R/divc.R

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

divc <- function(df, dis = NULL, scale = FALSE){
    # checking of user's data and initialization.
    if (!inherits(df, "data.frame")) stop("Non convenient df")
    if (any(df < 0)) stop("Negative value in df")
    if (!is.null(dis)) {
        if (!inherits(dis, "dist")) stop("Object of class 'dist' expected for distance")
        if (!is.euclid(dis)) warning("Euclidean property is expected for distance")
        dis <- as.matrix(dis)
        if (nrow(df)!= nrow(dis)) stop("Non convenient df")
        dis <- as.dist(dis)
    }
    if (is.null(dis)) dis <- as.dist((matrix(1, nrow(df), nrow(df))
        - diag(rep(1, nrow(df)))) * sqrt(2))
    div <- as.data.frame(rep(0, ncol(df)))
    names(div) <- "diversity"
    rownames(div) <- names(df)
    for (i in 1:ncol(df)) {
        if(sum(df[, i]) < 1e-16) div[i, ] <- 0
        else div[i, ] <- (t(df[, i]) %*% (as.matrix(dis)^2) %*% df[, i]) / 2 / (sum(df[, i])^2)
    }
    if(scale == TRUE){
        divmax <- divcmax(dis)$value
        div <- div / divmax
    }
    return(div)
}