R packge refactor for compatibility with devtools::install_github

.Rbuildignore

@@ -0,0 +1,79 @@
+^appveyor\.yml$
+^azure-pipelines\.yml$
+^bench$
+^.clangd$
+^codecov\.yml$
+^compile_commands.json$
+^CONDUCT\.md$
+^config\.yaml$
+^cran-comments\.md$
+^CRAN-RELEASE$
+^[^/]+.csv
+^[^/]+.sh
+^data-raw$
+^\.dir-locals\.el$
+^development.md$
+^doc$
+^docker$
+^.dockerignore.*$
+^docs$
+^etc$
+^\.github$
+^\.github/workflows/pkgdown\.yaml$
+^\.github/workflows/pr-commands\.yaml$
+^\.github/workflows/R-CMD-check\.yaml$
+^\.gitlab$
+^home$
+^\.httr-oauth$
+^inst/bench$
+^inst/db$
+^inst/extdata/ext$
+^inst/extdata/int$
+^inst/extdata/tmp$
+^inst/rcon$
+^Jenkinsfile.*$
+^LICENSE\.md$
+.*log$
+^logo\.png$
+^logs$
+^maven-project$
+^Makefile.*$
+^Makefile$
+^man-roxygen$
+^Meta$
+^\.mypy_cache$
+^notes$
+^pkgdown$
+^_pkgdown\.yml$
+^poetry\.lock$
+^Project\.toml$
+^pyproject\.toml$
+^\.python-version$
+^rcon$
+^renv$
+^renv\.lock$
+^.renvignore$
+^README-.*\.png$
+^README\.Rmd$
+^resources\.txt$
+^revdep$
+^Rplots.*
+^.Rprofile$
+^\.\.Rcheck$
+^.*\.Rproj$
+^\.Rproj\.user$
+^sanitize\.sh$
+^script\.R$
+^setup\.cfg$
+^setup\.py$
+^src/\.clang-format$
+^src/\.ycm_extra_conf\.pyc?$
+^TAGS$
+^_targets$
+^_targets\.R$
+^temp$
+^travis$
+^travis/check_format\.sh$
+^\.travis\.yml$
+^vignettes/rsconnect$
+^.vimrc$

.gitattributes

@@ -0,0 +1,39 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto eol=lf
+
+*.sh text eol=lf
+*.bat text eol=crlf
+*.cmd text eol=crlf
+pom.xml text eol=lf
+*.java text eol=lf
+*.scala text eol=lf
+*.xml text eol=lf
+*.properties text eol=lf
+
+# Denote all files that are truly binary and should not be modified.
+*.gpg binary
+*.png binary
+*.jpg binary
+*.gif binary
+*.jpeg binary
+*.zip binary
+*.phar binary
+*.ttf binary
+*.woff binary
+*.woff2 binary
+*.eot binary
+*.ico binary
+*.mo binary
+*.pdf binary
+*.xsd binary
+*.ts binary
+*.exe binary
+
+*.pt binary
+*.pickle binary
+
+*.docx binary
+*.xslx binary
+*.pptx binary
+/NEWS.md merge=union
+/.Rbuildignore merge=union

.gitignore

@@ -1,12 +1,149 @@
-/build
-/.classpath
-/.project
-/.settings
-/target
+**/.settings/
+**/.classpath
+**/.project
+**/.metadata
+#**/bin/
+**/*.2delete
+**/target/
+**/build/
+*.egg-info
+.idea/
+*.iml
+*.eml
+
+
+# Ignore all dotfiles...
+#.*
+
+.#*
+
+
+
+
+# except for .gitignore
+!.gitignore
+!.gitattributes
+
+!.dockerignore
+!.travis.yml
+
+
+!.python-version
+
+
+# python
+venv/
+
+
+###################
+# Compiled source #
+###################
+*.com
+*.class
+docs
+/src/*.o
+/src/*.o-*
+/src/*.d
+/src/*.so
+
+*.dll
+*.exe
+*.o
+*.so
+
+
+############
+# setup.py #
+############
+
+/build/
+/dist/
+
+*.pyc
+*.egg
+*.whl
+
+*.egg-info/
+
+##########
+# pytest #
+##########
+
+/.pytest_cache/
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+
+### *.jar
+
+*.rar
+*.tar
+#*.zip
+
+# Logs and databases #
+######################
+*.log
+*.tlog
+*.sqlite
+/logs/
+
+
+# OS generated files #
+######################
+.DS_Store*
+ehthumbs.db
+Icon?
+Thumbs.db
+
+
+# general
 *~
+
+# Eclipse
+.settings
+.project
+.classpath
+
+# IDEA
+/.idea
+/.idea_modules
+
+# Sublime
+*.sublime-project
+*.sublime-workspace
+
+# SPARK
+metastore_db/
+/doc/_build/
+*.~undo-tree~
+.RData
+.Rproj.user
+..Rcheck
 .Rhistory
-*.class
-# Package Files #
-*.jar
-*.war
-*.ear
+Rplots.*
+inst/doc
+.httr-oauth
+vignettes/*.R
+.DS_Store
+/clion-test.R
+/BROWSE
+/GPATH
+/GRTAGS
+/GTAGS
+/TAGS
+/.dir-locals.el
+.obsidian/
+/issues
+/home
+/logs
+/temp
+/.drake
+bench-libs
+doc
+Meta

