varPart

varPart <- function (A, B, C = NA, AB, AC = NA, BC = NA, ABC = NA, model.type = NULL, 
    A.name = "Factor A", B.name = "Factor B", C.name = "Factor C", 
    plot = TRUE, plot.digits = 3, cex.names = 1.5, cex.values = 1.2, 
    main = "", cex.main = 2, plot.unexpl = TRUE) 
{
    if (!is.null(model.type)) 
        message("NOTE: Argument 'model.type' is no longer used.")
    partials <- c(A, B, C, AB, BC, AC, ABC)
    if (is.finite(partials[c(1:2, 4)]) && is.na(partials[c(3, 
        5:7)])) 
        twofactors <- TRUE
    else if (all(is.finite(partials))) 
        twofactors <- FALSE
    else stop("You must provide numeric values for either A, B and AB (for variation partitioning among two factors) or A, B, C, AB, BC, AC and ABC (for variation partitioning among three factors). See Details.")
    if (!all(na.omit(partials) >= 0 & na.omit(partials) <= 1)) 
        stop("Values must be between 0 and 1.")
    totalexpl <- ifelse(twofactors, AB, ABC)
    unexpl <- 1 - totalexpl
    if (twofactors) {
        Apure <- totalexpl - B
        Bpure <- totalexpl - A
        ABoverlap <- totalexpl - Apure - Bpure
        output.names <- c(paste("Pure", A.name), paste("Pure", 
            B.name), paste0("Pure ", A.name, "_", B.name, " overlap"), 
            "Unexplained")
        results <- data.frame(c(Apure, Bpure, ABoverlap, unexpl), 
            row.names = output.names)
    }
    else {
        Apure <- totalexpl - BC
        Bpure <- totalexpl - AC
        Cpure <- totalexpl - AB
        ABoverlap <- totalexpl - Apure - Bpure - C
        BCoverlap <- totalexpl - Bpure - Cpure - A
        ACoverlap <- totalexpl - Apure - Cpure - B
        ABCoverlap <- totalexpl - Apure - Bpure - Cpure - ABoverlap - 
            BCoverlap - ACoverlap
        output.names <- c(paste("Pure", A.name), paste("Pure", 
            B.name), paste("Pure", C.name), paste0("Pure ", 
            A.name, "_", B.name, " overlap"), paste0("Pure ", 
            B.name, "_", C.name, " overlap"), paste0("Pure ", 
            A.name, "_", C.name, " overlap"), paste0(A.name, 
            "_", B.name, "_", C.name, " overlap"), "Unexplained")
        results <- data.frame(c(Apure, Bpure, Cpure, ABoverlap, 
            BCoverlap, ACoverlap, ABCoverlap, unexpl), row.names = output.names)
    }
    colnames(results) <- "Proportion"
    if (plot) {
        circle <- function(x, y, r) {
            ang <- seq(0, 2 * pi, length = 100)
            xx <- x + r * cos(ang)
            yy <- y + r * sin(ang)
            polygon(xx, yy)
        }
        Apure <- round(Apure, plot.digits)
        Bpure <- round(Bpure, plot.digits)
        ABoverlap <- round(ABoverlap, plot.digits)
        if (!twofactors) {
            Cpure <- round(Cpure, plot.digits)
            BCoverlap <- round(BCoverlap, plot.digits)
            ACoverlap <- round(ACoverlap, plot.digits)
            ABCoverlap <- round(ABCoverlap, plot.digits)
        }
        if (twofactors) {
            plot(0, 0, ylim = c(-1, 10), xlim = c(-1, 7), type = "n", 
                axes = FALSE, ylab = "", xlab = "", main = main, 
                cex.main = cex.main)
            circle(3, 3, 3)
            circle(3, 6, 3)
            text(x = c(3, 3), y = c(9.5, -0.5), labels = c(A.name, 
                B.name), cex = cex.names)
            text(x = c(3, 3, 3), y = c(7, 4.75, 2), c(Apure, 
                ABoverlap, Bpure), cex = cex.values)
        }
        else {
            plot(0, 0, ylim = c(-1, 10), xlim = c(-1, 10), type = "n", 
                axes = FALSE, ylab = "", xlab = "", main = main, 
                cex.main = cex.main)
            circle(3, 6, 3)
            circle(6, 6, 3)
            circle(4.5, 3, 3)
            text(x = c(2.5, 6.5, 4.5), y = c(9.5, 9.5, -0.5), 
                labels = c(A.name, B.name, C.name), cex = cex.names, 
                adj = c(0.5, 0.5, 0))
            text(x = c(1.8, 7.2, 4.5, 4.5, 2.8, 6.2, 4.5), y = c(6.6, 
                6.6, 2, 7, 4, 4, 5), labels = c(Apure, Bpure, 
                Cpure, ABoverlap, ACoverlap, BCoverlap, ABCoverlap), 
                cex = cex.values)
        }
        if (plot.unexpl) {
            rect(-1, -1, 10, 10)
            text(x = -0.9, y = -0.2, label = paste0("Unexplained\n", 
                round(unexpl, plot.digits)), adj = 0, cex = cex.values)
        }
    }
    if (all.equal(sum(results, na.rm = TRUE), 1)) 
        cat("")
    else warning("Results don't sum up to 1; are you sure your input data are correct?")
    results
}