Materials and Code

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 A of an undirected graph as A = HH^\top, where H is a nonnegative matrix with k (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]