R-skeleton/NAMESPACE → NAMESPACE

@@ -1,7 +1,7 @@
-import("rJava")
-export(extraTrees, toRMatrix, toJavaMatrix, toJavaCSMatrix, toJavaMatrix2D, selectTrees, setJavaMemory, prepareForSave)
-S3method(predict, extraTrees)
-S3method(print,   extraTrees)
-S3method(extraTrees, default)
-
-
+import("rJava")
+export(extraTrees, toRMatrix, toJavaMatrix, toJavaCSMatrix, toJavaMatrix2D, selectTrees, setJavaMemory, prepareForSave)
+S3method(predict, extraTrees)
+S3method(print,   extraTrees)
+S3method(extraTrees, default)
+
+

R-skeleton/R/extraTrees.R → R/extraTrees.R

@@ -1,4 +1,4 @@
-extraTrees <- function(x, ...) UseMethod("extraTrees", x)
-
-
-
+extraTrees <- function(x, ...) UseMethod("extraTrees", x)
+
+
+

R-skeleton/R/onLoad.R → R/onLoad.R

@@ -1,3 +1,3 @@
-.onLoad <- function(libname, pkgname) {
-  .jpackage(pkgname, lib.loc = libname)
+.onLoad <- function(libname, pkgname) {
+  .jpackage(pkgname, lib.loc = libname)
 }

R-skeleton/man/setJavaMemory.Rd → man/setJavaMemory.Rd

@@ -1,21 +1,21 @@
-\name{setJavaMemory}
-\alias{setJavaMemory}
-\title{Utility function for setting Java memory.}
-\description{
-  Function for setting JVM memory, specified in MB. If you get java.lang.OutOfMemoryError you can use this function to increase the memory available to ExtraTrees.
-}
-\usage{
-  setJavaMemory( memoryInMB )
-}
-\arguments{
-  \item{memoryInMB}{Integer specifying the amount of memory (MB)}
-}
-%\value{
-%}
-\author{Jaak Simm}
-\examples{
-  ## use 2G memory
-  setJavaMemory(2000)
-}
-\keyword{java.lang.OutOfMemoryError,memory,JVM}
-
+\name{setJavaMemory}
+\alias{setJavaMemory}
+\title{Utility function for setting Java memory.}
+\description{
+  Function for setting JVM memory, specified in MB. If you get java.lang.OutOfMemoryError you can use this function to increase the memory available to ExtraTrees.
+}
+\usage{
+  setJavaMemory( memoryInMB )
+}
+\arguments{
+  \item{memoryInMB}{Integer specifying the amount of memory (MB)}
+}
+%\value{
+%}
+\author{Jaak Simm}
+\examples{
+  ## use 2G memory
+  setJavaMemory(2000)
+}
+\keyword{java.lang.OutOfMemoryError,memory,JVM}
+

R-skeleton/man/toJavaMatrix.Rd → man/toJavaMatrix.Rd

@@ -1,18 +1,18 @@
-\name{toJavaMatrix}
-\alias{toJavaMatrix}
-\title{Utility function for converting an R matrix (numeric matrix) to Java matrix.}
-\description{
-  Internal function used for converting an R matrix to a Matrix object in Java. Matrix class is a custom Java class used for storing matrices by the implementation of ExtraTrees in Java.
-}
-\usage{
-  toJavaMatrix( m )
-}
-\arguments{
-  \item{m}{ matrix of numeric values. }
-}
-\value{
-  reference to Java matrix with the same contents as the input R matrix.
-}
-\author{Jaak Simm}
-\keyword{java,matrix,conversion}
-
+\name{toJavaMatrix}
+\alias{toJavaMatrix}
+\title{Utility function for converting an R matrix (numeric matrix) to Java matrix.}
+\description{
+  Internal function used for converting an R matrix to a Matrix object in Java. Matrix class is a custom Java class used for storing matrices by the implementation of ExtraTrees in Java.
+}
+\usage{
+  toJavaMatrix( m )
+}
+\arguments{
+  \item{m}{ matrix of numeric values. }
+}
+\value{
+  reference to Java matrix with the same contents as the input R matrix.
+}
+\author{Jaak Simm}
+\keyword{java,matrix,conversion}
+