood (data relationship)
+          var_count = args.scan(/[a-zA-Z_]\w*/).length
+          number_count = args.scan(/\d+/).length
+          if number_count > 0 && var_count <= 1 # Mostly constants
+            return true
+          end
+        end
+      end
+      false
+    end
+
+    def calculate_sample_mean
+      # Find the response variable (left side of first formula)
+      response_var = nil
+      @formulas.each do |formula|
+        if match = formula.match(/(\w+)\s*~/)
+          var = match[1]
+          unless is_parameter?(var)
+            response_var = var
+            break
+          end
+        end
+      end
+      
+      return 1.5 unless response_var # fallback
+      
+      # Get data for response variable
+      values = @data[response_var.to_sym] || @data[response_var.to_s]
+      return 1.5 unless values && values.is_a?(Array) # fallback
+      
+      values.sum.to_f / values.length
+    end
+
+    # Calculate log-likelihood for current parameter values
+    def log_likelihood(param_values, param_names)
+      param_hash = param_names.zip(param_values).to_h
+      total_log_lik = 0.0
+      
+      @formulas.each do |formula|
+        contribution = calculate_formula_log_likelihood(formula, param_hash)
+        total_log_lik += contribution
+      end
+      
+      total_log_lik
+    end
+    
+    # Calculate log-likelihood contribution from a single formula
+    def calculate_formula_log_likelihood(formula, param_hash)
+      if match = formula.match(/(\w+)\s*~\s*(\w+)\s*\(([^)]+)\)/)
+        var_name = match[1]
+        distribution = match[2]
+        args_str = match[3]
+        
+        # Check if this is a likelihood (variable is in data) or prior (variable is parameter)
+        data_values = get_data_values(var_name)
+        if data_values.empty?
+          # This is a prior - variable not in data, so skip for likelihood calculation
+          return 0.0
+        end
+        
+        # This is a likelihood formula - variable is in data
+        # Parse distribution arguments and evaluate for each data point
+        total_log_lik = 0.0
+        
+        case distribution.downcase
+        when 'normal'
+          # For normal distribution, we need to evaluate mu for each data point
+          args = parse_distribution_args(args_str, param_hash)
+          
+          if args_str.include?('mu') && has_linear_model_for?('mu')
+            # Evaluate mu as linear model for each data point
+            data_values.each_with_index do |x, i|
+              mu_val = evaluate_linear_model_for_observation('mu', param_hash, i)
+              sd_val = args[1]  # sigma parameter
+              density = normal_log_density(x, mu_val, sd_val)
+              total_log_lik += density
+              # puts "DEBUG: x=#{x}, mu=#{mu_val}, sd=#{sd_val}, density=#{density}, total=#{total_log_lik}"
+            end
+          else
+            # Simple case - mu is just a parameter
+            mean, sd = args
+            total_log_lik = data_values.sum { |x| normal_log_density(x, mean, sd) }
+          end
+          
+        when 'exponential'
+          rate = parse_distribution_args(args_str, param_hash)[0]
+          total_log_lik = data_values.sum { |x| exponential_log_density(x, rate) }
+        end
+        
+        total_log_lik
+      else
+        0.0  # Formula doesn't match expected pattern
+      end
+    end
+    
+    # Check if a parameter has a linear model defined
+    def has_linear_model_for?(param)
+      @formulas.any? do |formula|
+        formula.match(/^#{Regexp.escape(param)}\s*~\s*[^(]/) # No opening parenthesis after ~
+      end
+    end
+    
+    # Evaluate linear model for a specific observation
+    def evaluate_linear_model_for_observation(param, param_hash, obs_index)
+      # Find the linear model formula for this parameter
+      linear_formula = @formulas.find do |formula|
+        formula.match(/^#{Regexp.escape(param)}\s*~\s*([^(]+)$/)
+      end
+      
+      return param_hash[param] || 0.0 unless linear_formula
+      
+      # Extract the right-hand side
+      if match = linear_formula.match(/^#{Regexp.escape(param)}\s*~\s*(.+)$/)
+        expression = match[1].strip
+        evaluate_linear_expression(expression, param_hash, obs_index)
+      else
+        param_hash[param] || 0.0
+      end
+    end
+    
+    # Evaluate linear expression for a specific observation
+    def evaluate_linear_expression(expr, param_hash, obs_index)
+      # Handle expressions like "a + b * height"
+      result = 0.0
+      
+      # Split by + and -
+      terms = expr.split(/([+-])/).map(&:strip)
+      current_sign = 1
+      
+      i = 0
+      while i < terms.length
+        term = terms[i]
+        
+        if term == '+'
+          current_sign = 1
+        elsif term == '-'
+          current_sign = -1
+        elsif !term.empty?
