Merge pull request #116 from neurodata/staging

Merge v2.0.2 into master branch

.#build.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+Rscript -e "install.packages('Rcpp', repos = 'http://cran.us.r-project.org')"
+Rscript -e "Rcpp::compileAttributes()"
+
+# Rscript -e "install.packages('devtools', repos = 'http://cran.us.r-project.org')"
+# Rscript -e "install.packages('roxygen2', repos = 'http://cran.us.r-project.org')"
+## RUN styler on directory
+# Rscript -e "styler::style_dir(style = tidyverse_style)"
+Rscript -e "devtools::document('R')"
+
+R CMD build --resave-data .
+
+# Rscript -e "install.packages('dummies', repos = 'http://cran.us.r-project.org')"
+# Rscript -e "install.packages('RcppArmadillo', repos = 'http://cran.us.r-project.org')"
+# Rscript -e "install.packages('RcppZiggurat', repos = 'http://cran.us.r-project.org')"
+# Rscript -e "install.packages('testthat', repos = 'http://cran.us.r-project.org')"
+
+R CMD check --as-cran --no-manual rerf*.tar.gz

.#build_win.ps1

@@ -0,0 +1,18 @@
+
+Rscript.exe -e "install.packages('Rcpp', repos = 'http://cran.us.r-project.org')"
+Rscript.exe -e "Rcpp::compileAttributes()"
+
+# Rscript.exe -e "install.packages('devtools', repos = 'http://cran.us.r-project.org')"
+# Rscript.exe -e "install.packages('roxygen2', repos = 'http://cran.us.r-project.org')"
+## RUN styler on directory
+# Rscript.exe -e "styler::style_dir(style = tidyverse_style)"
+Rscript.exe -e "devtools::document('R')"
+
+R.exe CMD build --resave-data .
+
+# Rscript.exe -e "install.packages('dummies', repos = 'http://cran.us.r-project.org')"
+# Rscript.exe -e "install.packages('RcppArmadillo', repos = 'http://cran.us.r-project.org')"
+# Rscript.exe -e "install.packages('RcppZiggurat', repos = 'http://cran.us.r-project.org')"
+# Rscript.exe -e "install.packages('testthat', repos = 'http://cran.us.r-project.org')"
+
+R.exe CMD check --as-cran --no-manual rerf*.tar.gz

.Rbuildignore

@@ -1,4 +1,13 @@
+^README.html$
+^README.Rmd$
 ^travisTest$
 ^docs$
+^\.git$
 ^\.travis\.yml$
-^.*\\.gz$
+^.*\.gz$
+^.*\.out$
+^.*\.o$
+^.*\.so$
+^.*\.Rproj$
+^\.Rproj\.user$
+^CONTRIBUTING.md$

.gitattributes

@@ -0,0 +1,6 @@
+*.csv linguist-generated=true
+*.html linguist-documentation=true
+*.md linguist-documentation=true
+*.Rmd linguist-documentation=true
+man/* linguist-generated=true
+docs/* linguist-documentation=true

.gitignore

@@ -18,6 +18,9 @@
 # RStudio files
 .Rproj.user/
 
+# vscode settings
+.vscode/settings.json
+
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
@@ -43,6 +46,8 @@ vignettes/*.pdf
 *.csv
 *.swp
 
-# auto generated Rcpp code
-src/RcppExports.cpp
-R/RcppExports.R
+.Rproj.user
+
+#automatically generated on Windows
+rerf.dll
+src-i386

.travis.yml

@@ -1,23 +1,26 @@
 language: r
-cache: packages
+dist: trusty
+
 r:
-    - release
+  - release
 
 sudo: false
 
-branches:
-    only:
-        - master
-
 addons:
-      apt:
-          packages:
-              - libgsl0-dev
-
-before_install:
-    - #
+  apt:
+    packages:
+      - libgsl0-dev
+
+r_packages:
+  - devtools
+  - testthat
+  - Rcpp
 
 script:
-    - cd travisTest
-    - printf "starting run\n"
-    - Rscript test.R
+  - printf "Starting install and test with devtools.\n\n"
+  - Rscript -e "Rcpp::compileAttributes()"
+  - Rscript -e "devtools::install(local=FALSE);devtools::test()"
+  - Rscript travisTest/test-on-prior-release.R
+  - printf "Starting BUILD and CHECK --as-cran\n\n"
+  - R CMD build --resave-data .
+  - R CMD check --as-cran --no-manual rerf*tar.gz

