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fxtas

The goal of fxtas is to apply the Ordinal SuStaIn algorithm (Young et al. (2021)) to study disease progression in fragile X-associated tremor/ataxia syndrome,
as described in Morrison et al (not yet published), “Progression of fragile X-associated tremor/ataxia syndrome revealed by subtype and stage inference”.

Installation

You can install the development version of fxtas from GitHub with:

# install.packages("devtools")
devtools::install_github("UCD-IDDRC/fxtas")

Running the analyses

The manuscript is implemented in the file ordinal-sustain.qmd in the analyses subfolder, which incorporates several subfiles in this repository. The data-raw folder contains numerous auxiliary scripts, including:

  • data preprocessing scripts, which be run in the following order (after extracting the necessary files from the GP, GP4, and Trax research databases):

    • gp3.r
    • gp4.r
    • gp34.R
    • trax.R

  • SLURM batch scripts and corresponding R scripts for pre-running the computation-heavy sections of the analysis on an appropriately-preconfigured distributed computing server.

If the corresponding output files have not been pre-generated, ordinal-sustain.qmd should produce them.

References

Young, Alexandra L, Jacob W Vogel, Leon M Aksman, Peter A Wijeratne, Arman Eshaghi, Neil P Oxtoby, Steven CR Williams, Daniel C Alexander, and Alzheimer’s Disease Neuroimaging Initiative. 2021. “Ordinal SuStaIn: Subtype and Stage Inference for Clinical Scores, Visual Ratings, and Other Ordinal Data.” Frontiers in Artificial Intelligence 4: 613261. https://doi.org/10.3389/frai.2021.613261.