markkukuismin / mdsd

Network hub detection using the entire solution path information.

MDSD (The Mean Degree Squared Difference)

Description

The R package MDSD can be used to identify hubs using solution path information. The method is tested and compatible with glasso, hglasso, and space R packages. See the example below.

For more details on the MDSD distance, please refer to: (link comming soon...) Supplementary data and code needed to reproduce the results reported in the article are available at: https://github.com/markkukuismin/MDSD_supplementary.

Dependencies

Please make sure to install the following packages before using R package MDSD. R with version later than 4.3.1 is needed.

install.packages(c("igraph", "ggplot2", "huge"))

Installation

The R package MDSD can be installed from source files in the GitHub repository (R package devtools is needed):

library(devtools)
install_github(repo="markkukuismin/MDSD")

Main functions

• hub_detection_mdsd: Compute the MDSD distance from the solution path information.
• hub_detection_plot: Plots of the node degree with respect to the tuning parameter value or the MDSD values.
• cor_screening: Thresholding of the absolute values of correlation coefficients (aka. lossy screening). One can also use the function huge from the huge package (link). I faced with some memory leak issues while using huge so I made this.