first commit

.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -0,0 +1,7 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+src/*.o
+src/*.so
+src/*.dll

DESCRIPTION

@@ -0,0 +1,11 @@
+Package: gpuRNN
+Type: Package
+Title: What the package does (short line)
+Version: 1.0
+Date: 2017-10-16
+Author: Who wrote it
+Maintainer: Who to complain to <[email protected]>
+Description: More about what it does (maybe more than one line)
+License: What license is it under?
+Imports: Rcpp (>= 0.12.13), RcppEigen (>= 0.3.3.3.0)
+LinkingTo: Rcpp, RcppEigen

NAMESPACE

@@ -0,0 +1,4 @@
+useDynLib(gpuRNN)
+import(RcppEigen)
+importFrom(Rcpp, evalCpp)
+exportPattern("^[[:alpha:]]+")

R/RcppExports.R

@@ -0,0 +1,19 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+rcppeigen_hello_world <- function() {
+    .Call('_gpuRNN_rcppeigen_hello_world', PACKAGE = 'gpuRNN')
+}
+
+rcppeigen_outerproduct <- function(x) {
+    .Call('_gpuRNN_rcppeigen_outerproduct', PACKAGE = 'gpuRNN', x)
+}
+
+rcppeigen_innerproduct <- function(x) {
+    .Call('_gpuRNN_rcppeigen_innerproduct', PACKAGE = 'gpuRNN', x)
+}
+
+rcppeigen_bothproducts <- function(x) {
+    .Call('_gpuRNN_rcppeigen_bothproducts', PACKAGE = 'gpuRNN', x)
+}
+

README.md

@@ -0,0 +1,19 @@
+# gpuRNN
+
+Although there are many neural network implementations either directly
+written in R, such as [nnet](https://CRAN.R-project.org/package=nnet) and 
+[neuralnet](https://CRAN.R-project.org/package=neuralnet), and linked to
+other frameworks, such as [keras](https://CRAN.R-project.org/package=keras)
+and [tensorflow](https://CRAN.R-project.org/package=tensorflow), there is 
+no package that readily allows much flexibility in developing new neural 
+network models without needing to go to other languages or interfaces.
+
+This package is intended to provide R a neural network (or deep learning)
+framework to allow R users a means to not only build and train networks but
+to also allow users to more rapidly contribute novel methods and approaches
+in the R language.
+
+To make this package performant, it is based on the [gpuR](https://CRAN.R-project.org/package=gpuR) package to allow users
+to leverage GPUs.  However, it is my intent to not make this a strict
+requirement.
+

gpuRNN.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
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette

man/gpuRNN-package.Rd

@@ -0,0 +1,35 @@
+\name{gpuRNN-package}
+\alias{gpuRNN-package}
+\alias{gpuRNN}
+\docType{package}
+\title{
+\packageTitle{gpuRNN}
+}
+\description{
+\packageDescription{gpuRNN}
+}
+\details{
+
+The DESCRIPTION file:
+\packageDESCRIPTION{gpuRNN}
+\packageIndices{gpuRNN}
+~~ An overview of how to use the package, including the most important functions ~~
+}
+\author{
+\packageAuthor{gpuRNN}
+
+Maintainer: \packageMaintainer{gpuRNN}
+}
+\references{
+~~ Literature or other references for background information ~~
+}
+~~ Optionally other standard keywords, one per line, from file KEYWORDS in the R ~~
+~~ documentation directory ~~
+\keyword{ package }
+\seealso{
+~~ Optional links to other man pages, e.g. ~~
+~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
+}
+\examples{
+~~ simple examples of the most important functions ~~
+}

man/rcppeigen_hello_world.Rd

@@ -0,0 +1,50 @@
+\name{RcppEigen-Functions}
+\alias{rcppeigen_hello_world}
+\alias{rcppeigen_innerproduct}
+\alias{rcppeigen_outerproduct}
+\alias{rcppeigen_bothproducts}
+\title{Set of functions in example RcppEigen package}
+\description{
+  These four functions are created when
+  \code{RcppEigen.package.skeleton()} is invoked to create a
+  skeleton packages.
+}
+\usage{
+rcppeigen_hello_world()
+rcppeigen_outerproduct(x)
+rcppeigen_innerproduct(x)
+rcppeigen_bothproducts(x)
+}
+\arguments{
+  \item{x}{a numeric vector}
+}
+\value{
+  \code{rcppeigen_hello_world()} does not return a value, but displays a
+  message to the console.
+
+  \code{rcppeigen_outerproduct()} returns a numeric matrix computed as the
+  outer (vector) product of \code{x}.
+
+  \code{rcppeigen_innerproduct()} returns a double computer as the inner
+  (vector) product of \code{x}.
+
+  \code{rcppeigen_bothproducts()} returns a list with both the outer and
+  inner products.
+
+}
+\details{
+  These are example functions which should be largely
+  self-explanatory. Their main benefit is to demonstrate how to write a
+  function using the Eigen C++ classes, and to have to such a
+  function accessible from R.
+}
+\references{
+  See the documentation for Eigen, and RcppEigen, for more details.
+}
+\examples{
+  x <- sqrt(1:4)
+  rcppeigen_innerproduct(x)
+  rcppeigen_outerproduct(x)
+}
+\author{Dirk Eddelbuettel}
+

