spatial_stats 1.0.3 → 2.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,10 +1,12 @@
+![Spatial Stats](/assets/ruby.svg)
+
 [![Build Status](https://travis-ci.com/keithdoggett/spatial_stats.svg?branch=master)](https://travis-ci.com/keithdoggett/spatial_stats)
 
-![Spatial Stats](/assets/ruby.svg)
+[Docs](https://keithdoggett.github.io/spatial_stats)
 
 # SpatialStats
 
-SpatialStats is an ActiveRecord plugin that utilizes PostGIS and Ruby to compute weights/statistics of spatial data sets in Rails Apps.
+SpatialStats is an ActiveRecord/Rails plugin that utilizes PostGIS to compute weights/statistics of spatial data sets in Rails Apps.
 
 ## Installation
 
@@ -327,7 +329,9 @@ Summaries of milestones for v1.x and v2.0. These lists are subject to change. If
    - Add support for .gal/.swm file imports
    - Add support for Rate variables
    - Add support for Bayes smoothing
+   - ~Add support for Bonferroni Bounds and FDR~
 4. General
+   - ~Add new stat constructors that only rely on a weights matrix and data vector~
    - Point Pattern Analysis Module
    - Regression Module
 
@@ -336,6 +340,11 @@ Summaries of milestones for v1.x and v2.0. These lists are subject to change. If
 - Break gem into core `spatial_stats` that will not include queries module and `spatial_stats-activerecord`. This will remove the dependency on rails for the core gem.
 - Create `spatial_stats-import/geojson/shp` gem that will allow importing files and generating a `WeightsMatrix`. Will likely rely on `RGeo` or another spatial lib.
 
+### Other TODOs
+
+- Update Docs to show `from_observation` when version is bumped
+- Refactor `MultivariateGeary` so that it can be used without `activerecord` by adding `from_observations` and supporting methods.
+
 ## License
 
 The gem is available as open source under the terms of the [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause).

data/ext/spatial_stats/csr_matrix.c

@@ -22,9 +22,17 @@ size_t csr_matrix_memsize(const void *ptr)
     return sizeof(*csr);
 }
 
+const rb_data_type_t csr_matrix_type = {
+    "SpatialStats::Weights::CSRMatrix",
+    {NULL, csr_matrix_free, csr_matrix_memsize},
+    0,
+    0,
+    RUBY_TYPED_FREE_IMMEDIATELY
+};
+
 VALUE csr_matrix_alloc(VALUE self)
 {
-    csr_matrix *csr = malloc(sizeof(csr_matrix));
+    csr_matrix *csr = ALLOC(csr_matrix);
     return TypedData_Wrap_Struct(self, &csr_matrix_type, csr);
 }
 
@@ -64,7 +72,7 @@ void mat_to_sparse(csr_matrix *csr, VALUE data, VALUE keys, VALUE num_rows)
         // if it is, add array len to nnz
         row = rb_hash_aref(data, key);
         Check_Type(row, T_ARRAY);
-        nnz += rb_array_len(row);
+        nnz += (int)RARRAY_LEN(row); // Explicit cast to int
     }
 
     values = malloc(sizeof(double) * nnz);
@@ -82,7 +90,7 @@ void mat_to_sparse(csr_matrix *csr, VALUE data, VALUE keys, VALUE num_rows)
 
         key = rb_ary_entry(keys, i);
         row = rb_hash_aref(data, key);
-        m = rb_array_len(row);
+        m = (int)RARRAY_LEN(row); // Explicit cast to int
 
         for (j = 0; j < m; j++)
         {
@@ -140,7 +148,7 @@ VALUE csr_matrix_initialize(VALUE self, VALUE data, VALUE num_rows)
     keys = rb_funcall(data, rb_intern("keys"), 0);
 
     // check dimensions are correct
-    if (NUM2INT(num_rows) != rb_array_len(keys))
+    if (NUM2INT(num_rows) != (int)RARRAY_LEN(keys)) // Explicit cast to int
     {
         rb_raise(rb_eArgError, "n_rows != keys.size, check your dimensions");
     }
@@ -249,7 +257,7 @@ VALUE csr_matrix_mulvec(VALUE self, VALUE vec)
 
