# install.packages("devtools")
devtools::install_github("WY-Chen/DAGDNA")

LearnDNAforward(
  dat,  #dat$X hold the data matrix. 
  k,    #learning level
  CIFUN_skel, #Conditional independence test used for skeleton learning. 
              #CIFUN(x,y,S) returns 0 (dependence) or 1 (independence)
  CIFUN_DNA   #Conditional independence test used for DNA learning. 
              #CIFUN(x,y,S) returns 0 (dependence) or 1 (independence)
  )

allDNA(
  g #DAG matrix (g_ij=1 if and only if i->j)
  )

orderConstraining(
  D, #DNA output
  verbose=F
  )

SparsestPermutation(
  X,      #observed data
  DNA=F,  #use DNA learning or not
  k=0,    #if DNA=T, set level of DNA learning
  alpha=0.05,  #significance level in CI test (gaussCItest)
  r=5,    #number of restarts
  d=5,    #depth of SP search
  verbose=F #if true, prints the learning path with scores
  )