Merge remote-tracking branch 'origin/master' into dev/0.9

Conflicts:
	R/RcppExports.R
	R/hashed.model.matrix.R
	man/hashed.model.matrix.Rd
	src/RcppExports.cpp

..Rcheck/00install.out

@@ -0,0 +1,13 @@
+* installing *source* package ‘FeatureHashing’ ...
+** libs
+make: Nothing to be done for `all'.
+installing to /Users/wush/Projects/FeatureHashing/..Rcheck/FeatureHashing/libs
+** R
+** data
+** inst
+** preparing package for lazy loading
+** help
+*** installing help indices
+** building package indices
+** testing if installed package can be loaded
+* DONE (FeatureHashing)

..Rcheck/FeatureHashing-Ex.R

@@ -0,0 +1,107 @@
+pkgname <- "FeatureHashing"
+source(file.path(R.home("share"), "R", "examples-header.R"))
+options(warn = 1)
+base::assign(".ExTimings", "FeatureHashing-Ex.timings", pos = 'CheckExEnv')
+base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
+base::assign(".format_ptime",
+function(x) {
+  if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+  if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+  options(OutDec = '.')
+  format(x[1L:3L], digits = 7L)
+},
+pos = 'CheckExEnv')
+
+### * </HEADER>
+library('FeatureHashing')
+
+base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
+cleanEx()
+nameEx("CSCMatrix-class")
+### * CSCMatrix-class
+
+flush(stderr()); flush(stdout())
+
+base::assign(".ptime", proc.time(), pos = "CheckExEnv")
+### Name: CSCMatrix-class
+### Title: CSCMatrix
+### Aliases: CSCMatrix-class [,CSCMatrix,missing,numeric,ANY-method
+###   [,CSCMatrix,numeric,missing,ANY-method
+###   [,CSCMatrix,numeric,numeric,ANY-method %*%,CSCMatrix,numeric-method
+###   %*%,numeric,CSCMatrix-method dim,CSCMatrix-method
+###   dim<-,CSCMatrix-method
+
+### ** Examples
+
+# construct a CSCMatrix
+m <- hashed.model.matrix(~ ., CO2, 8)
+# convert it to dgCMatrix
+m2 <- as(m, "dgCMatrix")
+
+
+
+base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
+base::cat("CSCMatrix-class", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
+cleanEx()
+nameEx("hashed.model.matrix")
+### * hashed.model.matrix
+
+flush(stderr()); flush(stdout())
+
+base::assign(".ptime", proc.time(), pos = "CheckExEnv")
+### Name: hashed.model.matrix
+### Title: Create a model matrix with feature hashing
+### Aliases: hash_h hash_xi hashed.model.matrix
+
+### ** Examples
+
+# Construct the model matrix. The transposed matrix is returned by default.
+m <- hashed.model.matrix(~ ., CO2, 2^6, keep.hashing_mapping = TRUE)
+# Print the matrix via dgCMatrix
+as(m, "dgCMatrix")
+# Check the result of hashing
+mapping <- unlist(as.list(attr(m, "mapping")))
+# Check the rate of collision
+# mean(duplicated(mapping %% 2^6))
+# The result is CSCMatrix which supports simple subsetting and matrix-vector
+# multiplication
+# rnorm(2^6) %*% m
+
+# Detail of the hashing
+## The main effect is hashed via `hash_h`
+all(hash_h(names(mapping)) %% 2^6 == mapping %% 2^6)
+## The sign is corrected by `hash_xi`
+hash_xi(names(mapping))
+## The interaction term is implemented as follow:
+m2 <- hashed.model.matrix(~ .^2, CO2, 2^6, keep.hashing_mapping = TRUE)
+mapping2 <- unlist(as.list(attr(m2, "mapping")))
+mapping2[2] # PlantQn2:uptake
+h1 <- mapping2["PlantQn2"]
+h2 <- mapping2["uptake"]
+library(pack)
+hash_h(rawToChar(c(numToRaw(h1, 4), numToRaw(h2, 4)))) # should be mapping2[2]
+
+# The tag-like feature
+data(test.tag)
+df <- data.frame(a = test.tag, b = rnorm(length(test.tag)))
+m <- hashed.model.matrix(~ tag(a, split = ",", type = "existence"):b, df, 2^6,
+ keep.hashing_mapping = TRUE)
+# The column `a` is splitted by "," and have an interaction with "b":
+mapping <- unlist(as.list(attr(m, "mapping")))
+names(mapping)
+
+
+
+base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
+base::cat("hashed.model.matrix", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
+### * <FOOTER>
+###
+options(digits = 7L)
+base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+grDevices::dev.off()
+###
+### Local variables: ***
+### mode: outline-minor ***
+### outline-regexp: "\\(> \\)?### [*]+" ***
+### End: ***
+quit('no')

