Replaced standardized and windowed methods with standardize and windo…

…w, respectively. Changed local moran variance method to use sparse matrix

lib/spatial_stats/global/bivariate_moran.rb

@@ -19,7 +19,7 @@ def initialize(scope, x_field, y_field, weights)
         @scope = scope
         @x_field = x_field
         @y_field = y_field
-        @weights = weights.standardized
+        @weights = weights.standardize
       end
       attr_writer :x, :y
 
@@ -29,8 +29,7 @@ def initialize(scope, x_field, y_field, weights)
       #
       # @return [Float]
       def stat
-        w = @weights.standardized
-        y_lag = SpatialStats::Utils::Lag.neighbor_sum(w, y)
+        y_lag = SpatialStats::Utils::Lag.neighbor_sum(weights, y)
         numerator = 0
         x.each_with_index do |xi, idx|
           numerator += xi * y_lag[idx]

lib/spatial_stats/global/stat.rb

@@ -11,7 +11,7 @@ class Stat
       def initialize(scope, field, weights)
         @scope = scope
         @field = field
-        @weights = weights.standardized
+        @weights = weights.standardize
       end
       attr_accessor :scope, :field, :weights
 

lib/spatial_stats/local/bivariate_moran.rb

@@ -19,7 +19,7 @@ def initialize(scope, x_field, y_field, weights)
         @scope = scope
         @x_field = x_field
         @y_field = y_field
-        @weights = weights.standardized
+        @weights = weights.standardize
       end
       attr_accessor :scope, :x_field, :y_field, :weights
 

lib/spatial_stats/local/getis_ord.rb

@@ -73,9 +73,9 @@ def mc_i(wi, perms, idx)
 
       def calc_weights
         @weights = if star?
-                     weights.windowed.standardized
+                     weights.window.standardize
                    else
-                     weights.standardized
+                     weights.standardize
                    end
       end
 

lib/spatial_stats/local/moran.rb

@@ -55,12 +55,11 @@ def expectation
       # @return [Array] of variances for each observation
       def variance
         # formula is A - B - (E[I])**2
-        wt = w.row_standardized
         exp = expectation
 
         vars = []
-        a_terms = a_calc(wt)
-        b_terms = b_calc(wt)
+        a_terms = a_calc
+        b_terms = b_calc
 
         a_terms.each_with_index do |a_term, idx|
           vars << (a_term - b_terms[idx] - (exp**2))
@@ -109,20 +108,27 @@ def si2
       end
 
       # https://pro.arcgis.com/en/pro-app/tool-reference/spatial-statistics/h-local-morans-i-additional-math.htm
-      def a_calc(wt)
-        n = wt.shape[0]
+      # TODO: sparse
+      def a_calc
+        n = weights.n
         b2i = b2i_calc
+
+        wts = weights.sparse.values
+        row_index = weights.sparse.row_index
+
         a_terms = []
 
         (0..n - 1).each do |idx|
-          sigma_term = wt[idx, true].to_a.sum { |v| v**2 }
+          row_range = row_index[idx]..(row_index[idx + 1] - 1)
+          wt = wts[row_range]
+          sigma_term = wt.sum { |v| v**2 }
           a_terms << (n - b2i) * sigma_term / (n - 1)
         end
         a_terms
       end
 
-      def b_calc(wt)
-        n = wt.shape[0]
+      def b_calc
+        n = weights.n
         b2i = b2i_calc
         b_terms = []
 

lib/spatial_stats/local/multivariate_geary.rb

@@ -23,7 +23,7 @@ class MultivariateGeary < Stat
       def initialize(scope, fields, weights)
         @scope = scope
         @fields = fields
-        @weights = weights.standardized
+        @weights = weights.standardize
       end
       attr_accessor :scope, :fields, :weights
 

lib/spatial_stats/local/stat.rb

@@ -12,7 +12,7 @@ class Stat
       def initialize(scope, field, weights)
         @scope = scope
         @field = field
-        @weights = weights.standardized
+        @weights = weights.standardize
       end
       attr_accessor :scope, :field, :weights
 

lib/spatial_stats/narray_ext.rb

@@ -12,11 +12,11 @@ class NArray
     #
     # @ example
     #
-    #   Numo::DFloat [[0, 1, 1], [1, 1, 1]].row_standardized
+    #   Numo::DFloat [[0, 1, 1], [1, 1, 1]].row_standardize
     #   Numo::DFloat [[0, 0.5, 0.5], [0.33333, 0.33333, 0.33333]]
     #
     # @return [Numo::NArray]
-    def row_standardized
+    def row_standardize
       # every row will sum up to 1, or if they are all 0, do nothing
       standardized = each_over_axis.map do |row|
         sum = row.sum
@@ -38,16 +38,16 @@ def row_standardized
     #
     # @ example
     #
-    #   Numo::DFloat [[0, 1, 0], [1, 0, 1], [0, 1, 0]].windowed
+    #   Numo::DFloat [[0, 1, 0], [1, 0, 1], [0, 1, 0]].window
     #   Numo::DFloat [[1, 1, 0], [1, 1, 1], [0, 1, 1]]
     #
     # @ example
     #   # Input will be equivalent to output in this case
-    #   Numo::DFloat [[1, 1, 0], [1, 0, 1], [0, 1, 0]].windowed
+    #   Numo::DFloat [[1, 1, 0], [1, 0, 1], [0, 1, 0]].window
     #   Numo::DFloat [[1, 1, 0], [1, 0, 1], [0, 1, 0]]
     #
     # @return [Numo::NArray]
-    def windowed
+    def window
       # in windowed calculations, the diagonal is set to 1
       # if trace (sum of diag) is 0, add it, else return input
       if trace.zero?