CONTRIBUTING.md

@@ -0,0 +1,60 @@
+# Contributing
+
+You are here to help on R-RerF?  First off, thank you!  Please read the following sections in order to know how to ask questions and how to work work on something.
+
+## Get in touch
+
+* Report bugs, suggest features or view the source code [on GitHub](https://github.com/neurodata/R-RerF)
+
+## Organization
+
+### Branches
+
+* `master`: inline with current release on CRAN
+* `staging`: development branch from which PRs should be made
+
+## Making Changes
+
+### Formatting
+
+* Run your code through [styler](http://styler.r-lib.org/) auto-formater
+* Avoid modifying formatting outside the scope of your pull request
+* Use **TRUE** and **FALSE**, not **T** and **F**
+* Check for unnecessary whitespace with `git diff --check` before committing
+
+### Testing
+
+We use the [testthat](https://github.com/r-lib/testthat) library for testing in R.  You can run your tests locally using `devtools::test()`.  Testthat tests are also run on [TravisCI](https://travis-ci.org/neurodata/R-RerF) automatically.
+
+* New features need tests
+* Tests should be fast, ideally each test should complete in under 5 seconds
+* Mark longer running tests with 
+* Bug fixes need [testthat](https://github.com/r-lib/testthat) functions (test the condition that was failing)
+
+### Make your Pull Request
+
+Congrats, you are ready for your PR!
+
+* If adding a new feature, add a summary of your feature to the NEWS.md file.
+* Create your pull request on GitHub
+
+### Code review
+
+Code reviews will take place for all Pull Requets.  It is our intention for code reviews to be a pleasant experience - we appreciate PRs and all the work that goes into them.  The purpose for the code review is to:
+
+* Ensure working code
+* Maintainable code
+* Consistent style throughout the package
+
+We aim to give feedback in a timely fashion
+
+### Merge
+
+When merging, choose the `squash and merge` type on GitHub
+
+## Resources for best practices
+
+* For additions to the R code, we will be following [Google's](https://google.github.io/styleguide/Rguide.xml) style guide
+* [Comments on Style by H.W.](http://adv-r.had.co.nz/Style.html)
+* [Advanced R by H.W.](http://adv-r.had.co.nz)
+* [R packages by H.W.](http://r-pkgs.had.co.nz)

DESCRIPTION

@@ -1,32 +1,38 @@
 Package: rerf
 Type: Package
 Title: Randomer Forest
-Version: 1.1.3
-Date: 2018-07-05
-Authors@R: c(person("James", "Browne", role = c("aut", "cre"),
-	   	    email = "jbrowne6@jhu.edu"),
-	     person("Tyler", "Tomita", role = "aut",
-	            email = "ttomita2@jhmi.edu"),
-	     person("Joshua", "Vogelstein", role = "ths",
-	     	    email = "jovo@jhu.edu"))
-Description: Random Forester (RerF) is an algorithm developed by Tomita
-  (2016) <arXiv:1506.03410v2> which is similar to Random Forest - Random
-  Combination (Forest-RC) developed by Breiman (2001)
-  <doi:10.1023/A:1010933404324>.  Random Forests create axis-parallel, or
-  orthogonal trees. That is, the feature space is recursively split along
-  directions parallel to the axes of the feature space. Thus, in cases in
-  which the classes seem inseparable along any single dimension, Random
-  Forests may be suboptimal.  To address this, Breiman also proposed and
-  characterized Forest-RC, which uses linear combinations of coordinates
-  rather than individual coordinates, to split along.  This package,
-  'rerf', implements RerF which is similar to Forest-RC.  The difference
-  between the two algorithms is where the random linear combinations
-  occur: Forest-RC combines features at the per tree level whereas RerF
-  takes linear combinations of coordinates at every node in the tree.
-License: GPL-2
+Version: 2.0.2
+Date: 2018-12-03
+Authors@R: c(
+        person("Jesse", "Patsolic", role = c("ctb", "cre"), email = "software@neurodata.io"),
+        person("Benjamin", "Falk", role = "ctb", email = "falk.ben@jhu.edu"),
+        person("Jaewon", "Chung", role = "ctb", email = "j1c@jhu.edu"),
+        person("James", "Browne", role = "aut", email = "jbrowne6@jhu.edu"),
+        person("Tyler", "Tomita", role = "aut", email = "ttomita2@jhmi.edu"),
+        person("Joshua", "Vogelstein", role = "ths", email = "jovo@jhu.edu")
+    )
+Description: R-RerF (aka Randomer Forest (RerF) or Random Projection
+  Forests) is an algorithm developed by Tomita (2016) <arXiv:1506.03410v2>
+  which is similar to Random Forest - Random Combination (Forest-RC)
+  developed by Breiman (2001) <doi:10.1023/A:1010933404324>.  Random
+  Forests create axis-parallel, or orthogonal trees. That is, the feature
+  space is recursively split along directions parallel to the axes of the
+  feature space. Thus, in cases in which the classes seem inseparable
+  along any single dimension, Random Forests may be suboptimal.  To
+  address this, Breiman also proposed and characterized Forest-RC, which
+  uses linear combinations of coordinates rather than individual
+  coordinates, to split along.  This package, 'rerf', implements RerF
+  which is similar to Forest-RC.  The difference between the two
+  algorithms is where the random linear combinations occur: Forest-RC
+  combines features at the per tree level whereas RerF takes linear
+  combinations of coordinates at every node in the tree.
+Depends: R (>= 3.3.0)
+License: Apache License 2.0 | file LICENSE
 URL: https://github.com/neurodata/R-RerF
+BugReports: https://github.com/neurodata/R-RerF/issues
 Imports: parallel, RcppZiggurat, utils, stats, dummies
+Suggests: roxygen2 (>= 5.0.0), testthat
 LinkingTo: Rcpp, RcppArmadillo
 SystemRequirements: GNU make
 ByteCompile: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0