Adding AIF360-R components (#168)

* Adding AIF360 R components * Updating README to refer to R documentation for R users * adding updated test * adding updated test * update readme * update readme * update readme * update readme * update tf * update pandas * update pandas * update readme example * add travis * add travis * update travis * update travis * update travis * update travis * update travis * update travis * update travis * update travis * update travis * update travis * add python * update python * update python * update python * update python * update python virtual env tool * remove virtual env * update test file * update test file * update test * add folder change * change folder path * change folder path * change folder path * change folder path * change folder path * change folder path * change folder path * merge * merge * Add gitignore * Add .Rbuildignore * Add cran-comments.md * Add GH repo url and issues url to DESCRIPTION * oops - Rename .gitgnore * Update .Rbuildignore * Typos Co-authored-by: srnghn <[email protected]> Co-authored-by: Gabriela de Queiroz <[email protected]>
Trusted-AI · May 23, 2020 · ae55ccc · ae55ccc
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diff --git a/.gitignore b/.gitignore
@@ -24,4 +24,5 @@ docs/source/modules/generated
 aif360/version.py
 aif360/data/raw/**
 !aif360/data/raw/*/*.md
-aif360/sklearn/data/
+aif360/sklearn/data/
+.Rproj.user
diff --git a/.travis.yml b/.travis.yml
@@ -1,30 +1,52 @@
-language: python
-
-python: "3.6"
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
 env:
   global:
     - UCI_HTTPS_URL="https://archive.ics.uci.edu/ml/machine-learning-databases"
 
-branches:
-  only:
-    - master
-
-install:
-  - pip install -r requirements.txt
-  - pip install flake8
-  - if ! wget ${UCI_HTTPS_URL}/adult/adult.data -P aif360/data/raw/adult/ ; then wget ${UCI_HTTPS_URL}/adult/adult.data --no-check-certificate -P aif360/data/raw/adult/ ; fi
-  - if ! wget ${UCI_HTTPS_URL}/adult/adult.test -P aif360/data/raw/adult/ ; then wget ${UCI_HTTPS_URL}/adult/adult.test --no-check-certificate -P aif360/data/raw/adult/; fi
-  - if ! wget ${UCI_HTTPS_URL}/adult/adult.names -P aif360/data/raw/adult/ ; then wget ${UCI_HTTPS_URL}/adult/adult.names --no-check-certificate -P aif360/data/raw/adult/; fi
-  - if ! wget ${UCI_HTTPS_URL}/statlog/german/german.data -P aif360/data/raw/german/ ; then wget ${UCI_HTTPS_URL}/statlog/german/german.data --no-check-certificate -P aif360/data/raw/german/; fi
-  - if ! wget ${UCI_HTTPS_URL}/statlog/german/german.doc -P aif360/data/raw/german/ ; then wget ${UCI_HTTPS_URL}/statlog/german/german.doc --no-check-certificate -P aif360/data/raw/german/; fi
-  - wget https://raw.githubusercontent.com/propublica/compas-analysis/master/compas-scores-two-years.csv -P aif360/data/raw/compas/
-
-before_script:
-  # exit-zero treats all errors as warnings.  The GitHub editor is 127 chars wide
-  - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-script:
-  # stop the build if there are Python syntax errors or undefined names
-  - flake8 . --count --select=E901,E999,F821,F822,F823 --show-source --statistics
-  - travis_wait pytest tests
+matrix:
+  include:
+    - language: python
+      python: "3.6"
+      install:
+          - pip install -r requirements.txt
+          - pip install flake8
+          - if ! wget ${UCI_HTTPS_URL}/adult/adult.data -P aif360/data/raw/adult/ ; then wget ${UCI_HTTPS_URL}/adult/adult.data --no-check-certificate -P aif360/data/raw/adult/ ; fi
+          - if ! wget ${UCI_HTTPS_URL}/adult/adult.test -P aif360/data/raw/adult/ ; then wget ${UCI_HTTPS_URL}/adult/adult.test --no-check-certificate -P aif360/data/raw/adult/; fi
+          - if ! wget ${UCI_HTTPS_URL}/adult/adult.names -P aif360/data/raw/adult/ ; then wget ${UCI_HTTPS_URL}/adult/adult.names --no-check-certificate -P aif360/data/raw/adult/; fi
+          - if ! wget ${UCI_HTTPS_URL}/statlog/german/german.data -P aif360/data/raw/german/ ; then wget ${UCI_HTTPS_URL}/statlog/german/german.data --no-check-certificate -P aif360/data/raw/german/; fi
+          - if ! wget ${UCI_HTTPS_URL}/statlog/german/german.doc -P aif360/data/raw/german/ ; then wget ${UCI_HTTPS_URL}/statlog/german/german.doc --no-check-certificate -P aif360/data/raw/german/; fi
+          - wget https://raw.githubusercontent.com/propublica/compas-analysis/master/compas-scores-two-years.csv -P aif360/data/raw/compas/
+      before_script:
+          # exit-zero treats all errors as warnings.  The GitHub editor is 127 chars wide
+          - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      script:
+          # stop the build if there are Python syntax errors or undefined names
+          - flake8 . --count --select=E901,E999,F821,F822,F823 --show-source --statistics
+          - travis_wait pytest tests
+
+    - language: R
+      cache: packages
+      warnings_are_errors: false
+      before_install:
+          - cd aif360/aif360-r
+      install:
+          - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+          - bash miniconda.sh -b -p $HOME/miniconda
+          - export PATH="$HOME/miniconda/bin:$PATH"
+          - hash -r
+          - conda config --set always_yes yes --set changeps1 no
+          - conda update -q conda
+          - conda info -a
+          - conda create -q -n test-env python=3.7
+          - source activate test-env
+          - R -q -e "install.packages('reticulate')"
+          - R -q -e "install.packages('rstudioapi')"
+          - R -q -e "install.packages('testthat')"
+          - pip install aif360 -q
+          - pip install numba -q
+          - pip install BlackBoxAuditing -q
+          - pip install tensorflow==1.15.0 -q
+          - pip install pandas -q
+      before_script:
+          - R CMD INSTALL .
diff --git a/AIF360.Rproj b/AIF360.Rproj
@@ -0,0 +1,18 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackagePath: aif360/aif360-r
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/README.md b/README.md
@@ -56,7 +56,9 @@ Get in touch with us on [Slack](https://aif360.slack.com) (invitation
 
