R/getRwls.R

In xRing: Identify and Measure Tree Rings on X-Ray Micro-Density Profiles

#' @title Get Data-Frames With Ring Width and Density Values
#' @description Produce a list with 8 data.frames (trw, ew, lw, Dmean, Dew, Dlw, Dmin, Dmax ) that can be used by other packages (dplR, detrendeR)
#' @param x an "xRingList" object
#' @return a list with 8 elements:
##' \describe{
##'  \item{trw}{a data.frame with tree-ring widths}
##'  \item{ew}{a data.frame with earlywood widths}
##'  \item{lw }{a data.frame with latewood widths}
##'  \item{Dmean}{a data.frame with mean tree-ring density}
##'  \item{Dew}{a data.frame with mean earlywood density}
##'  \item{Dlw}{a data.frame with mean latewood density}
##'  \item{Dmin}{a data.frame with the minimum ring density}
##'  \item{Dmax}{a data.frame with the maximum ring density}
##' }
#' @export
#' @importFrom dplR combine.rwl
#' @examples
#'
#' data(PaPiRaw)
#' data(PaPiSpan)
#' PaPi <- detectRings(PaPiRaw, PaPiSpan)
#' PaPi <- combineFrag(PaPi)
#' PaPi <- detectEwLw(PaPi)
#' rwls <- getRwls(PaPi)
#' names(rwls)
#' library(dplR)
#' rwl.report(rwls$trw)
#' library(detrendeR)
#' RwlInfo(rwls$trw)
#'
getRwls <- function(x) {
  if (ncol(x[[1]]$trw) < 2) {
    return(message("You should first detect the earlywood and latewood rings."))
  }
  if (is.null(x[[1]]$density)) {
    x <- getDensity(x)
  }
  nSeries <- length(x)
  name <- rep(NA, nSeries)
  trw <-
    ew <-
    lw <-
    Dtr <-
    Dmin <-
    Dmax <-
    Dew <-
    Dlw <- vector("list", nSeries)

  for (i in 1:length(x)) {
    name[i] <- x[[i]]$name
    trw[[i]] <- x[[i]]$trw[, 1, drop = FALSE]
    ew[[i]] <- x[[i]]$trw[, 2, drop = FALSE]
    lw[[i]] <- x[[i]]$trw[, 3, drop = FALSE]
    Dtr[[i]] <- x[[i]]$density[, "Dmean", drop = FALSE]
    Dmin[[i]] <- x[[i]]$density[, "Dmin", drop = FALSE]
    Dmax[[i]] <- x[[i]]$density[, "Dmax", drop = FALSE]
    Dew[[i]] <- x[[i]]$density[, "Dew", drop = FALSE]
    Dlw[[i]] <- x[[i]]$density[, "Dlw", drop = FALSE]
  }


  trw <- combine.rwl(trw)
  ew <- combine.rwl(ew)
  lw <- combine.rwl(lw)
  Dtr <- combine.rwl(Dtr)
  Dmin <- combine.rwl(Dmin)
  Dmax <- combine.rwl(Dmax)
  Dew <- combine.rwl(Dew)
  Dlw <- combine.rwl(Dlw)


  names(trw) <-
    names(ew) <-
    names(lw) <-
    names(Dtr) <-
    names(Dmin) <-
    names(Dmax) <-
    names(Dew) <-
    names(Dlw) <- name

  out <- list(trw, ew, lw, Dtr, Dew, Dlw, Dmin, Dmax)
  names(out) <-
    c("trw", "ew", "lw", "Dmean", "Dew", "Dlw", "Dmin", "Dmax")
  out
}