..Rcheck/FeatureHashing-Ex.timings

@@ -0,0 +1,2 @@
+name	user	system	elapsed
+CSCMatrix-class	0.003	0.000	0.005	

..Rcheck/FeatureHashing/DESCRIPTION

@@ -0,0 +1,24 @@
+Package: FeatureHashing
+Type: Package
+Title: Creates a Model Matrix via Feature Hashing With a Formula
+        Interface
+Version: 0.8.1
+Date: 2014-08-01
+Authors@R: as.person(c( "Wush Wu <wush978@gmail.com> [aut, cre]"))
+Author: Wush Wu [aut, cre]
+Maintainer: Wush Wu <wush978@gmail.com>
+Description: Feature hashing, also called as the hashing trick, is a method to 
+  transform features to vector. Without looking up the indices in an 
+  associative array, it applies a hash function to the features and uses their 
+  hash values as indices directly. The method of feature hashing in this package
+  was proposed in Weinberger et al. (2009). The hashing algorithm is the murmurhash3 
+  from the digest package. Please see the README.md for more information.
+License: GPL(>= 3)
+Depends: R (>= 3.1), methods
+Imports: Rcpp (>= 0.11), Matrix, digest(>= 0.6.8)
+LinkingTo: Rcpp, digest(>= 0.6.8), BH
+Suggests: pack, RUnit
+SystemRequirements: C++11
+BugReports: https://github.com/wush978/FeatureHashing/issues
+URL: https://github.com/wush978/FeatureHashing
+Built: R 3.1.2; x86_64-apple-darwin13.4.0; 2015-02-21 09:20:06 UTC; unix

..Rcheck/FeatureHashing/INDEX

@@ -0,0 +1,4 @@
+CSCMatrix-class         CSCMatrix
+hashed.model.matrix     Create a model matrix with feature hashing
+tag                     Expand concatenated feature
+test.tag                test.tag

..Rcheck/FeatureHashing/NAMESPACE

@@ -0,0 +1,12 @@
+# Generated by roxygen2 (4.0.1): do not edit by hand
+
+export(hash_h)
+export(hash_xi)
+export(hashed.model.matrix)
+export(tag)
+import(digest)
+importClassesFrom(Matrix,dgCMatrix)
+importFrom(Rcpp,evalCpp)
+importFrom(methods,checkAtAssignment)
+importFrom(methods,new)
+useDynLib(FeatureHashing)

..Rcheck/FeatureHashing/R/FeatureHashing

@@ -0,0 +1,27 @@
+#  File share/R/nspackloader.R
+#  Part of the R package, http://www.R-project.org
+#
+#  Copyright (C) 1995-2012 The R Core Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  http://www.r-project.org/Licenses/
+
+local({
+    info <- loadingNamespaceInfo()
+    pkg <- info$pkgname
+    ns <- .getNamespace(as.name(pkg))
+    if (is.null(ns))
+        stop("cannot find namespace environment for ", pkg, domain = NA);
+    dbbase <- file.path(info$libname, pkg, "R", pkg)
+    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})

..Rcheck/FeatureHashing/help/AnIndex

@@ -0,0 +1,13 @@
+%*%,CSCMatrix,numeric-method	CSCMatrix-class
+%*%,numeric,CSCMatrix-method	CSCMatrix-class
+CSCMatrix-class	CSCMatrix-class
+dim,CSCMatrix-method	CSCMatrix-class
+dim<-,CSCMatrix-method	CSCMatrix-class
+hashed.model.matrix	hashed.model.matrix
+hash_h	hashed.model.matrix
+hash_xi	hashed.model.matrix
+tag	tag
+test.tag	test.tag
+[,CSCMatrix,missing,numeric,ANY-method	CSCMatrix-class
+[,CSCMatrix,numeric,missing,ANY-method	CSCMatrix-class
+[,CSCMatrix,numeric,numeric,ANY-method	CSCMatrix-class