     TypedData_Get_Struct(self, csr_matrix, &csr_matrix_type, csr);
 
-    if (rb_array_len(vec) != csr->n)
+    if (RARRAY_LEN(vec) != csr->n)
     {
         rb_raise(rb_eArgError, "Dimension Mismatch CSRMatrix.n != vec.size");
     }
@@ -294,7 +302,7 @@ VALUE csr_matrix_dot_row(VALUE self, VALUE vec, VALUE row)
 
     TypedData_Get_Struct(self, csr_matrix, &csr_matrix_type, csr);
 
-    if (rb_array_len(vec) != csr->n)
+    if (RARRAY_LEN(vec) != csr->n)
     {
         rb_raise(rb_eArgError, "Dimension Mismatch CSRMatrix.n != vec.size");
     }

data/ext/spatial_stats/csr_matrix.h

@@ -14,13 +14,7 @@ typedef struct csr_matrix
 void csr_matrix_free(void *mat);
 size_t csr_matrix_memsize(const void *ptr);
 
-// ruby VALUE for csr_matrix
-static const rb_data_type_t csr_matrix_type = {
-    "SpatialStats::Weights::CSRMatrix",
-    {NULL, csr_matrix_free, csr_matrix_memsize},
-    0,
-    0,
-    RUBY_TYPED_FREE_IMMEDIATELY};
+extern const rb_data_type_t csr_matrix_type;
 
 void mat_to_sparse(csr_matrix *csr, VALUE data, VALUE keys, VALUE num_rows);
 VALUE csr_matrix_alloc(VALUE self);

data/ext/spatial_stats/spatial_stats.c

@@ -15,7 +15,7 @@ void Init_spatial_stats()
 {
     VALUE spatial_stats_mod = rb_define_module("SpatialStats");
     VALUE weights_mod = rb_define_module_under(spatial_stats_mod, "Weights");
-    VALUE csr_matrix_class = rb_define_class_under(weights_mod, "CSRMatrix", rb_cData);
+    VALUE csr_matrix_class = rb_define_class_under(weights_mod, "CSRMatrix", rb_cObject);
 
     rb_define_alloc_func(csr_matrix_class, csr_matrix_alloc);
     rb_define_method(csr_matrix_class, "initialize", csr_matrix_initialize, 2);

data/lib/spatial_stats/global/bivariate_moran.rb

@@ -22,6 +22,23 @@ module SpatialStats
         @weights = weights.standardize
       end
 
+      ##
+      # A new instance of BivariateMoran, from vector and weights.
+      #
+      # @param [Array] x observations of dataset
+      # @param [WeightsMatrix] weights to define relationships between observations
+      #
+      # @return [BivariateMoran]
+      def self.from_observations(x, y, weights)
+        n = weights.n
+        raise ArgumentError, 'Data size != weights.n' if x.size != n || y.size != n
+
+        instance = new(nil, nil, nil, weights.standardize)
+        instance.x = x
+        instance.y = y
+        instance
+      end
+
       ##
       # Computes the global spatial correlation of x against spatially lagged
       # y.

data/lib/spatial_stats/global/stat.rb

@@ -15,6 +15,21 @@ module SpatialStats
       end
       attr_accessor :scope, :field, :weights
 
+      ##
+      # A new instance of Stat, from vector and weights.
+      #
+      # @param [Array] x observations of dataset
+      # @param [WeightsMatrix] weights to define relationships between observations
+      #
+      # @return [Stat]
+      def self.from_observations(x, weights)
+        raise ArgumentError, 'Data size != weights.n' if x.size != weights.n
+
+        instance = new(nil, nil, weights.standardize)
+        instance.x = x
+        instance
+      end
+
       def stat
         raise NotImplementedError, 'method stat not defined'
       end

data/lib/spatial_stats/local/bivariate_moran.rb

@@ -23,6 +23,24 @@ module SpatialStats
       end
       attr_accessor :scope, :x_field, :y_field, :weights
 
