R/io.R

In tzimiskes/causality: Examine The Causal Structure of Data

#' Read and write causality graphs
#'
#' \code{write_causality_graph} writes a causality graph to file
#'
#' \code{read_causality_graph} reads a causality graph from file
#' @param file The file you wish to read/write \code{graph} from/to
#' @param graph The graph you wish to save.
#' @note \code{file} will be output as a TETRAD compatible graph, and file must
#' be a TETRAD compatible graph if you wish to read it into R.
#' @examples
#' \dontrun{write_causality_graph(sachs.dag, file = "sachs")}
#' # Will throw an error if PATH_TO_FILE is invalid
#' \dontrun{graph <-read_causality_graph(file = "PATH_TO_FILE")}
#' @return \code{read_causality_graph} returns an object of class
#'     "causality.graph". An error will be thrown if there does not exist a
#'      valid path to file, graph is not a graph, or the file you wish to read
#'      does not contain a graph in TETRAD format.
#' @author Alexander Rix
#' @name causality-IO
#' @aliases NULL
NULL

#' @rdname causality-IO
#' @export
write_causality_graph <- function(graph, file)
{
    if (!is.cgraph(graph))
        stop("graph must be a causality graph!")
    if (file.exists(file))
        warning(sprintf("File \"%s\" already exists; overwriting...\n", file))
    write("Graph Nodes:", file = file, append = F)
    cat(graph$nodes, file = file, append = T, sep = ",")
    write('\n', file = file, append = T)
    write("Graph Edges:", file = file, append = T)
    for (i in 1:nrow(graph$edges)) {
        x <- graph$edges[i, 1]
        y <- graph$edges[i, 2]
        e <- graph$edges[i, 3]
        write(sprintf("%i. %s %s %s", i, x, e, y), file = file, append = T)
    }
}

#' @rdname causality-IO
#' @export
read_causality_graph <- function(file)
{
    if (!file.exists(file))
        stop("Cannot find file!")
    tmp <- readLines(file)
    if (tmp[1] != "Graph Nodes:")
        stop("file does not contain a compatible graph.")
    if (grepl(";", tmp[2]))
        split <- ";"
    else 
        split <- ","
    nodes <- unlist(strsplit(tmp[2], split = split))
    nodes <- sort(nodes)
    if (tmp[4] != "Graph Edges:")
        stop("file does not contain a compatible graph.")
    tmp <- tmp[-(1:4)]
    edges <- c()
    # process the file one line at a time
    edges <- c()
    line <- tmp[1]
    while (!is.na(line) && line != "") {
        line <- sub("[0-9]+\\. ", "", line)
        edge <- unlist(strsplit(line, split = " "))
        if (is.na(sum(match(c(edge[1], edge[3]), nodes)))) {
            print(line)
            stop("file contains a malformed causality graph.")
        }
        edges <- c(edges, c(edge[1], edge[3], edge[2]))
        tmp   <- tmp[-1]
        line  <- tmp[1]
    }
    cgraph(nodes, edges)
}