charlesdgburns / rwr

Resampling with replacement? This can lead to biased statistical error estimates.

README

Biased statistical error estimates when resampling with replacement. PREPRINT: https://www.biorxiv.org/content/10.1101/2023.09.21.558661v1

Thanks for reading this!

Here's a short overview over the files in this repository.

MATLAB is a folder containing matlab code used for exploratory tests of Marek et al.'s (2022) code. This work would not have been possible without the availability of their code, for which we are grateful. The project was since moved to the R environment for open-source reproducibility and figures have been included for reproducibility purposes as well.

Please contact [email protected] for any issues with reproducibility.

MATLAB

Before running 'TestingStatErrors.m', please download the following and add it to your matlab directory:

'abcd_edgewise_correlation_iterative_reliability_single_factor.m' and 'abcd_statisticalerrors.m'

from the Marek et al. (2022) BWAS code repository:

https://gitlab.com/DosenbachGreene/bwas

R

Analyses have been coded in separate R markdown files.

1. "subject_level.Rmd"" (Figures 1, 2 and Supplementary figures)

2. "correlation_level.Rmd" (Figure 3)

3. "Fig2SrcSim.Rmd" (Supplementary Figure 1)

We recommend navigating through the Chunks, as these have been separated for different tasks, such as generating data, resampling with replacement, arranging plots, et.c.

The workflow in R was enabled thanks to the following packages:

Kassambara, A. (2020). ggpubr:'ggplot2'Based Publication Ready Plots. R package version 0.4. 0. Computer software]. https://cran-r-project. org/web/packages/ggpubr/indes. html.

Ripley, B., Venables, B., Bates, D. M., Hornik, K., Gebhardt, A., Firth, D., & Ripley, M. B. (2013). Package ‘mass’. Cran r, 538, 113-120.

Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L. D. A., François, R., ... & Yutani, H. (2019). Welcome to the Tidyverse. Journal of open source software, 4(43), 1686.