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Category: Library Category: Librarianship. 3E](#pone.0087967.s005){ref-type="supplementary-material"}). The other threepatients for whom we had data for both the AT and SATS were excluded from the analysis due to the small number of people. It
was not possible to use the intercepts from the Partial Least Squares regression to test for a difference between conditions
because of the small number of patients with the intercept data. The protocol is similar to protocols used in previous studies bythe group including Niedziela, Robinson, Debray, and Mayhew [@pone.0087967-Robinson1],[@pone.0087967-Mayhew1]--[@pone.0087967-Niedziela1]. Statistical analysis {#s4f} -------------------- We used a random
effects Bayesian hierarchical model to assess the effect of AT versus SAT on QOL, as well as the effect of SATS versus noSATS on QOL while accounting for the effects of multiple tests performed in the same participants. We used a random effects
Bayesian model (MRMR method) to estimate the treatment effect. We included three random effects at the level of theintercept, the slope, and treatment type (AT vs. SAT) to account for the repeated measures. A random intercept was set at thesubject level and a random slope was set at the within-subject level (subject 1 by subject 2). The model was implemented in
WinBUGS version 1.4.3. [@pone.0087967-Lunn1] Three different chains with 100,000 iterations (burnin = 1,000; thinning =10) were run from four different starting values. We inspected the samples of parameter estimates and their standard deviations
to check for convergence. From the four chains we used one for the posterior distribution inference and one for the trace plots
to display the convergence of the chains. All Bayesian analyses were performed using the WinBUGS package and R version
2.13.0 for Mac OSX (R Foundation for Statistical Computing, Vienna, Austria). For all analyses, the prior standard deviations
and the precision of the inference were the same as in previous studies [@pone.0087967-Niedziela1]. Supporting Information{#s5}

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