src/Makevars

@@ -0,0 +1,7 @@
+## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is
+## no user-facing library. The include path to headers is already set by R.
+#PKG_LIBS = 
+
+## With R 3.1.0 or later, you can uncomment the following line to tell R to 
+## enable compilation with C++11 (or even C++14) where available
+#CXX_STD = CXX11

src/Makevars.win

@@ -0,0 +1,7 @@
+## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is
+## no user-facing library. The include path to headers is already set by R.
+#PKG_LIBS = 
+
+## With R 3.1.0 or later, you can uncomment the following line to tell R to 
+## enable compilation with C++11 (or even C++14) where available
+#CXX_STD = CXX11

src/RcppExports.cpp

@@ -0,0 +1,64 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <RcppEigen.h>
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+// rcppeigen_hello_world
+Eigen::MatrixXd rcppeigen_hello_world();
+RcppExport SEXP _gpuRNN_rcppeigen_hello_world() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(rcppeigen_hello_world());
+    return rcpp_result_gen;
+END_RCPP
+}
+// rcppeigen_outerproduct
+Eigen::MatrixXd rcppeigen_outerproduct(const Eigen::VectorXd& x);
+RcppExport SEXP _gpuRNN_rcppeigen_outerproduct(SEXP xSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Eigen::VectorXd& >::type x(xSEXP);
+    rcpp_result_gen = Rcpp::wrap(rcppeigen_outerproduct(x));
+    return rcpp_result_gen;
+END_RCPP
+}
+// rcppeigen_innerproduct
+double rcppeigen_innerproduct(const Eigen::VectorXd& x);
+RcppExport SEXP _gpuRNN_rcppeigen_innerproduct(SEXP xSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Eigen::VectorXd& >::type x(xSEXP);
+    rcpp_result_gen = Rcpp::wrap(rcppeigen_innerproduct(x));
+    return rcpp_result_gen;
+END_RCPP
+}
+// rcppeigen_bothproducts
+Rcpp::List rcppeigen_bothproducts(const Eigen::VectorXd& x);
+RcppExport SEXP _gpuRNN_rcppeigen_bothproducts(SEXP xSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Eigen::VectorXd& >::type x(xSEXP);
+    rcpp_result_gen = Rcpp::wrap(rcppeigen_bothproducts(x));
+    return rcpp_result_gen;
+END_RCPP
+}
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_gpuRNN_rcppeigen_hello_world", (DL_FUNC) &_gpuRNN_rcppeigen_hello_world, 0},
+    {"_gpuRNN_rcppeigen_outerproduct", (DL_FUNC) &_gpuRNN_rcppeigen_outerproduct, 1},
+    {"_gpuRNN_rcppeigen_innerproduct", (DL_FUNC) &_gpuRNN_rcppeigen_innerproduct, 1},
+    {"_gpuRNN_rcppeigen_bothproducts", (DL_FUNC) &_gpuRNN_rcppeigen_bothproducts, 1},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_gpuRNN(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}

src/rcppeigen_hello_world.cpp

@@ -0,0 +1,51 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; indent-tabs-mode: nil; -*-
+
+// we only include RcppEigen.h which pulls Rcpp.h in for us
+#include <RcppEigen.h>
+
+// via the depends attribute we tell Rcpp to create hooks for
+// RcppEigen so that the build process will know what to do
+//
+// [[Rcpp::depends(RcppEigen)]]
+
+// simple example of creating two matrices and
+// returning the result of an operatioon on them
+//
+// via the exports attribute we tell Rcpp to make this function
+// available from R
+//
+// [[Rcpp::export]]
+Eigen::MatrixXd rcppeigen_hello_world() {
+    Eigen::MatrixXd m1 = Eigen::MatrixXd::Identity(3, 3);
+    Eigen::MatrixXd m2 = Eigen::MatrixXd::Random(3, 3);
+
+    return m1 + 3 * (m1 + m2);
+}
+
+
+// another simple example: outer product of a vector, 
+// returning a matrix
+//
+// [[Rcpp::export]]
+Eigen::MatrixXd rcppeigen_outerproduct(const Eigen::VectorXd & x) {
+    Eigen::MatrixXd m = x * x.transpose();
+    return m;
+}
+
+// and the inner product returns a scalar
+//
+// [[Rcpp::export]]
+double rcppeigen_innerproduct(const Eigen::VectorXd & x) {
+    double v = x.transpose() * x;
+    return v;
+}
+
+// and we can use Rcpp::List to return both at the same time
+//
+// [[Rcpp::export]]
+Rcpp::List rcppeigen_bothproducts(const Eigen::VectorXd & x) {
+    Eigen::MatrixXd op = x * x.transpose();
+    double          ip = x.transpose() * x;
+    return Rcpp::List::create(Rcpp::Named("outer")=op,
+                              Rcpp::Named("inner")=ip);
+}