This repository contains replication codes for the article about the gips R package.
The article is available on Journal of Statistical Software and on arXiv.
The code is design to run under gips 1.2.3.
To run it, install the following packages (in this order):
install.packages("gips")
install.packages(c("ggplot2", "HSAUR2", "DAAG", "dplyr", "tidyr", "BiocManager",
"igraph", "gRim", "magrittr", "huge", "mvtnorm"))
BiocManager::install(c("GEOquery", "RBGL"))
install.packages("rags2ridges")
All folders are independent and produce plots to the plots folder. Inside the 3_(1|2|3)_* folders, the scripts are numbered in the order of running. If the code produces some output files, they are saved in this repository in the appropriate data folders. Time-consuming scripts have information in the first line on how long it took us to run.