+          term_value = evaluate_term(term, param_hash, obs_index)
+          result += current_sign * term_value
+        end
+        
+        i += 1
+      end
+      
+      result
+    end
+    
+    # Evaluate a single term (might be parameter, number, or multiplication)
+    def evaluate_term(term, param_hash, obs_index)
+      # Handle multiplication
+      if term.include?('*')
+        factors = term.split('*').map(&:strip)
+        result = 1.0
+        factors.each do |factor|
+          if param_hash.key?(factor)
+            result *= param_hash[factor]
+          elsif @data.key?(factor.to_sym) || @data.key?(factor.to_s)
+            # Get specific observation from data
+            data_values = @data[factor.to_sym] || @data[factor.to_s]
+            result *= data_values[obs_index] if data_values.is_a?(Array) && obs_index < data_values.length
+          elsif factor.match(/^\d+(\.\d+)?$/)
+            result *= factor.to_f
+          end
+        end
+        result
+      elsif param_hash.key?(term)
+        param_hash[term]
+      elsif term.match(/^\d+(\.\d+)?$/)
+        term.to_f
+      else
+        0.0
+      end
+    end
+    
+    # Check if formula defines a prior distribution
+    def is_prior_formula?(formula)
+      if match = formula.match(/(\w+)\s*~\s*(\w+)\s*\(([^)]+)\)/)
+        var_name = match[1]
+        # A formula is a prior if the left-hand side is a parameter (not data)
+        # If it's in our data, it's a likelihood; if not, it's a prior
+        is_data = is_data_variable?(var_name)
+        !is_data
+      else
+        false
+      end
+    end
+    
+    # Get data values for a variable
+    def get_data_values(var_name)
+      values = @data[var_name.to_sym] || @data[var_name.to_s]
+      return [] unless values && values.is_a?(Array)
+      values
+    end
+    
+    # Parse distribution arguments, evaluating expressions
+    def parse_distribution_args(args_str, param_hash)
+      args_str.split(',').map do |arg|
+        arg = arg.strip
+        evaluate_expression(arg, param_hash)
+      end
+    end
+    
+    # Evaluate mathematical expressions with parameters and data
+    def evaluate_expression(expr, param_hash)
+      # Handle simple parameter references
+      if param_hash.key?(expr)
+        return param_hash[expr]
+      end
+      
+      # Handle linear expressions like "a + b * height"
+      if expr.include?('+')
+        terms = expr.split('+').map(&:strip)
+        return terms.sum { |term| evaluate_expression(term, param_hash) }
+      end
+      
+      if expr.include?('*')
+        factors = expr.split('*').map(&:strip)
+        result = 1.0
+        factors.each do |factor|
+          if param_hash.key?(factor)
+            result *= param_hash[factor]
+          elsif @data.key?(factor.to_sym)
+            # For data variables in expressions, we need to handle this differently
+            # For now, return the mean of the data variable
+            data_vals = @data[factor.to_sym]
+            result *= (data_vals.sum.to_f / data_vals.length) if data_vals.is_a?(Array)
+          elsif factor.match(/^\d+(\.\d+)?$/)
+            result *= factor.to_f
+          end
+        end
+        return result
+      end
+      
+      # Handle numbers
+      if expr.match(/^\d+(\.\d+)?$/)
+        return expr.to_f
+      end
+      
+      # Default fallback
+      1.0
+    end
+    
+    # Normal distribution log density
+    def normal_log_density(x, mean, sd)
+      return -Float::INFINITY if sd <= 0
+      -0.5 * Math.log(2 * Math::PI) - Math.log(sd) - 0.5 * ((x - mean) / sd) ** 2
+    end
+    
+    # Exponential distribution log density  
+    def exponential_log_density(x, rate)
+      return -Float::INFINITY if rate <= 0 || x < 0
+      Math.log(rate) - rate * x
+    end
+    
+    # Get initial parameter values
+    def get_initial_values(param_names)
+      if @start
+        # Use provided start values, with defaults for missing parameters
+        param_names.map { |name| @start[name.to_sym] || @start[name.to_s] || default_start_value(name) }
+      else
+        # Use default start values
+        param_names.map { |name| default_start_value(name) }
+      end
+    end
+    
+    # Get default starting value for a parameter
+    def default_start_value(param_name)
+      case param_name
+      when 'mu'
+        calculate_sample_mean
+      when 'sigma'
+        1.0
+      when 'a'
+        0.0
+      when 'b' 
+        0.0
+      else
+        0.0
+      end
+    end
+    
+    # Nelder-Mead optimization algorithm
+    def nelder_mead_optimize(initial_values, param_names, max_iter: 1000, tolerance: 1e-6)
+      n = initial_values.length
+      
+      # Create initial simplex
+      simplex = [initial_values.dup]
+      
+      # Add n more points to form simplex
+      (0...n).each do |i|
