R/PlotChron.R

In detrendeR: A Graphical User Interface (GUI) to Visualize and Analyze Dendrochronological Data

PlotChron <- function(crn,
                      BANDWITH_SPLINE = 10,
                      P_SPLINE = 0.5) {
  nCrn <- ncol(crn)
  yr.vec <- as.numeric(rownames(crn))
  crn.names <- colnames(crn)
  if (nCrn > 2) {
    op <-
      par(
        mfrow = c(2, 1),
        mar = c(3, 3, 3, 2),
        mgp = c(1.25, 0.25, 0),
        tcl = 0.25
      )
    on.exit(par(op))
    for (i in 1:(nCrn - 2)) {
      plot(
        yr.vec,
        crn[, i],
        type = "l",
        xlab = "",
        ylab = "Tree-ring index",
        main = crn.names[i],
        las = 1,
        lab = c(10, 2, 0)
      )
      spl <- crn[, i]
      tmp <- na.omit(spl)
      tmp <-
        SPLINE(tmp, bandwidth = BANDWITH_SPLINE, p = P_SPLINE)
      spl[!is.na(spl)] <- tmp
      lines(yr.vec, spl, col = "red", lwd = 2)
      abline(h = 1)
    }

    plot(
      data.frame(yr.vec, crn[, nCrn]),
      type = "l",
      xlab = "Years",
      ylab = "Sample depth",
      las = 1,
      lab = c(10, 5, 0)
    )
    lines(yr.vec, crn[, nCrn - 1], col = "red", lwd = 1)
  }
}
# PlotChron(crn)