Table of Contents

# R packages

## spdm

Operations in the cone of symmetric, positive definite matrices (aka covariance matrices). Includes tools for estimation, interpolation, distance and mean calculations, and kernel methods.

## synmf

Symmetric nonnegative matrix factorization for undirected graph clustering. The package implements the SymmNMF algorithm outlined in Kuang, Ding, and Park (2012), and is more or less a direct translation of the author’s Matlab code. SymmNMF factorizes the adjacency matrix of an undirected graph as , where is a nonnegative matrix with (generally sparse) columns, providing a clustering of the vertices of the graph.

Also implemented is the weighted symmetric NMF with multiplicative updates described in Ding, He, and Simon (2005).

**References**

Ding, C., He, X., & Simon, H. D. (2005, April). On the equivalence of nonnegative matrix factorization and spectral clustering. In Proceedings of the 2005 SIAM International Conference on Data Mining (pp. 606-610). *Society for Industrial and Applied Mathematics*.

Kuang, D., Ding, C., & Park, H. (2012, April). Symmetric nonnegative matrix factorization for graph clustering. In Proceedings of the 2012 SIAM international conference on data mining (pp. 106-117). *Society for Industrial and Applied Mathematics*.

## garm

Network analysis from the perspective of graphs as discrete Riemannian manifolds. Although only the heat equation is currently implemented, the end goal is to implement a suite of methods for analyzing various dynamic and analytic constructions on graphs.

# Open Data and Code

Karr, J. E., **Areshenkoff, C. N.**, Rast, P., Iverson, G.L., & Garcia-Barrera, M. A. (2018). The Unity and Diversity of Executive Functions: A Systematic Review and Re-Analysis of Latent Variable Studies. *Psychological Bulletin*.

[Materials]

Smart, C. M., Karr, J. E., **Areshenkoff, C. N.**, Rabin, L. A., Hudon, C., Gates, N., … & Hampel, H. (2017). Non-pharmacologic interventions for older adults with subjective cognitive decline: systematic review, meta-analysis, and preliminary recommendations. *Neuropsychology review*, 27(3), 245-257.

[Materials]