..Rcheck/FeatureHashing/html/00Index.html

@@ -0,0 +1,45 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Creates a Model Matrix via Feature Hashing With a Formula
+Interface</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Creates a Model Matrix via Feature Hashing With a Formula
+Interface
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package &lsquo;FeatureHashing&rsquo; version 0.8.1</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="CSCMatrix-class.html">%*%-method</a></td>
+<td>CSCMatrix</td></tr>
+<tr><td width="25%"><a href="CSCMatrix-class.html">CSCMatrix-class</a></td>
+<td>CSCMatrix</td></tr>
+<tr><td width="25%"><a href="CSCMatrix-class.html">dim-method</a></td>
+<td>CSCMatrix</td></tr>
+<tr><td width="25%"><a href="CSCMatrix-class.html">dim&lt;--method</a></td>
+<td>CSCMatrix</td></tr>
+<tr><td width="25%"><a href="hashed.model.matrix.html">hashed.model.matrix</a></td>
+<td>Create a model matrix with feature hashing</td></tr>
+<tr><td width="25%"><a href="hashed.model.matrix.html">hash_h</a></td>
+<td>Create a model matrix with feature hashing</td></tr>
+<tr><td width="25%"><a href="hashed.model.matrix.html">hash_xi</a></td>
+<td>Create a model matrix with feature hashing</td></tr>
+<tr><td width="25%"><a href="tag.html">tag</a></td>
+<td>Expand concatenated feature</td></tr>
+<tr><td width="25%"><a href="test.tag.html">test.tag</a></td>
+<td>test.tag</td></tr>
+<tr><td width="25%"><a href="CSCMatrix-class.html">[-method</a></td>
+<td>CSCMatrix</td></tr>
+</table>
+</body></html>

..Rcheck/FeatureHashing/html/R.css

@@ -0,0 +1,57 @@
+BODY{		background: white;
+		color: black }
+
+A:link{         background: white;
+                color: blue }
+A:visited{	background: white;
+		color: rgb(50%, 0%, 50%) }
+
+H1{		background: white;
+		color: rgb(55%, 55%, 55%);
+		font-family: monospace;
+		font-size: x-large;
+		text-align: center }
+
+H2{		background: white;
+		color: rgb(40%, 40%, 40%);
+		font-family: monospace;
+		font-size: large;
+		text-align: center }
+
+H3{		background: white;
+		color: rgb(40%, 40%, 40%);
+		font-family: monospace;
+		font-size: large }
+
+H4{		background: white;
+		color: rgb(40%, 40%, 40%);
+		font-family: monospace;
+		font-style: italic;
+		font-size: large }
+
+H5{		background: white;
+		color: rgb(40%, 40%, 40%);
+		font-family: monospace }
+
+H6{		background: white;
+		color: rgb(40%, 40%, 40%);
+		font-family: monospace;
+		font-style: italic }
+
+IMG.toplogo{	vertical-align: middle }
+
+IMG.arrow{	width: 30px;
+		height: 30px;
+		border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+  background: rgb(85%, 85%, 85%);
+}
+

..Rcheck/FeatureHashing/runTest.R

@@ -0,0 +1,3 @@
+library(RUnit)
+test <- defineTestSuite("FeatureHashing", dirs = "tests", testFileRegexp = "^test-")
+runTestSuite(test)

DESCRIPTION

@@ -12,14 +12,15 @@ Description: Feature hashing, also called as the hashing trick, is a method to
   hash values as indices directly. The method of feature hashing in this package
   was proposed in Weinberger et al. (2009). The hashing algorithm is the murmurhash3 
   from the digest package. Please see the README.md for more information.
-License: GPL(>= 3)
+License: GPL(>= 3) | file LICENSE
 Depends: 
   R (>= 3.1),
   methods
 Imports: 
   Rcpp (>= 0.11),
   Matrix,
-  digest(>= 0.6.8)
+  digest(>= 0.6.8),
+  magrittr (>= 1.5)
 LinkingTo: Rcpp, digest(>= 0.6.8), BH
 Suggests: pack, RUnit
 SystemRequirements: C++11

FeatureHashing.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
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
+PackageRoxygenize: rd,namespace

NAMESPACE

@@ -7,6 +7,8 @@ export(tag)
 import(digest)
 importClassesFrom(Matrix,dgCMatrix)
 importFrom(Rcpp,evalCpp)
+importFrom(magrittr,"%<>%")
+importFrom(magrittr,"%>%")
 importFrom(methods,checkAtAssignment)
 importFrom(methods,new)
 useDynLib(FeatureHashing)

R/RcppExports.R

@@ -27,8 +27,13 @@ hash_h <- function(src) {
     .Call('FeatureHashing_h', PACKAGE = 'FeatureHashing', src)
 }
 
+<<<<<<< HEAD
 .hashed.model.matrix.dataframe <- function(tf, data, hash_size, transpose, retval, keep_hashing_mapping, is_xi) {
     .Call('FeatureHashing_hashed_model_matrix_dataframe', PACKAGE = 'FeatureHashing', tf, data, hash_size, transpose, retval, keep_hashing_mapping, is_xi)
+=======
+.hashed.model.matrix.dataframe <- function(tf, data, hash_size, transpose, retval, keep_hashing_mapping) {
+    .Call('FeatureHashing_hashed_model_matrix_dataframe', PACKAGE = 'FeatureHashing', tf, data, hash_size, transpose, retval, keep_hashing_mapping)
+>>>>>>> origin/master
 }
 
 Xv <- function(m, v, retval) {