johncolby

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class="in-text">
  <info>
    <title>My First Style</title>
    <id>my-first-style</id>
    <updated>2008-10-29T21:01:24+00:00</updated>
  </info>
  <macro name="author-short">
    <names variable="author">

johncolby

diff --git a/trk_compile_data.m b/trk_compile_data.m
index 0b2ddfe..90d3d15 100644
--- a/trk_compile_data.m
+++ b/trk_compile_data.m
@@ -52,17 +52,12 @@ function [track_means,starting_pts_out] = trk_compile_data(subsDir,subIDs,tract_
 if nargin < 7 || isempty(saveASCII), saveASCII = 0; end
 if nargin < 6 || isempty(saveTrk), saveTrk = 0; end
 if nargin < 5 || isempty(starting_pts_in)
-    starting_pts_in = dataset();
-elseif ~iscell(starting_pts_in.Subject) % Reformat to cells if subIDs are all numeric

johncolby

exptDir = '/Users/jcolby/Documents/LONI/along-tract-stats/along-tract-stats.git/example/between_group'
grpLabs = c('Control', 'FASD')
thresh  = 0.05
nPerms  = 100

library(nlme)         # Mixed-effects models
library(ggplot2)      # Plotting tools
library(plyr)         # Data manipulation
library(RColorBrewer) # Color tables

johncolby

diff --git a/example/between_group/between_grp.R b/example/between_group/between_grp.R
index ffeeaeb..e2d1c08 100644
--- a/example/between_group/between_grp.R
+++ b/example/between_group/between_grp.R
@@ -77,16 +77,7 @@ doPerms <- function(df, demog, nPerms=100){
     maxT
 }
 
-# Only correct for multiple comparisons across the tracts with a significant
-# Point:Group interaction F-test. Set the corrected p-values of other tracts to 1

johncolby

diff --git a/trk_plot.m b/trk_plot.m
index 30e0a4a..26cf093 100644
--- a/trk_plot.m
+++ b/trk_plot.m
@@ -37,6 +37,9 @@ if nargin < 4  || isempty(slices), slices = header.dim/2; end
 
 if ~isstruct(tracks), error('Tracks must be in structure form. Try running TRK_RESTRUC first.'), end
 
+levels = [0 25 50 75 100];^M
+levels = round(levels*(97-1)/100 + 1);^M

johncolby

# Function to plot color bar
color.bar <- function(lut, min, max=-min, nticks=11, ticks=seq(min, max, len=nticks), title='') {
    scale = (length(lut)-1)/(max-min)

    dev.new(width=1.75, height=5)
    plot(c(0,10), c(min,max), type='n', bty='n', xaxt='n', xlab='', yaxt='n', ylab='', main=title)
    axis(2, ticks, las=1)
    for (i in 1:(length(lut)-1)) {
    	y = (i-1)/scale + min
    	rect(0,y,10,y+1/scale, col=lut[i], border=NA)

johncolby

library(plyr)
library(ggplot2)

# Simulate data
numSubs = 40

x = runif(numSubs, 0, 30)
x = c(x, x + abs(rnorm(numSubs, 2)))
y = 2 + x - 0.02*x^2 + rnorm(2*numSubs, 0, 1)

johncolby

library(plyr)

data = arrange(data.frame(ID=1:10, FA=runif(50, 0.2, 0.8)), ID)

ddply(data, 'ID', mean) # using plyr library
aggregate(data, list(ID=data$ID), mean) # using base

johncolby

-1.22920245520088 1.26297072626596 1.83337525320795
1.20936180458861 0.611215979963239 -1.30133702133403
0.522987838117479 -0.451731971345027 -0.58388185591968
0.101340272969554 -0.435726497850704 0.569398963635685
0.426031516466784 0.151080475310323 0.956491447694583
-0.252059713648723 -0.175471660877733 -0.980883888395024
0.662052189667485 1.33212600996006 -1.47268894052709
1.48817331808508 -0.0473711069814109 -0.492789669961388
-0.503441036994115 -0.294926138113795 0.366179342735957
-2.12920560829524 1.02332212331524 -1.58266122316052

johncolby

# Download example data from: https://github.com/johncolby/SVM-RFE/zipball/master 

setwd('/path/to/SVM-RFE/') # Change this to your setup

load('demo/input.Rdata')
data  = input[, 2:3]
input = input[, -(1:3)]

# Function to residualize a vector x for the covariates in data
residualize <- function(x, fun=x~., data) {