This directory holds the data and scripts to generate figure 1.
CRAN_analysis.R: this is an R script to calculate the degree and revision rate of an R package.
calc_size.m: this is a matlab script to calcuate the size of of package (the package needs to be downloaded first). Size is defined as the number of lines in all files under /src and /R of a package (excluding comment lines and empty lines).
CRAN_package_degree.txt: this is the in-degree of R packages. The analysis was done by Sept. 2014.
CRAN_package_update_rate.txt: this is the update rates of R packages. The analysis was done by Sept. 2014.
CRAN_package_size.txt: this is the sizes of R packages. This is calculated by the oldest version of a package available on CRAN by Oct. 2019.
Data of the protein-protein interaction network can be found at www.gersteinlab.org/proj/netpossel/index.html:
"Different estimations for positive selection" contains the dN/dS used for the scatter plot and the p-value (Bustamante_possel) used to color nodes.
"Network centrality statistics" holds the degree of each protein.