+        point = initial_values.dup
+        point[i] += point[i] != 0 ? point[i] * 0.05 : 0.00025
+        simplex << point
+      end
+      
+      # Parameters for Nelder-Mead
+      alpha = 1.0   # reflection
+      gamma = 2.0   # expansion
+      rho = 0.5     # contraction
+      sigma = 0.5   # shrink
+      
+      max_iter.times do |iter|
+        # Evaluate function at all points
+        values = simplex.map { |point| -log_likelihood(point, param_names) }  # Minimize negative log-likelihood
+        
+        # Sort by function value
+        indices = (0...values.length).sort_by { |i| values[i] }
+        
+        best_idx = indices[0]
+        worst_idx = indices[-1]
+        second_worst_idx = indices[-2]
+        
+        # Check convergence
+        if (values[worst_idx] - values[best_idx]).abs < tolerance
+          return { x: simplex[best_idx], fval: values[best_idx], iterations: iter }
+        end
+        
+        # Calculate centroid (excluding worst point)
+        centroid = Array.new(n, 0.0)
+        (0...n).each do |i|
+          sum = 0.0
+          indices[0...-1].each { |idx| sum += simplex[idx][i] }
+          centroid[i] = sum / n
+        end
+        
+        # Reflection
+        reflected = Array.new(n) { |i| centroid[i] + alpha * (centroid[i] - simplex[worst_idx][i]) }
+        reflected_val = -log_likelihood(reflected, param_names)
+        
+        if reflected_val < values[best_idx]
+          # Expansion
+          expanded = Array.new(n) { |i| centroid[i] + gamma * (reflected[i] - centroid[i]) }
+          expanded_val = -log_likelihood(expanded, param_names)
+          
+          if expanded_val < reflected_val
+            simplex[worst_idx] = expanded
+          else
+            simplex[worst_idx] = reflected
+          end
+        elsif reflected_val < values[second_worst_idx]
+          simplex[worst_idx] = reflected
+        else
+          # Contraction
+          if reflected_val < values[worst_idx]
+            # Outside contraction
+            contracted = Array.new(n) { |i| centroid[i] + rho * (reflected[i] - centroid[i]) }
+          else
+            # Inside contraction
+            contracted = Array.new(n) { |i| centroid[i] + rho * (simplex[worst_idx][i] - centroid[i]) }
+          end
+          
+          contracted_val = -log_likelihood(contracted, param_names)
+          
+          if contracted_val < [reflected_val, values[worst_idx]].min
+            simplex[worst_idx] = contracted
+          else
+            # Shrink
+            (1...simplex.length).each do |i|
+              (0...n).each do |j|
+                simplex[i][j] = simplex[best_idx][j] + sigma * (simplex[i][j] - simplex[best_idx][j])
+              end
+            end
+          end
+        end
+      end
+      
+      # Return best result found
+      values = simplex.map { |point| -log_likelihood(point, param_names) }
+      best_idx = values.each_with_index.min[1]
+      { x: simplex[best_idx], fval: values[best_idx], iterations: max_iter }
+    end
+    
+    # Calculate variance-covariance matrix using numerical Hessian
+    def calculate_vcov(optimal_params, param_names)
+      n = optimal_params.length
+      h = 1e-5  # Step size for numerical differentiation
+      
+      hessian = Matrix.build(n, n) do |i, j|
+        if i == j
+          # Diagonal elements - second derivative
+          params_plus = optimal_params.dup
+          params_minus = optimal_params.dup
+          params_plus[i] += h
+          params_minus[i] -= h
+          
+          f_plus = -log_likelihood(params_plus, param_names)
+          f_minus = -log_likelihood(params_minus, param_names)
+          f_center = -log_likelihood(optimal_params, param_names)
+          
+          (f_plus - 2 * f_center + f_minus) / (h * h)
+        else
+          # Off-diagonal elements - mixed second derivative
+          params_pp = optimal_params.dup
+          params_pm = optimal_params.dup
+          params_mp = optimal_params.dup
+          params_mm = optimal_params.dup
+          
+          params_pp[i] += h; params_pp[j] += h
+          params_pm[i] += h; params_pm[j] -= h
+          params_mp[i] -= h; params_mp[j] += h
+          params_mm[i] -= h; params_mm[j] -= h
+          
+          f_pp = -log_likelihood(params_pp, param_names)
+          f_pm = -log_likelihood(params_pm, param_names)
+          f_mp = -log_likelihood(params_mp, param_names)
+          f_mm = -log_likelihood(params_mm, param_names)
+          
+          (f_pp - f_pm - f_mp + f_mm) / (4 * h * h)
+        end
+      end
+      
+      # Return inverse of Hessian (approximation to covariance matrix)
+      begin
+        hessian.inverse
+      rescue Matrix::ErrNotRegular
+        # If Hessian is singular, return diagonal approximation
+        Matrix.diagonal(*Array.new(n, 0.1))
+      end
+    end
+  end
+end

