net_sim_funcs.R: functions used to simulate complete networks and networks with missing data.
exp_funcs.R: functions used for data imputation.
result_funcs.R: functions used to obtain network statistics and ERGM coefficients.
net_sim.R: simulating complete networks and also networks with missing data.
analyze_complete.R: obtaining network statistics and ERGM coefficients of the simulated complete networks.
exp_*.R files (e.g., exp_pa.R): these files are used to run the imputation processes and obtain network statistics for each of the imputation methods.
coef_*.R files (e.g., coef_pa.R): these files are used to obtain ERGM coefficient estimates of networks imputed by each method. 
ergm_mlist.R: obtaining ergm coefficients of the simulated networks with missing data.
data/nlist.RData: the complete network data used in the experiments. 
analysis.R: code for producing results including tables and plots.

Note: Note that running all the simulations will take approximately 2 weeks even with parallelization on HPC. There will be some randomness in data generation and the imputation processes, but the main conclusions should follow. Some files are run using job arrays in a portable batch system to remote servers. In these files, there are lines on reading arguments from the command line which might not run locally. These files include any coef_*.R files and also exp_bergm1.R, exp_bergm2.R, and exp_mice.R.
A sample job array file contains the following:
#!/bin/bash
#$ -pe smp 4
#$ -q long
#$ -t 1-96
module load R/4.1.1/gcc gcc
Rscript coef_bergm1.R ${SGE_TASK_ID} > bergm1_${SGE_TASK_ID}.out 