lib/spatial_stats/utils/lag.rb

@@ -16,7 +16,7 @@ module Lag
       #
       # @return [Array] resultant vector
       def self.neighbor_average(matrix, variables)
-        matrix = matrix.standardized
+        matrix = matrix.standardize
         neighbor_sum(matrix, variables)
       end
 
@@ -40,7 +40,7 @@ def self.neighbor_sum(matrix, variables)
       #
       # @return [Array] resultant vector
       def self.window_average(matrix, variables)
-        matrix = matrix.windowed.standardized
+        matrix = matrix.window.standardize
         window_sum(matrix, variables)
       end
 
@@ -53,7 +53,7 @@ def self.window_average(matrix, variables)
       #
       # @return [Array] resultant vector
       def self.window_sum(matrix, variables)
-        matrix = matrix.windowed
+        matrix = matrix.window
         matrix.sparse.mulvec(variables)
       end
     end

lib/spatial_stats/weights/weights_matrix.rb

@@ -60,10 +60,11 @@ def sparse
 
       ##
       # Row standardized version of the weights matrix.
-      # Will return a new version of the weights matrix standardized weights.
+      # Will return a new version of the weights matrix with standardized
+      # weights.
       #
       # @return [WeightsMatrix]
-      def standardized
+      def standardize
         new_weights = weights
 
         new_weights.transform_values do |neighbors|
@@ -83,7 +84,7 @@ def standardized
       # If a row already has an entry for itself, it will be skipped.
       #
       # @return [WeightsMatrix]
-      def windowed
+      def window
         new_weights = weights
 
         new_weights.each do |key, neighbors|

test/narray_ext_test.rb

@@ -7,29 +7,29 @@ def setup
     @matrix = Numo::DFloat[[0, 1, 0], [1, 0, 1], [0, 1, 0]]
   end
 
-  def test_row_standardized
+  def test_row_standardize
     expected = Numo::DFloat[[0, 1, 0], [1.0 / 2, 0, 1.0 / 2], [0, 1, 0]]
-    result = @matrix.row_standardized
+    result = @matrix.row_standardize
     assert_equal(expected, result)
   end
 
-  def test_row_standardized_zeros
+  def test_row_standardize_zeros
     zero_matrix = Numo::DFloat[[0, 1, 0], [1, 0, 1], [0, 0, 0]]
     expected = Numo::DFloat[[0, 1, 0], [1.0 / 2, 0, 1.0 / 2], [0, 0, 0]]
-    result = zero_matrix.row_standardized
+    result = zero_matrix.row_standardize
     assert_equal(expected, result)
   end
 
-  def test_windowed_success
+  def test_window_success
     expected = Numo::DFloat[[1, 1, 0], [1, 1, 1], [0, 1, 1]]
-    result = @matrix.windowed
+    result = @matrix.window
     assert_equal(expected, result)
   end
 
-  def test_windowed_failure
+  def test_window_failure
     # will fail if the trace isn't already 0 and just return input
     input = Numo::DFloat[[1, 1, 0], [1, 0, 1], [0, 1, 0]]
-    result = input.windowed
+    result = input.window
     assert_equal(input, result)
   end
 end

test/weights/weights_matrix_test.rb

@@ -49,9 +49,9 @@ def test_sparse
     assert_equal(expected.row_index, result.row_index)
   end
 
-  def test_standardized
+  def test_standardize
     mat = SpatialStats::Weights::WeightsMatrix.new(@weights)
-    standardized_mat = mat.standardized
+    standardized_mat = mat.standardize
 
     expected = {
       1 => [{ id: 2, weight: 1.0 / 2 }, { id: 4, weight: 1.0 / 2 }],
@@ -62,9 +62,9 @@ def test_standardized
     assert_equal(expected, standardized_mat.weights)
   end
 
-  def test_windowed
+  def test_window
     mat = SpatialStats::Weights::WeightsMatrix.new(@weights)
-    windowed_mat = mat.windowed
+    windowed_mat = mat.window
 
     expected = {
       1 => [{ id: 1, weight: 1 }, { id: 2, weight: 1 }, { id: 4, weight: 1 }],