Added PVLE

PVLE/DESCRIPTION

@@ -0,0 +1,16 @@
+Package: PVLE
+Version: 0.1.0
+Date: 2013-08-14
+Title: Parallel Voxel Level Everything
+Description: Parallel voxel-level analysis for neuro-images
+Suggests: stats
+Author: Xiaoqiang Xu <cppexp@gmail.com>, Brian Caffo <bcaffo@gmail.com>
+Maintainer: Brian Caffo <bcaffo@gmail.com>
+Depends: R (>= 3.0.1), methods, fmri, tools, Matrix, gdata, stringr,
+        parallel, AnalyzeFMRI
+License: GPL-3
+URL: http://www.bcaffo.com
+Packaged: 2013-04-14 11:58:52 UTC; bcaffo
+Repository: github
+Collate: 'PVLE.R'
+Built: R 3.0.1; ; 2013-08-16 03:33:41 UTC; windows

PVLE/INDEX

@@ -0,0 +1,8 @@
+AddImageFile            Add image file to the project.
+LoadArrayMask           Load mask from an array.
+LoadMask                Load mask from file.
+LoadPvleProj            Load a previously saved Pvle project
+PvleProj                Constructor for S4 class PvleProj
+PvleProj-class          Parallel Voxel Level Everything Project
+RetrieveMaskArray       return a previously loaded mask
+RunPvle                 Execute voxel level analysis

PVLE/MD5

@@ -0,0 +1,20 @@
+469937497e7e817da7eee24b788284b2 *DESCRIPTION
+4442ca07afa4756e24aa0cbe59d1cc36 *INDEX
+03b4c3091124d3019850edd7f75e0a02 *Meta/Rd.rds
+367f92ef1e516170a6d074cb330f5e98 *Meta/demo.rds
+02d5987d0dfa2cdc2f1a12af6701aaca *Meta/hsearch.rds
+c5f8c93fd26658676dd07813550c06f2 *Meta/links.rds
+629424384c97d8858aecaabb04c8a9f9 *Meta/nsInfo.rds
+93420f608c14deeea9e00c463aec9e6f *Meta/package.rds
+20e88f84d0d9ade64549949370a7b46a *NAMESPACE
+ebf0fc819595d631b8bf280c4b049940 *R/PVLE
+7c4ff98aee661f751ddef29f84a03586 *R/PVLE.rdb
+4f297f60b5a1405783058ed5c8c408ef *R/PVLE.rdx
+1860924a4b5694a74ffb141b9b24b3e2 *demo/face.R
+6bdbbec017e313784a46c60d910e4e3d *help/AnIndex
+d90316a35bab94ac8cdf3026fb61b820 *help/PVLE.rdb
+e73573609d9c368ebb21912ed4b1b275 *help/PVLE.rdx
+af181ed78002c9c6603c96074faae9ad *help/aliases.rds
+40189a3ae495652f406192aea18a874a *help/paths.rds
+065bce8f5dc610af438a9f0ef1711f02 *html/00Index.html
+444535b9cb76ddff1bab1e1865a3fb14 *html/R.css

PVLE/NAMESPACE

@@ -0,0 +1,4 @@
+export(PvleProj)
+exportClasses (PvleProj)
+exportMethods (LoadMask,LoadArrayMask,RetrieveMaskArray,AddImageFile,RunPvle)
+export (LoadPvleProj)

PVLE/R/PVLE

@@ -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__.")
+})

PVLE/demo/face.R

@@ -0,0 +1,34 @@
+facePath<-"e:/Pvle_proj/pvle/demo"
+faceProjFolder<-paste(facePath,"/FaceProj",sep="")
+
+unlink(faceProjFolder,recursive=TRUE)
+system.time(faceProj<-PvleProj("FaceProj",facePath,"FaceProj"))
+
+#Create mask array from the image files.
+files <- dir(paste(facePath,"/rawImgs",sep=""), pattern = "*.img", full.names= TRUE)
+imageDim <- f.read.analyze.header(files[1])$dim[2 : 4]
+mask3D <- array(1, imageDim)
+
+files<-files
+for (file in files)
+{
+	img <- f.read.analyze.volume(file)[,,,1]
+	mask3D <- mask3D * ( !is.na(img) )
+}
+faceProj<-LoadArrayMask(faceProj,mask3D)
+
+#Load image files
+for (file in files)
+	faceProj<-AddImageFile(faceProj,file)
+
+
+
+interceptModel<-function(y,show) #Return a vector of coefficient estimate, standard error, t value, and p value
+	{
+		return(coef(summary(lm(formula=y~1))))
+	}
+
+system.time(testRst<-RunPvle(faceProj,interceptModel,8))
+
+
+