+      ##
+      # A new instance of BivariateMoran, from vector and weights.
+      #
+      # @param [Array] x observations of dataset
+      # @param [Array] y observations of dataset
+      # @param [WeightsMatrix] weights to define relationships between observations
+      #
+      # @return [BivariateMoran]
+      def self.from_observations(x, y, weights)
+        n = weights.n
+        raise ArgumentError, 'Data size != weights.n' if x.size != n || y.size != n
+
+        instance = new(nil, nil, nil, weights.standardize)
+        instance.x = x
+        instance.y = y
+        instance
+      end
+
       ##
       # Computes the local indicator of spatial correlation for
       # x against lagged y.

data/lib/spatial_stats/local/stat.rb

@@ -16,6 +16,21 @@ module SpatialStats
       end
       attr_accessor :scope, :field, :weights
 
+      ##
+      # A new instance of Stat, from vector and weights.
+      #
+      # @param [Array] x observations of dataset
+      # @param [WeightsMatrix] weights to define relationships between observations
+      #
+      # @return [Stat]
+      def self.from_observations(x, weights)
+        raise ArgumentError, 'Data size != weights.n' if x.size != weights.n
+
+        instance = new(nil, nil, weights.standardize)
+        instance.x = x
+        instance
+      end
+
       def stat
         raise NotImplementedError, 'method stat not defined'
       end

data/lib/spatial_stats/utils.rb

@@ -6,5 +6,30 @@ module SpatialStats
   ##
   # The Utils module contains various utilities used in the gem.
   module Utils
+    ##
+    # Compute the false discovery rate (FDR) of a set of p-values given
+    # an alpha value.
+    #
+    # If there is no FDR available in the dataset, the Bonferroni Bound is
+    # returned instead.
+    #
+    # @param [Array] pvals from an mc test
+    # @param [Float] alpha value for the fdr
+    #
+    # @returns [Float] either the FDR or Bonferroni Bound
+    def self.fdr(pvals, alpha)
+      n = pvals.size
+      b_bound = alpha / n
+      pvals.sort!
+
+      p_val = b_bound
+      (0..n - 1).each do |i|
+        p_fdr = (i + 1) * b_bound
+        break unless pvals[i] <= p_fdr
+
+        p_val = p_fdr
+      end
+      p_val
+    end
   end
 end

data/lib/spatial_stats/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module SpatialStats
-  VERSION = '1.0.3'
+  VERSION = '2.0.0'
 end

data/lib/spatial_stats/weights/weights_matrix.rb

@@ -21,6 +21,16 @@ module SpatialStats
       end
       attr_accessor :keys, :weights, :n
 
+      ##
+      # Equality operator
+      #
+      # @param [WeightsMatrix] other WeightsMatrix
+      #
+      # @return [TrueClass, FalseClass] equality result
+      def ==(other)
+        weights == other.weights
+      end
+
       ##
       # Compute the n x n Numo::Narray of the weights hash.
       #

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: spatial_stats
 version: !ruby/object:Gem::Version
-  version: 1.0.3
+  version: 2.0.0
 platform: ruby
 authors:
 - Keith Doggett
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-05-22 00:00:00.000000000 Z
+date: 2024-06-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray
@@ -28,28 +28,28 @@ dependencies:
   name: rails
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 6.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 6.0.0
 - !ruby/object:Gem::Dependency
   name: activerecord-postgis-adapter
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 6.0.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 6.0.0
 - !ruby/object:Gem::Dependency
@@ -58,14 +58,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.3
+        version: 2.0.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.3
+        version: 2.0.2
 - !ruby/object:Gem::Dependency
   name: pg
   requirement: !ruby/object:Gem::Requirement
@@ -112,14 +112,14 @@ dependencies:
   name: tzinfo
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.2.6
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.2.6
 description: An ActiveRecord/PostGIS extension that provides statistical methods to
@@ -182,14 +182,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.3.0
+      version: 3.1.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.5.3
 signing_key: 
 specification_version: 4
 summary: An ActiveRecord/PostGIS extension that provides statistical methods to spatial