R/score.R

In tzimiskes/causality: Examine The Causal Structure of Data

#' @useDynLib causality r_causality_score_graph
#' @export
score <- function(graph, df, score = c("bic", "bdue"), penalty = 1.0,
                             sample.prior = 1.0, structure.prior = 1.0)
{
    if (!is.cgraph(graph))
        stop("graph is not a causality.graph!")
    if (!is.dag(graph))
        graph <- as.dag(graph)
    score <- match.arg(score, c("bic", "bdeu"))
    # the first step is to convert the data frame into one that only contains
    # numerics and integers. numerics are normalized.
    dimensions <- rep(0L, ncol(df))
    for (j in 1:ncol(df)) {
        col <- df[[j]]
        if (is.integer(col)) {
            dimensions[j] <- length(unique(col))
            df[[j]]       <- col - min(col)
        }
        else if (is.factor(col)) {
            dimensions[j] <- nlevels(col)
            df[[j]]       <- as.integer(col) - 1L
        }
        else if (is.character(col)) {
            col           <- as.factor(col)
            dimensions[j] <- nlevels(col)
            df[[j]]       <- as.integer(col) - 1L
        }
        if (score == "bic" && is.integer(col))
            col <- as.double(col)
        if (score == "bdeu" && is.double(col))
            stop("bdeu scoring cannot be used in conjuction with continuous data.
                  Use bic or cg")
    }
    # deterime the floating and integer arguments depending on the score
    if (score == "bic") {
        floating.args <- c(penalty)
        integer.args  <- c()
    }
    else if (score == "bdeu") {
        floating.args <- c(sample.prior, structure.prior)
        integer.args  <- c()
    }
    else if (score == "cg")
        stop("not implemented")
    else
        stop("error")
    score.func.args <- switch(score,
        "bic"  = list(penalty = penalty),
        "bdeu" = list(sample.prior = sample.prior,
                      structure.prior = structure.prior)
    )
    score <- .Call("r_causality_score_graph", graph, df, score, dimensions,
                       floating.args, integer.args)
    return(score)
}