PVLE/help/AnIndex

@@ -0,0 +1,8 @@
+AddImageFile	AddImageFile
+LoadArrayMask	LoadArrayMask
+LoadMask	LoadMask
+LoadPvleProj	LoadPvleProj
+PvleProj	PvleProj
+PvleProj-class	PvleProj-class
+RetrieveMaskArray	RetrieveMaskArray
+RunPvle	RunPvle

PVLE/html/00Index.html

@@ -0,0 +1,40 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Parallel Voxel Level Everything</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Parallel Voxel Level Everything
+<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;PVLE&rsquo; version 0.1.0</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../demo">Code demos</a>.  Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="AddImageFile.html">AddImageFile</a></td>
+<td>Add image file to the project.</td></tr>
+<tr><td width="25%"><a href="LoadArrayMask.html">LoadArrayMask</a></td>
+<td>Load mask from an array.</td></tr>
+<tr><td width="25%"><a href="LoadMask.html">LoadMask</a></td>
+<td>Load mask from file.</td></tr>
+<tr><td width="25%"><a href="LoadPvleProj.html">LoadPvleProj</a></td>
+<td>Load a previously saved Pvle project</td></tr>
+<tr><td width="25%"><a href="PvleProj.html">PvleProj</a></td>
+<td>Constructor for S4 class PvleProj</td></tr>
+<tr><td width="25%"><a href="PvleProj-class.html">PvleProj-class</a></td>
+<td>Parallel Voxel Level Everything Project</td></tr>
+<tr><td width="25%"><a href="RetrieveMaskArray.html">RetrieveMaskArray</a></td>
+<td>return a previously loaded mask</td></tr>
+<tr><td width="25%"><a href="RunPvle.html">RunPvle</a></td>
+<td>Execute voxel level analysis</td></tr>
+</table>
+</body></html>

PVLE/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%);
+}
+

rsfmriGraph/R/groupMatrixPermutationTest.R

@@ -12,9 +12,9 @@ groupMatrixPermutationTest <- function(group1MatrixData, group2MatrixData,
     ##if paired, they have to have the same number of subjects in the same order
     if (paired) stopifnot(nrow(group1MatrixData) == nrow(group2MatrixData))
 
-    v <- ncol(group1Matrix)
-    n <- nrow(group1Matrix)
-    m <- nrow(group2Matrix)
+    v <- ncol(group1MatrixData)
+    n <- nrow(group1MatrixData)
+    m <- nrow(group2MatrixData)
 
     ##the observed statistics value
     observedStat <- sapply(1 : ncol(group1MatrixData),
@@ -29,15 +29,15 @@ groupMatrixPermutationTest <- function(group1MatrixData, group2MatrixData,
     ##permutations are generated at first
     if (paired){
         ##each column is an indicator of whether that pair should switch groups
-        permIDs <- matrix(sample(c(1, 0), size = n * permutations, replace = TRUE), n, permutations)
+        permIDXs <- matrix(sample(c(1, 0), size = n * permutations, replace = TRUE), n, permutations)
     }
     else {
         ##each column is a reshuffling of the subject IDs
-        permIDs <- sapply(1 : permutations, function(x) sample(1 : (m + n)))
+        permIDXs <- sapply(1 : permutations, function(x) sample(1 : (m + n)))
     }
 
     ##a parallel function
-    myApply <- function(cl, cores, X, FUN){
+    myApply <- function(X, FUN){
         if (cores > 1){
             parApply(cl, X, 2, FUN)
         }
@@ -47,12 +47,12 @@ groupMatrixPermutationTest <- function(group1MatrixData, group2MatrixData,
     }
 
     if (cores == 1) cl <- NULL
-    else makeCluster(getOption("cl.cores", cores))
+    else cl <-makeCluster(getOption("cl.cores", cores))
 
-    permutationDistribution <- myApply(permID, 
-        ##for each permutation take the maximum statistic value
-        max(
-            function(perm){
+    permutationDistribution <- myApply(permIDXs, 
+        function(perm){
+            ##for each permutation take the maximum statistic value
+            max(
                 ##loop over all v
                 sapply(1 : v, 
                     function(i) {
@@ -70,9 +70,14 @@ groupMatrixPermutationTest <- function(group1MatrixData, group2MatrixData,
                         return(stat(x, y))
                     }
                 )
-            }
-        )
+            )
+        }
     )
+    if (cores > 1) stopCluster(cl)
 
+    out <- list(pvalues = sapply(observedStat, function(x) mean(x > permutationDistribution)),
+                observedStat = observedStat,
+                permutationDistribution = permutationDistribution)
+
     return(out)
 }