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#' @title Plot random forests significance
#' @description Plot function for significance object
#'
#' @param x A significance object
#' @param ... Additional arguments passed to plot
#'
#' @author Jeffrey S. Evans <jeffrey_evans@@tnc.org>
#'
#' @method plot significance
#'
#' @export
plot.significance <- function(x, ...) {
dots <- as.list(match.call(expand.dots = TRUE)[-1])
dots[["type"]] <- "n"
if( x$rf.type == "classification" ) {
if (is.null(dots[["xlab"]]) & "xlab" %in% names(dots) == FALSE) dots[["xlab"]] <- "Error"
if (is.null(dots[["ylab"]]) & "ylab" %in% names(dots) == FALSE) dots[["ylab"]] <- ""
if (is.null(dots[["main"]]) & "main" %in% names(dots) == FALSE) dots[["main"]] <- "Distribution of randomized OOB error"
dots[["x"]] <- stats::density(x$RandOOB)
dots[["x"]]$y <- dots[["x"]]$y/max(dots[["x"]]$y)
dots[["xlim"]] <- c(min(c(x$RandOOB,x$test.OOB)), 1)
do.call("plot", dots)
graphics::polygon(dots[["x"]], col="blue")
graphics::abline(v = x$test.OOB, col="black", lwd=1.5, lty=2)
graphics::abline(v = stats::quantile(x$RandOOB, p = x$TestQuantile),lwd=1.5, lty=2, col="red")
graphics::legend("topright", c("model", "null"), bg="white", col=c("black","red"),
lty=c(2,2), lwd=c(1.5,1.5) )
} else if(x$rf.type == "regression" ) {
if (is.null(dots[["xlab"]]) & "xlab" %in% names(dots) == FALSE) dots[["xlab"]] <- "Error"
if (is.null(dots[["ylab"]]) & "ylab" %in% names(dots) == FALSE) dots[["ylab"]] <- ""
if (is.null(dots[["main"]]) & "main" %in% names(dots) == FALSE) dots[["main"]] <- "Distribution of R-square in randomized models"
dots[["x"]] <- stats::density(x$RandRsquare)
dots[["x"]]$y <- dots[["x"]]$y/max(dots[["x"]]$y)
dots[["xlim"]] <- c(min(x$RandRsquare), 1)
do.call("plot", dots)
graphics::polygon(dots[["x"]], col="blue")
graphics::abline(v = x$Rsquare, col="black", lwd = 1.5, lty = 2)
graphics::abline(v = stats::quantile(x$RandRsquare, p = x$TestQuantile),lwd = 1.5, lty = 2, col = "red")
graphics::legend("topright", c("model", "null"), bg="white",
col=c("black","red"), lty=c(2,2), lwd=c(1.5,1.5) )
}
}
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