Added changelog, created v1.x and 2.0 plan, added logo, added pr template, changed license, changed stat attr_writer x methods to automatically standardize

Author: keithdoggett

.github/pull_request_template.md

@@ -0,0 +1,5 @@
+Fixes #
+
+## Proposed Changes
+
+## Additional Info

CHANGELOG.md

@@ -0,0 +1,63 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [1.0.3] - 2020-05-22
+
+### Added
+
+- CONTRIBUTING.md
+- PR Template
+- logo
+
+### Changed
+
+- `x/z` attr_writer changed to a function that standardizes input
+- MIT -> GPL-3-Clause License
+
+## [1.0.2] - 2020-05-08 (First Changelog Commit)
+
+### Added
+
+- Global Statistical Classes
+- Local Statistical Classes
+- WeightsMatrix
+- Weights Queries
+- Data queries
+- Spatial Lag computations
+- Array extensions
+- Numo extensions
+- Add examples/usage to docs
+- Create RDocs
+- Write SparseMatrix C ext
+- Add `#summary` method to statistics that will combine stat vals with p-vals, and quads or hot/cold spot info.
+- Add ability to assign `x` or `z` on stat classes so users are not forced to query data to input it into models. Add example to README.
+
+### Changed
+
+- Memoize expensive functions within classes
+- Make star a parameter to getis-ord class
+- Refactor Global Moran and BVMoran
+- Support non-numeric keys in WeightsMatrix/General refactor
+- Change instances of `standardized` and `windowed` to `standardize` and `window`, respectively.
+- Add `positive` and `negative` groups for `GetisOrd` and `Geary`, similar to how `#quads` is implemented.
+- Refactor stats to inherit an abstract class.
+
+### Removed
+
+- Pure Ruby CSR Matrix
+
+[unreleased]: https://github.com/olivierlacan/keep-a-changelog/compare/v1.0.3...HEAD
+[1.0.3]: https://github.com/keithdoggett/spatial_stats/compare/v1.0.1...v1.0.3
+[1.0.2]: https://github.com/keithdoggett/spatial_stats/compare/v1.0.1...v1.0.2
+[1.0.1]: https://github.com/keithdoggett/spatial_stats/compare/v1.0.0...v1.0.1
+[1.0.0]: https://github.com/keithdoggett/spatial_stats/compare/v0.2.2...v1.0.0
+[0.2.2]: https://github.com/keithdoggett/spatial_stats/compare/v0.2.1...v0.2.2
+[0.2.1]: https://github.com/keithdoggett/spatial_stats/compare/v0.1.1...v0.2.1
+[0.1.1]: https://github.com/keithdoggett/spatial_stats/compare/v0.1.0...v0.1.1
+[0.1.0]: https://github.com/keithdoggett/spatial_stats/releases/tag/v0.1.0

CONTRIBUTING.md

@@ -0,0 +1,42 @@
+## Contributing
+
+Once cloned, run the following commands to setup the test database.
+
+```bash
+cd ./spatial_stats
+bundle install
+cd test/dummy
+rake db:create
+rake db:migrate
+```
+
+If you are getting an error, you may need to set the following environment variables.
+
+```bash
+$PGUSER # default "postgres"
+$PGPASSWORD # default ""
+$PGHOST # default "127.0.0.1"
+$PGPORT # default "5432"
+$PGDATABASE # default "spatial_stats_test"
+```
+
+If the dummy app is setup correctly, run the following:
+
+```bash
+cd ../..
+rake
+```
+
+This will run the tests. If they all pass, then your environment is setup correctly.
+
+Note: It is recommended to have GEOS installed and linked to RGeo. You can test this by running the following:
+
+```bash
+cd test/dummy
+rails c
+
+RGeo::Geos.supported?
+# => true
+```
+
+Please submit PRs with a description of the problem, the solution and link any issues that it closes.

Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    spatial_stats (1.0.2)
+    spatial_stats (1.0.3)
       numo-narray (~> 0.9.1)
       rails (~> 6.0.0)
 

LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2020 Keith Doggett.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MIT-LICENSE

@@ -1,5 +1,7 @@
 [![Build Status](https://travis-ci.com/keithdoggett/spatial_stats.svg?branch=master)](https://travis-ci.com/keithdoggett/spatial_stats)
 
+![Spatial Stats](/assets/ruby.svg)
+
 # SpatialStats
 
 SpatialStats is an ActiveRecord plugin that utilizes PostGIS and Ruby to compute weights/statistics of spatial data sets in Rails Apps.
@@ -138,8 +140,8 @@ field = nil
 moran = SpatialStats::Global::Moran.new(scope, field, weights)
 # => <SpatialStats::Global::Moran>
 
-# important to standardize the data!
-data = [1,2,3,4,5,6].standardize
+# data is automatically standardized on input
+data = [1,2,3,4,5,6]
 moran.x = data
 
 moran.stat
@@ -219,8 +221,8 @@ field = nil
 moran = SpatialStats::Local::Moran.new(scope, field, weights)
 # => <SpatialStats::Local::Moran>
 
-# important to standardize the data!
-data = [1,2,3,4,5,6].standardize
+# data is automatically standardized on input
+data = [1,2,3,4,5,6]
 moran.x = data
 
 moran.stat
@@ -310,50 +312,30 @@ RGeo::Geos.supported?
 # => true
 ```
 
-## TODO
-
-- ~~Memoize expensive functions within classes~~
-- ~~Make star a parameter to getis-ord class~~
-- ~~Add examples/usage to docs~~
-- ~~Create RDocs~~
-- ~~Refactor Global Moran and BVMoran~~
-- ~~Support non-numeric keys in WeightsMatrix/General refactor~~
-- ~~Write SparseMatrix C ext~~
-- ~~Change instances of `standardized` and `windowed` to `standardize` and `window`, respectively.~~
-- ~~Add `positive` and `negative` groups for `GetisOrd` and `Geary`, similar to how `#quads` is implemented.~~
-- ~~Add `#summary` method to statistics that will combine stat vals with p-vals, and quads or hot/cold spot info.~~
-- ~~Add ability to assign `x` or `z` on stat classes so users are not forced to query data to input it into models. Add example to README.~~
-
-## Future Work
-
-#### General
-
-- ~~Refactor stats to inherit an abstract class.~~
-- ~~Change WeightsMatrix class and Stat classes to utilize sparse matrix methods.~~
-- Split into two separate gems spatial_stats and spatial_stats-activerecord
-
-#### Weights
-
-- Add Kernel based weighting
-
-#### Utils
-
-- Rate smoothing
-- Bayes smoothing
-
-#### Global
+## Path Forward
 
-- Geary class
-- GetisOrd class
+Summaries of milestones for v1.x and v2.0. These lists are subject to change. If you have an additional feature you want to see for either milestone, open up an issue or PR.
 
-#### Local
+### v1.x
 
-- Join Count Statistic
+1. Global Measurements
+   - `Geary`'s C
+   - `GetisOrd`
+2. Local Measurements
+   - `Join Count`
+3. Utilities
+   - Add support for .gal/.swm file imports
+   - Add support for Rate variables
+   - Add support for Bayes smoothing
+4. General
+   - Point Pattern Analysis Module
+   - Regression Module
 
-#### PPA
+### v2.0
 
-- Add descriptive stat methods for point clusters.
+- 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.
 
 ## License
 
-The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+The gem is available as open source under the terms of the [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause).

README.md

@@ -21,7 +21,6 @@ def initialize(scope, x_field, y_field, weights)
         @y_field = y_field
         @weights = weights.standardize
       end
-      attr_writer :x, :y
 
       ##
       # Computes the global spatial correlation of x against spatially lagged

assets/ruby.svg

@@ -18,7 +18,6 @@ class Moran < Stat
       def initialize(scope, field, weights)
         super(scope, field, weights)
       end
-      attr_writer :x
 
       ##
       # Computes the global spatial autocorrelation of x against a spatially

lib/spatial_stats/global/bivariate_moran.rb

@@ -39,6 +39,15 @@ def z_score
         (stat - expectation) / Math.sqrt(variance)
       end
 
+      def x=(values)
+        @x = values.standardize
+      end
+      alias z= x=
+
+      def y=(values)
+        @y = values.standardize
+      end
+
       def mc(permutations, seed)
         rng = gen_rng(seed)
         shuffles = []

lib/spatial_stats/global/moran.rb

@@ -22,7 +22,6 @@ def initialize(scope, x_field, y_field, weights)
         @weights = weights.standardize
       end
       attr_accessor :scope, :x_field, :y_field, :weights
-      attr_writer :x, :y
 
       ##
       # Computes the local indicator of spatial correlation for