R/renyicomp.R

In BiodiversityR: Package for Community Ecology and Suitability Analysis

`renyicomp` <- function(
    x, y, factor, sites=Inf, 
    scales=c(0, 0.25, 0.5, 1, 2, 4, 8, Inf), permutations=100,
    plotit=FALSE, ...) 
{

    factors <- NULL
    for (i in 1:length(names(y)) ) {
        if (is.factor(y[ , i]) == T) {factors <- c(factors, names(y)[i])}
    }

    if((factor %in% factors) == F) {stop("specified factor '", factor, "' is not an available factor variable")}

    groups <- table(y[,factor])
    if (sites == Inf) {sites <- min(groups)}
    m <- length(groups)
    n <- max(groups)
    s <- length(scales)
    levels <- names(groups)
    result <- array(NA,dim=c(m,s,6))
    dimnames(result) <- list(level=levels, scale=scales, c("mean", "stdev", "min", "max", "Qnt 0.025", "Qnt 0.975"))
    names(dimnames(result)) <- c(factor,"scale","")
    for (i in 1:m) {
       if (groups[i] == sites) {result[i, , 1] <- as.matrix(renyiresult(x, y, factor, levels[i], scales=scales))}
       if (groups[i] > sites) {result[i, , ] <- renyiaccumresult(x, y, factor, levels[i], scales=scales, permutations=permutations)[sites,,]}
    }
    if (plotit == T) {renyiplot(result[, , 1], ...)}
    return(result)
}