pruningComparisons

Overview

This repository contains scripts for fNIRS data pruning using different methods and parameters, plus analysis of the effects on data quality and retention.

• MATLAB (pruningComparisonsMatlab/): Processes raw data and generates output tables.
• R (pruningComparisonsMatlab/): Runs multilevel models (MLMs) on processed data. Also includes a parameter choice script.

Repository Structure

pruningComparisons/
│ 
│── pruningComparisonsMatlab/
│   ├── pruneRunAll.m
│   ├── +pruneTools/ # modular helpfer functions
|   ├── collationScripts/ # collates results form pruning into tables which are called using R scripts
│   ├── stats/  # Folder for statistical outcomes
│ 
│── pruningComparisonsR/
│   ├── compareCVandSCI.R #compares CV, SCI Only and full QT-NIRS pruning
│   ├── prepBrightMotionMLM.R # uses MLM to invesitgate predictorsd associated with motion occurrence
│   ├── prepBrightSciPspMLM.R # uses MLM to investigate effects on average SCi and PSP measures
│   ├── prepBrightQtParamsMLM  # uses MLM to invesitgate effects of changing SCI- and PSP Thresholds in QT-NIRS
│   ├── parameterChoice.R # script to aid QT-NIRS parameter selection
│ 
│── README.md

Requirements

• MATLAB (Tested on version R2022b)
• R (Tested on version 4.4.1)
• Required Matlab toolboxes: qt-nirs, Homer2
• Required R packages: lme4, tidyr, foreach, doParallel, dplyr, effectsize, MuMIn, ggplot2, viridis, arules, data.table, effects, lmerTest, scales, Matrix, gridExtra, MASS, car

License

MIT License