R/getTableAddressing.R

In HelpersMG: Tools for Environmental Analyses, Ecotoxicology and Various R Functions

.getTableAddressing <- function (variableNames, truth){		
  
  # Get the adjacency list addressing template. 
  # 
  # Useful if you want to store the networks in their condensed upper-diagonal form while still
  # having the benefit of convenient addressing and/or if you are using a simulated dataset in
  # which you know the truth and want to store all the values in a single data.frame.
  # 
  # Internal function used to get the addressing template for a data.frame to contain the adjacency 
  # list representation of a matrix.
  # @param variableNames the names of all genes to include in the adjacency list
  # @param truth The true adjacency matrix. Often will not be available, but is useful for 
  # debugging and testing.
  # @return A data.frame representing the adjacency list of the matrix provided.
  # @description This function was part of the package ENA. This package is no more available
  # and it cannot be installed from archive because some dependencies are no more
  # available.
  # @export
  # @author Jeffrey D. Allen \email{Jeffrey.Allen@@UTSouthwestern.edu}
  # @examples
  # # getTableAddressing example
  # 
  
	joint <- matrix(0, nrow=length(variableNames), ncol=length(variableNames))
	rownames(joint) <- variableNames
	colnames(joint) <- variableNames
	
	#extract the row, col indices for the upper-triangular portion of the matrix
	address <- cbind(row(joint)[upper.tri(joint)], col(joint)[upper.tri(joint)])
	address <- matrix(row.names(joint)[address], ncol=2)
	
	upper <- upper.tri(joint);
	
	if (missing(truth)){
		aggregate <- data.frame(address)
		colnames(aggregate) <- c("Source", "Dest")
	}
	else{
		aggregate <- data.frame(address, truth[upper])
		colnames(aggregate) <- c("Source", "Dest", "Truth")
	}
	return(aggregate);
}