 ## Setup
 
-Supported Configurations:
+AIF360 is available for both Python and R. For R setup, please refer to instructions [here](aif360/aif360-r/README.md).
+
+Supported Python Configurations:
 
 | OS      | Python version |
 | ------- | -------------- |

diff --git a/aif360/aif360-r/.Rbuildignore b/aif360/aif360-r/.Rbuildignore
@@ -0,0 +1,12 @@
+^.*\.Rproj$         # Automatically added by RStudio,
+^\.Rproj\.user$     # used for temporary files.
+^README\.Rmd$       # An Rmarkdown file used to generate README.md
+^NEWS\.md$          # A news file written in Markdown
+^\.travis\.yml$     # Used for continuous integration testing with travis
+^LICENSE\.md$
+^raif360\.Rproj$
+^README\.Rmd$
+^CONDUCT\.md$
+^CONTRIBUTING\.md$
+^CODEOFCONDUCT\.md$
+^cran-comments\.md$
diff --git a/aif360/aif360-r/.gitignore b/aif360/aif360-r/.gitignore
@@ -0,0 +1,7 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.httr-oauth
+.*.Rnb.cached
+.DS_Store
diff --git a/aif360/aif360-r/CODEOFCONDUCT.md b/aif360/aif360-r/CODEOFCONDUCT.md
@@ -0,0 +1,44 @@
+
+# Contributor Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/),
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
diff --git a/aif360/aif360-r/CONTRIBUTING.md b/aif360/aif360-r/CONTRIBUTING.md
@@ -0,0 +1,30 @@
+# Contributing to the AIF360 R package
+
+This guide is divided into three main parts:
+
+1. Filing a bug report or feature request in an issue.
+2. Suggesting a change via a pull request.
+3. New features or enhancements to AIF360 functionality.
+
+If you're not familiar with git or GitHub, please start by reading <http://r-pkgs.had.co.nz/git.html>
+
+Please note that the AIF360 R package is released with a [Contributor Code of Conduct](CODEOFCONDUCT.md). By contributing to this project, 
+you agree to abide by its terms.
+
+## Issues
+
+If you find a bug, please search GitHub under [Issues](https://github.com/IBM/AIF360/issues) to ensure the bug was not already reported. 
+If you’re unable to find an open issue addressing the problem, [open a new one](https://github.com/IBM/AIF360/issues/new). Please include a title and clear description, as much relevant information as possible (such as required packages, data, etc.), and a code sample to replicate the issue.
+
+## Pull requests
+
+To contribute a change to the AIF360 R package, you follow these steps:
+
+* Create a branch in git and make your changes.
+* Push branch to GitHub and open a new pull request (PR).
+* Ensure the PR description clearly describes the problem and solution. Include the relevant issue number if applicable.
+
+## New Features
+
+The AIF360 R package is part of [AI Fairness 360](https://github.com/IBM/AIF360), developed with extensibility in mind. If you wish to suggest new metrics, explainers, algorithms or datasets. Please get in touch on [Slack]( https://aif360.slack.com) (invitation [here](https://aif360.slack.com/join/shared_invite/zt-5hfvuafo-X0~g6tgJQ~7tIAT~S294TQ))!
+
diff --git a/aif360/aif360-r/DESCRIPTION b/aif360/aif360-r/DESCRIPTION
@@ -0,0 +1,24 @@
+Package: aif360
+Type: Package
+Title: Help Detect and Mitigate Bias in Machine Learning Models
+Version: 0.1.0
+Authors@R: c(
+    person("Gabriela", "de Queiroz", email = "[email protected]", role = "aut"),
+    person("Stacey", "Ronaghan", email = "[email protected]", role = "aut"),
+    person("Saishruthi", "Swaminathan", email = "[email protected]", 
+    role = c("aut", "cre")))
+Description: The AI Fairness 360 toolkit is an open-source library to help detect 
+    and mitigate bias in machine learning models. The AI Fairness 360 R package includes 
+    a comprehensive set of metrics for datasets and models to test for biases, 
+    explanations for these metrics, and algorithms to mitigate bias in datasets and models.
+License: Apache License (>= 2.0)
+Encoding: UTF-8
+LazyData: true
+URL: https://github.com/IBM/AIF360
+BugReports: https://github.com/IBM/AIF360/issues
+Imports: 
+    reticulate,
+    rstudioapi
+RoxygenNote: 7.1.0
+Suggests: 
+    testthat