R/plot.RNE.r

In richardjtelford/palaeoSig: Significance Tests for Palaeoenvironmental Reconstructions

#' @describeIn rne Plot RNE object
#' @param   x RNE object to be plotted
#' @param   which Which column of the results to plot eg if more than one WAPLS
#'  component is calculated
#' @param   ylim Y-limits of the plot
#' @param   ... Arguments passed to plot
#'
#' @importFrom graphics plot matpoints text
#' @export

plot.RNE <- function(x, which = 1, ylim, ...) {
  z <- list()
  z$r <- x$random[, c(1, 1 + which)]
  z$n <- t(sapply(x$neigh, function(b) {
    c(b$neigh, b$effn, b$hb.r2[which])
  }))
  z$e <- sapply(x$neighbour, function(b) {
    b$eb.r2[which]
  })
  if (missing(ylim)) {
    ylim <- range(c(z$r[, 2], z$n[, 3]))
  }
  plot(
    1 - z$r[, 1],
    z$r[, 2],
    ylim = ylim,
    type = "b",
    xlab = "Fraction of sites deleted",
    ylab = expression("r"^2),
    ...
  )
  matpoints(
    z$n[, 2],
    cbind(z$n[, 3], z$e),
    type = "b",
    pch = c(16, 3),
    lty = c(1, 2)
  )
  text(z$n[, 2:3], label = paste(z$n[, 1], "km"), adj = -0.1)
  z
}