spatial_stats 1.0.3 → 1.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3e79499aff738642d7e50a0255239de6627e68b3e1553f8aa6fa21364c3b5acb
-  data.tar.gz: 26a98ee5cb279af10e2cc324663e06ddfc7217eb6a6adc3d4052cc6469b5b6be
+  metadata.gz: 053a1b234d54d2231e35c7eb74547b086f7415fc96190bc7d3afb25f51dd879e
+  data.tar.gz: a85d682009559812fb20695c5bea8f2978acf49a12d0b3df2506d58ced8c5e77
 SHA512:
-  metadata.gz: a184a7e6561ec950ecc97e08840c8e88ba7bb20567d140036c34e0552a0e11a339885094fa5380e59f1a7ebe4eee0cb371368e6a7384531c7704e9894c8c1948
-  data.tar.gz: cd971928ff328e8daca3b0176b01903bdc98d7fcf1109cdbf9937dd84ff737d2d8072b7437e21dc0c2f26c73738c7c7f30c9a7bdca30b5cfd655ef5f3f760df1
+  metadata.gz: 868ec3b50f4b1b9fc261d6dd94439bba62a08d4c496a48d164c41590d1cd5a088c87de682a7cb96bcf4dbe0d534b5cf35e136e39d42c505ba8cc1f4c3569a3d4
+  data.tar.gz: b767cc6ed7f22ce4096965a6172f77d21a348d51bd84dc3b96f0d51bf16e2f4f92617e21e9bcda1a36eeda2cd5c07c51452dd55d9e5a62567e206bf7a06c8fe0

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/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 = '1.0.4'
 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: 1.0.4
 platform: ruby
 authors:
 - Keith Doggett
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-05-22 00:00:00.000000000 Z
+date: 2020-12-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray
@@ -28,14 +28,14 @@ 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
@@ -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
@@ -189,7 +189,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.0.8
 signing_key: 
 specification_version: 4
 summary: An ActiveRecord/PostGIS extension that provides statistical methods to spatial