demo.R

# The path of "R-proj"
proj_path<-getwd()
src_path<-paste(proj_path,'/src',sep="")
res_path<-paste(proj_path,'/result',sep="")
data_path<-paste(proj_path,'/data',sep="")

source(paste(src_path,'/CITest.R',sep=""))
source(paste(src_path,'/Evaluation.R',sep=""))
source(paste(src_path,'/MissingValuePC.R',sep=""))
source(paste(src_path,'/SyntheticDataGeneration.R',sep=""))

# Synthethic data generation
num_var=20
num_sample = 10000

myDAG <- randomDAG(num_var,2/(num_var-1))

gen_result_list<-gen_data(num_sample = num_sample, 
                          mode = "mnar",
                          myDAG = myDAG,
                          num_extra_e=5, 
                          num_m = 10, 
                          seed = 777)

data_complete = gen_result_list$data_complete
data_m = gen_result_list$data_m
myCPDAG = gen_result_list$ground_truth$cpdag

suffStat_m <- list(data=data_m)
suffStat  = list(C = cor(data_complete),n=num_sample)

# PC on the complete dataset
res_com_pc<-pc(suffStat, 
               gaussCItest, 
               alpha=0.01, 
               p=num_var)

# Test-wise deletion PC 
res_tw<-pc(suffStat_m,
           gaussCItest.td,
           alpha=0.01, 
           p=num_var)

# MVPC with the PermC correction method 
res.mvpc.permc <-mvpc(suffStat_m,
                      gaussCItest.td, 
                      gaussCItest.permc,
                      alpha=0.01,
                      p=num_var)

# MVPC with the DRW correction method 
res.mvpc.drw <-mvpc(suffStat_m,
                    gaussCItest.td,
                    gaussCItest.drw,
                    alpha=0.01, 
                    p=num_var)


# Evaluation: Compare with the structural Hamming distance
shd(res.mvpc.drw,myCPDAG)
shd(res.mvpc.permc,myCPDAG)
shd(res_tw,myCPDAG)
print(shd(res_com_pc,myCPDAG))