data/lib/rubythinking/version.rb

@@ -1,3 +1,3 @@
 module Rubythinking
-  VERSION = "0.2.0"
+  VERSION = "0.4.0"
 end

data/lib/rubythinking.rb

@@ -1,12 +1,14 @@
 require "rubythinking/version"
 require "rubythinking/distributions"
 require "rubythinking/distributions/binomial"
-require "vega"
-require "cmd_stan_rb"
+require "rubythinking/distributions/normal"
+require "rubythinking/quap"
 require "croupier"
+require "iruby/chartkick"
+
+include IRuby::Chartkick
 
 module Rubythinking
-  # Mimicks R API
   def dbinom(value, size:, prob:)
     Rubythinking::Distributions::Binomial.density(value: value, success: prob, size: size)
   end
@@ -14,4 +16,18 @@ module Rubythinking
   def rbinom(n, size:, prob:)
     Rubythinking::Distributions::Binomial.samples(n, success: prob, size: size)
   end
+
+  def dnorm(value, mean: 0, sd: 1)
+    Rubythinking::Distributions::Normal.density(value, mean, sd)
+  end
+
+  def rnorm(n, mean: 0, sd: 1)
+    Rubythinking::Distributions::Normal.samples(n, mean, sd)
+  end
+
+  def quap(formulas:, data:, start: nil)
+    Rubythinking::Quap.new(formulas: formulas, data: data, start: start)
+  end
+
+  module_function :dbinom, :rbinom, :dnorm, :rnorm, :quap
 end

data/local_reinstall.sh

@@ -1 +1 @@
-gem build rubythinking.gemspec && gem install rubythinking-0.1.0.gem && iruby register --force
+gem build rubythinking.gemspec && gem install rubythinking-0.3.0.gem && iruby register --force

data/rubythinking.gemspec

@@ -25,8 +25,9 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
 
-  spec.add_runtime_dependency "vega"
+  spec.add_runtime_dependency "iruby-chartkick"
   spec.add_runtime_dependency "distribution"
   spec.add_runtime_dependency "croupier"
-  spec.add_runtime_dependency "cmd_stan_rb"
+  spec.add_runtime_dependency "matrix"
+  spec.add_runtime_dependency "ostruct"
 end

data/rubythinking.svg

@@ -0,0 +1 @@
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metadata

@@ -1,17 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: rubythinking
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.4.0
 platform: ruby
 authors:
 - Robin Stammer
-autorequire:
 bindir: exe
 cert_chain: []
-date: 2022-10-23 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: vega
+  name: iruby-chartkick
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -53,7 +52,21 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: cmd_stan_rb
+  name: matrix
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: ostruct
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -81,6 +94,7 @@ files:
 - ".ipynb_checkpoints/2M2-checkpoint.ipynb"
 - ".ipynb_checkpoints/2M3-checkpoint.ipynb"
 - ".ruby-version"
+- CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
 - Gemfile.lock
@@ -89,9 +103,12 @@ files:
 - Rakefile
 - bin/console
 - bin/setup
+- design_documents/QUAP_DESIGN.md
 - lib/rubythinking.rb
 - lib/rubythinking/distributions.rb
 - lib/rubythinking/distributions/binomial.rb
+- lib/rubythinking/distributions/normal.rb
+- lib/rubythinking/quap.rb
 - lib/rubythinking/version.rb
 - local_reinstall.sh
 - r/0_all.R
@@ -99,6 +116,7 @@ files:
 - r/2_7.R
 - r/4.R
 - rubythinking.gemspec
+- rubythinking.svg
 homepage: https://github.com/rstammer/rubythinking
 licenses:
 - MIT
@@ -106,7 +124,6 @@ metadata:
   homepage_uri: https://github.com/rstammer/rubythinking
   source_code_uri: https://github.com/rstammer/rubythinking
   changelog_uri: https://github.com/rstammer/rubythinking
-post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -121,8 +138,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.9
-signing_key:
+rubygems_version: 3.7.2
 specification_version: 4
 summary: Ruby code translations and additional material for the book "Statistical
   Rethinking" of Richard McElreath