R/plot.fittedAgelme.R

In richardjtelford/palaeoSig: Significance Tests for Palaeoenvironmental Reconstructions

#' Plots fitted agelme model and dates
#' @param x Fitted agelme model.
#' @param main Title of the plot.
#' @param xlab x axis label of the plot.
#' @param ylab y axis label of the plot.
#' @param \dots Other arguments to plot.
#' @examples
#' data(STOR)

#' fit.mod <- with(STOR, agelme(depthup, depthdo, cageup, cagedo))

#' #Predicting using the constant variance model,
#' #for each cm between 70 and 400 cm.
#' fit.pre <- predict(fit.mod, 1, 70:400)
#' plot(fit.pre)
#' @export
#' @importFrom mgcv gam
#' @importFrom stats quasi loess.smooth predict approx qqnorm qqline
#' @importFrom graphics plot arrows title matlines par lines abline

plot.fittedAgelme <- function(x, main, xlab = "Depth",
                              ylab = "Calibrated Age", ...) {
  if (missing(main)) {
    main <- x$v
  }
  xlim <- range(c(x$data$depup, x$data$depthdo, x$fit$depth))
  ylim <- range(c(x$data$cageup, x$data$cagedo, x$fit[, 2:4]))
  with(
    x$data,
    plot((depthup + depthdo) / 2, (cageup + cagedo) / 2,
      xlim = xlim, ylim = ylim, ylab = ylab, xlab = xlab, pch = 20, ...
    )
  )
  with(
    x$data,
    arrows(
      x0 = depthup, y0 = (cageup + cagedo) / 2, x1 = depthdo,
      y1 = (cageup + cagedo) / 2, length = 0,
      col = ifelse(use, "black", "grey70")
    )
  )
  with(
    x$data,
    arrows(
      x0 = (depthup + depthdo) / 2, y0 = cageup,
      x1 = (depthup + depthdo) / 2, y1 = cagedo, length = 0,
      col = ifelse(use, "black", "grey70")
    )
  )
  title(main = main)
  matlines(x$fit$depth, x$fit[, 2:4], lty = c(1, 2, 2), col = c(2, 4, 4))
}