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rb643 authored Sep 4, 2020
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Expand Up @@ -145,5 +145,10 @@ This code has been tested with RStudio 3.4.1 on the following OS+Systems:

# Quality control
In response to reviewer comments we now included further extensive quality control

Main plots generated using ggstatsplot

> Patil, I. (2018). ggstatsplot: 'ggplot2' Based Plots with Statistical Details. CRAN. Retrieved from https://cran.r-project.org/web/packages/ggstatsplot/index.html
![image](./Plots/MotionOverview-01.png)
Panel A shows the case-control difference in mean framewise displacement, indicating a significantly higher mean framewise displacement in the autism group t(1125.68)= 5.07, p < .001. Panel B shows the Pearson r correlations between age and the confound variables included in our models. Correlations not passing FDR correction of p <.05 are marked with a cross. Panel C shows the spatial correlation of each ROI with the three included confound regressors in our model, all three show small correlations ranging from r = -.18 to r = .14 and were thus included in all subsequent analyses. Panel D shows the spatial correlation between Cohen’s D maps from analyses where subject with either high motion (upper triangle) or high Euler indices (lower triangle) were iteratively excluded. The fold refers to the cohorts of exclusion ranging from 1 = 5% exclusion to 5 = 25% excluded. Panel E shows the correspondence in the one-sample model with and without motion included. Models show highly similar spatial topology (r = 1.00, p < .001, BF = Inf). Panel F shows the significant spatial correspondence for the between group linear mixed effects model (r = 0.96, p < .001, BF = Inf). Panel G shows the small relation between the absolute w-score and mean framewise displacement (r = 0.15, p < .001, BF -4.89). Panels H and J shows the same for the positive (r = 0.09, p < .05, BF = 0.13) and negative (r = 0.16, p < .001, BF = -6.67) ratio’s respectively. Panel J shows the residual correlation between motion and the absolute ration after excluding the top 5% of motion subjects from the ASD sample (r = 0.10, p <.05, BF = - 0.43). Panel K shows the absolute w-score ratio with the dotted line indicating the cut-off of 0.5 after excluding the top 5% of motion individuals from the ASD sample. Panel L replicates the main figure 3 of this thresholded sample. Panel M shows the residual correlation between the absolute w-score ratio and the Euler index after thresholding the ASD sample at 5% of Euler scores (r = -0.07, p = .08, BF = 1.33). Panel N shows the absolute w-score in the thresholded sample with the dotted line indicating the 0.5 cut-off. Panel O replicated main figure 3 in this thresholded sample.

5 comments on commit 6c8af8d

@IndrajeetPatil
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Hmm, I am curious why the log(BF)values in E and F plots here are NAs.

@rb643
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@rb643 rb643 commented on 6c8af8d Sep 6, 2020

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Good spot, will have a look at that, but best guess it that there may be an NA or Inf in one of the values (which the conventional correlation ignores/removes). Not sure either if for E it matters cause the correlation is near perfect.

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@rb643 rb643 commented on 6c8af8d Sep 6, 2020

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Seems it neither, attached is the data for Panel E if you want to check it
Panel_E.xlsx

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Thanks, will have a look.

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Ah, apparently this is to be expected since BayesFactor package itself produces NAs here:

> BayesFactor::correlationBF(df$oldD, df$newD)
Bayes factor analysis
--------------
[1] Alt., r=0.333 : NA ±0%

Against denominator:
  Null, rho = 0 
---
Bayes factor type: BFcorrelation, Jeffreys-beta*

Warning message:
In genhypergeo_series_pos(U = c((n - 1)/2, (n - 1)/2), L = ((n +  :
  Series not converged.

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