Description Details Author(s) References Examples
This package implements the algorithms underlying the shuffle estimators, variance estimators for one-way analysis of variance designs. The estimators can overcome correlated noise by recomputing the mean-square-between statistics on a permuted version of the data. The permutations should preserve the noise covariance matrix, but a parametric model for the noise covariance is not necessary. For more details see Benjamini and Yu, and here http://statweb.stanford.edu/~yuvalben.
Two functions implement the important stages of estimation:
prepareShuffle(design_vec, premutation), which preprocess the design and computes the normalization constant for a given permutation.
estimateShuffle(response_vec, prepare), which estimates variances and effect sizes for a specific data vector.
Package: | shuffle |
Type: | Package |
Version: | 1.0.1 |
Date: | 2013-4-24 |
License: | GPL (>= 2) |
Yuval Benjamini <yuvalbenj@gmail.com>
Benjamini and Yu (2013), "The shuffle estimator for explainable variance in fMRI experiments", Annals of Applied Statistics 7 (4) http://projecteuclid.org/euclid.aoas/1387823308
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | data(design_vec,fMRI_responses,prediction_res)
# Make example shorter - for paper example use T = ncol(fMRI_responses)
T = 156*4
fMRI_responses_sm = fMRI_responses[,1:T]
design_sm = design_vec[1:T]
permutation = rev(1:T)
prep_shuffle = prepareShuffle(design_sm,permutation)
var_explained = numeric(nrow(fMRI_responses_sm))
for (i in 1:nrow(fMRI_responses_sm)) {
var_explained[i] = estimateShuffle(fMRI_responses_sm[i,],prep_shuffle)$effect
}
plot(var_explained, pmax(prediction_res,0)^2,
xlim = c(0,0.7), ylim = c(0,0.7),
xlab = "Explainable variance", ylab = "Corr^2")
abline(0,1,col=4)
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