R/pcalg2dagitty.R

In pcalg: Methods for Graphical Models and Causal Inference

## adapting the dagitty functions to our problem

##we need the pcalgTodagitty function to utilize the functionality of dagitty

## as input this function takes the adjacency matrix of a graph, 
## labels=list of (observed) variable names and 
## type which can take values DAG, CPDAG, MAG, PAG
## the function outputs an object of class dagitty that corresponds
## to the same graph.

##the adjacency matrix encoding is amat.cpdag
pcalg2dagitty <- function(amat,labels,type="cpdag")
{
  if (type == "cpdag" | type=="pdag"){
    result <- "pdag{"
  }  else {
    if (type=="dag"){
      result <- "dag{"  
    } else{
      if (type=="mag"){
        result <- "mag{"
      } else {
        if (type=="pag"){
          result <- "pag{"
        }
      }
    }
  }
  
  n <- length(amat[1,])
  
  ## if type of graph is DAG/CPDAG then edges are denoted with 0 and 1
  if (type %in% c("pdag","dag","cpdag")){
    
    for (i in 1:(n-1))
    {
      ## for single (unconnected) nodes
      if (sum(amat[,i]+amat[i,])==0){
        result <- paste0(result," ",labels[i]," ")
      }
      for(j in (i+1) : n)
      {
        
        if (amat[i,j] & amat[j,i]){
          result <- paste(result,labels[i],"--",labels[j],sep=" ")
        } else {
          
          if (amat[i,j] & !amat[j,i]){
            result <- paste(result,labels[i],"<-",labels[j],sep=" ")
          } else { 
            if (!amat[i,j] & amat[j,i]){
              result <- paste(result,labels[i],"->",labels[j],sep=" ")
            }
          }
        }
      }
    }
    
  } else {
    
    ## if the type of graph is MAG/PAG then edgemarks are encoded with
    ## 1,2 and 3 in the adjacency matrix
    if (type %in% c("mag","pag")){
      
      for (i in 1:(n-1))
      {
        ##for single nodes
        if (sum(amat[,i]+amat[i,])==0){
          result <- paste0(result," ",labels[i]," ")
        }
        for(j in (i+1) : n)
        {
          if (amat[i,j]==1 & amat[j,i]==1){
            result <- paste(result,labels[i],"@-@",labels[j],sep=" ")
          } else {
            
            if (amat[i,j]==2 & amat[j,i]==3){
              result <- paste(result,labels[i],"->",labels[j],sep=" ")
            } else { 
              if (amat[i,j]==3 & amat[j,i]==2){
                result <- paste(result,labels[i],"<-",labels[j],sep=" ")
              } else {
                if (amat[i,j]==3 & amat[j,i]==3){
                  result <- paste(result,labels[i],"--",labels[j],sep=" ")
                } else {
                  if (amat[i,j]==2 & amat[j,i]==2){
                    result <- paste(result,labels[i],"<->",labels[j],sep=" ")
                  } else {
                    if (amat[i,j]==2 & amat[j,i]==1){
                      result <- paste(result,labels[i],"@->",labels[j],sep=" ")
                    } else {
                      if (amat[i,j]==1 & amat[j,i]==2){
                        result <- paste(result,labels[i],"<-@",labels[j],sep=" ")
                      }
                    }
                  }
                }
              }
            }
          }
        }
      }}
  }
  ## if last node is unconnected
  if (sum(amat[,n]+amat[n,])==0){
    result <- paste0(result," ",labels[n]," ")
  }
  result <- paste0(result,"}")
  
  ## transform the resulting string into a daggity object
  dagitty::dagitty(result)
}